WO2001066593A1

WO2001066593A1 - Structural coordinate of protein complex and utilization of the structural coordinate

Info

Publication number: WO2001066593A1
Application number: PCT/JP2001/001666
Authority: WO
Inventors: Hiroyuki Toh; Takaaki Hiroike; Masaharu Aritomi; Naoki Kunishima; Kosuke Morikawa
Original assignee: Biomolecular Engineering Research Institute
Priority date: 2000-03-07
Filing date: 2001-03-05
Publication date: 2001-09-13

Abstract

A three-dimensional structural coordinate of a protein complex consisting of leptin and a domain of leptin receptor binding to leptin. Use of this structural coordinate makes it possible to identify, search for, evaluate or design leptin mutants, which have a biological activity higher than that of natural leptin or a leptin inhibitory activity, obtained by the substitution, deletion, insertion or chemical modification of one or more amino acid residues, agonists which are compounds having a biological activity comparable or even superior to that of leptin, and antagonists which are compounds inhibiting the biological activity of leptin.

Description

Description Structural coordinates of protein complex and use of structural coordinates

The present invention relates to a three-dimensional structural coordinate of a complex of lebutin and a part of a lebutin receptor that binds to lebutin (hereinafter, abbreviated as CRH—lebutin receptor). The present invention also relates to variants of lebutin using the three-dimensional structural coordinates of a complex of lebutin and a lebutin receptor, and the identification, search, evaluation or design of an agonist or antagonist for the lebutin receptor.

Furthermore, the present invention also relates to the three-dimensional structural coordinates of a complex of a cytokine protein having a 4-helix 'bundle structure and its receptor, like G_CSF and leptin. The present invention also relates to the design, selection, and retrieval of a mutant of the cytoforce in protein and an agonist or antagonist for the leptin receptor using the three-dimensional structural coordinates. Background art

Lebutin is a type of cytokine derived from fat cells, and is known as an obesity gene because it acts on the hypothalamus of the brain, especially on the arcuate nucleus, suppresses appetite, and loses weight ( Zhang, Y. et al., Nature, 372: 425-431.

(1994)). Leptin consists of 167 amino acids, including the 21 amino acid signal peptide, has 96% and 83% homology between mouse and rat, and between mouse and human, respectively, and is well conserved across races. (Ogawa, Y., etc.

J. CHn. Invest., 96: 1647-1652 (1995)).

This factor is generally produced by Escherichia coli and animal cells using gene recombination technology, and clinical trials are being conducted as weight loss drugs for obese patients. In addition, since leptin also has an action to enhance insulin sensitivity (Ogawa, Y., et al.

Diabetes, 48: 1822–1829 (1999)), and clinical trials for the treatment of type II diabetes have been conducted. In addition to these effects, it inhibits bone formation and regulates bone mass (Ducy, R et al., Cell, 100: 197-207 (2000)), or Physiological actions such as promoting the proliferation of hematopoietic cells (Bennet, BD, et al., Currnt Biology, 6: 1170-1180 (1996)) have been reported.

However, since the factor is a protein, it is difficult to produce it, and there is a need for leptin having high biological activity, which is effective in a smaller amount. In addition, leptin preparations undergoing clinical trials are proteins and cannot be administered orally, but are administered intravenously or subcutaneously by injection. They cannot be administered by the patient themselves, must be administered by a medical professional such as a physician, and are painful to the patient. There is a need for an active agent having the biological activity of lebutin that can be administered in different ways.

In addition, antagonists that suppress the activity of lebutin are also needed for detailed studies of the mechanism of obesity or for studying the involvement of lebutin and diabetes.

On the other hand, the leptin receptor, which has the function of transmitting leptin activity to cells, is present on the surface of cells responding to leptin stimulation, and is a protein consisting of about 1200 amino acid residues. CDNA encoding mouse, rat and human leptin receptors has been cloned and the nucleotide sequence has been determined.

(TaxtagHa, LA etc., Cell, 83: 1263-1271 (1995 ), Phillips, MS , etc., Nature Genet, 13: 18- 19 (1996), the protein amino acid sequence database Swiss Prot (LEPR HUMAN)) ₀ The leptin receptor Is a single transmembrane receptor, and its amino acid sequence has been found to be highly homologous to the G-CSF receptor, one of the cytokine receptors. This leptin receptor has the ability to bind to leptin in specific regions outside the cell. This region has a similar amino acid sequence to other cytokine receptors and is commonly called the cytokin receptor homologous region (CRH). This CRH region contains G-CSF, GM-CSF, growth honoremon, interleukin-1, 2, 6, interferon-1 α, β, γ, leukemia inhibitory factor (LIF), ciliary neurotrophic Factors such as Ciliary neurotrophic factor (CNTF) are homologous regions of about 200 amino acid residues found in the extracytoplasmic domain of receptors, and are ligand binding sites for these receptors. These receptors are cytokines It is called the receptor family, and its three-dimensional structure is considered to be similar. (Bazan, JF, Proc. Natl. Acad. Sci. USA., 87: 6934-6938 (1990)).

The CRH region is considered to be the most important unit for ligand binding and signaling in this family. In other words, elucidating the binding of the ligand to the CRH region of the receptor is essential for elucidating the interaction between the ligand and the entire receptor.

Lebutin binds to the lebutin receptor, so that its stimulation is transmitted into cells via the intracellular domain of the lebutin receptor and signal transmission is performed. However, the details of the mechanism have not been elucidated. The intracellular domain of the leptin receptor has three regions, called Boxes 1, 2, and 3, with slightly different configurations depending on the isoform. These regions are used to identify JAKs (Janus activated kinases) and STATs It is thought to combine with signal transducers and activators of transcription to perform signal transmission and is transcription control. In addition, the existence of a secreted isoform that does not have an intracellular domain and a transmembrane site has been confirmed, and this is thought to be related to the function of lebutin.

Also, the three-dimensional structural coordinates of leptin are known (Zhang, Y. et al., Nature, 387: 206-209 (1997); Protein'Data Bank registration number: 1 AX8). The three-dimensional structure of leptin is a 4-helix-bundle structure, and the long-chain helical site of G-CSF, growth hormone, interleukin-1, leukemia cell inhibitory factor, ciliary neurotrophic factor, etc. It is classified into families, and each has an approximate structure (Wells, JA et al., Annu. Rev. Biochem., 65: 609-634 (1996)). On the other hand, the three-dimensional structure of the leptin receptor has not been revealed. Regarding sites other than leptin, for example, the crystal structure of a complex in which a growth factor binds to the extracellular part of its receptor has also been solved (de Vos, AM et al., Science, 255: 306-312 ( 1992); Registration No. of Protein II Data Bank: 3 hhr).

Also, it has been reported by kinetic analysis that the binding between lebutin and the lebutin receptor forms a two-to-two complex (Devos.R. Et al., J. Biol. Chem., 272: 18304-18310 (1997)), while leptin receptor It has been shown that G-CSF and CRH-G-CSF-R form a two-to-two complex with respect to the G-CSF receptor with high homology to the amino acid sequence. These facts strongly suggest that the binding pattern of leptin and leptin receptor is similar to that of G-CSF and CRH-G-CSF-R.

Growth hormones other than leptin (deVos, A.M., et al., Science, 255: 3

06-312 (1992)), interleukin-6 (Somers, W. et al., EMBO J., 16: 989-997 (1997)), leukemia cell inhibitory factor (Robinson, RC, etc., Cell, 77: 1101-1-1) 116 (1994)), ciliary neurotrophic factor (McDonald, NQ et al., EMBO J., 14: 2689-2699 (1995)), GM-CSF (Walter, MR et al., J. Mol. Biol., 224) : 1075—1085

(1992)), interleukin-1 (Sano, C. et al., J. Biol. Chem., 262: 4766-4769 (1987)), interferon-1a, β, γ

(Senda ゝ Τ ·, et al., EMBO J-, 11: 3193—3201 (1992), Ealick, SE, Science, 252: 698-702 (1991)) It regulates physiological functions and plays an important role in maintaining the body. Three-dimensional structural coordinates have also been reported for some of these cytokine proteins.

However, despite this information, the three-dimensional structural coordinates of the complex of leptin and the leptin receptor themselves are not known, and therefore, for details of the chemical interaction between leptin and the leptin receptor, No reasonable understanding in three-dimensional space has been obtained. That is, as shown in the protein 'data' bank (1AX8), the structural coordinates of lebutin are solved, and even if a general mutant creation method is used based on the structural coordinates, the conventional method cannot Since the actual state of the chemical interaction with the protein has not been ascertained, no mutant has been created that takes into account the receptor side in three-dimensional space. In addition, a computerized electronic design method (CG Wermuth et al., He Practice of Medicinal Chemistry, 167: 178 (1996)), which has been remarkably developed in recent years as a method for designing low molecular weight compounds that bind to and act on receptor binding sites. However, since the three-dimensional structural coordinates of the complex of leptin and leptin receptor were unknown, the leptin-binding site on the leptin receptor was unclear. Instead, it was not possible to design agonists or drugs using these methods. Disclosure of the invention

In recent years, the elect-nick nick design method, in which the design or search of a compound having a bioactive effect based on the three-dimensional structure coordinates of a protein, that is, the `` structure-based drug design '' is performed on a computer, has been rapidly progressing. Methods for this are also widely known (CG Wermuth et al., He Practice of Medicinal Chemistry, 167: 178 (1996)). In many cases, in these methods, in order to design or search for a compound having a desired biological activity, a region important for expressing the biological activity of the target protein, that is, the target protein is a receptor or a ligand. In this case, it is important to design a compound that binds to the region to which each binds, or if the target protein is an enzyme, a compound that binds to the region to which the substrate binds. For this purpose, it is not enough to clarify the three-dimensional structural coordinates of the protein of interest, and it is important to clarify the region to which the receptor, ligand or substrate binds to the protein. . As a means to clarify this region, by obtaining the three-dimensional structural coordinates of the complex of the target protein and its receptor, ligand or substrate, the binding state of these regions can be determined in detail It is one of the effective methods to clarify including the binding style.

The present inventors first attempted to solve the above problems by first using G—C S F and C R H

— The crystal of the complex of G—CSF—R was prepared, and the three-dimensional structural coordinates of the complex of G—CSF and CRH—G—CSF—R were revealed. Regarding the interaction with G—CSF, CRH—G—CSF—R is considered to be the equivalent of G—CSF—R, so the three-dimensional space of G—CSF and G—CSF—R For the first time, the details of the chemical interaction at have been clarified.

The G-CSF portion of the G-CSF and G-CSF-R complex was then replaced by a known leptin molecule conformation and optimal superposition. For the receptor part of this hypothetical complex of lebutin and G-CSF-R, sequence alignment was performed with the relevant part of the lebutin receptor, and the homology of the hypothetical complex G-CSF-R By substituting the three-dimensional structure of CRH-lebutin receptor by modeling, the three-dimensional structure coordinates of the complex of leptin and CRH-lebutin receptor have been revealed.

That is, according to the present invention, the tertiary structure of a complex of leptin and a CRH-leptin receptor was clarified, and thereby the leptin binding site on the leptin receptor and the binding mode were clarified. Also, based on the three-dimensional structural coordinates, it has become possible to change the amino acid residues of the protein of lebutin and to design a more active lebutin or a mutant lebutin that inhibits the active production of lebutin. . Also, based on the three-dimensional structural coordinates, it was possible to identify, search, evaluate or design compounds such as agonists having the biological activity of lebutin or antagonists that inhibit the biological activity of lebutin.

Furthermore, the present invention relates to a complex formed by lebutin and CRH-levbutin receptor, which is used for identifying, searching, evaluating or designing a lebutin mutant or a lebutin receptor agonist or antagonist. Make the three-dimensional structure coordinates the abstract.

Further, the present invention stores all or a part of the above three-dimensional structural coordinates used for identifying, searching, evaluating or designing a lebutin mutant or a lebutin receptor agonist or antagonist. The storage medium for a computer that is used is also a gist.

Further, the present invention provides a method for identifying, searching, evaluating, or designing a mutant or an antagonist of a lebutin receptor or a lebutin receptor, all or a part of the above three-dimensional structural coordinates, or The use of the storage medium for a computer described above is also a gist. Further, the present invention has a biological activity equivalent to or superior to that of natural lebutin, characterized by using all or a part of the three-dimensional structural coordinates or the storage medium for a computer. A gist of the present invention is a method for identifying, searching, evaluating, or designing a mutant of lebutin in which one, a few or several amino acid residues have been substituted, deleted, inserted, or chemically modified.

Further, the present invention has an activity as an antagonist of lebutin, characterized by using all or a part of the above three-dimensional structure coordinates or the above storage medium for computer, and has one or several A gist of the present invention is a method for identifying, searching, evaluating, or designing a mutant of lebutin in which the amino acid residue is substituted, deleted, inserted, or chemically modified. Further, the present invention provides a method for controlling all or a part of the three-dimensional structure coordinates described above, A gist of the present invention is a method for identifying, searching, evaluating, or designing an agonist of lebutin, which is characterized by using a storage medium for a computer.

Further, the present invention provides a method for identifying, searching, evaluating or designing a lebutin antagonist, which comprises using all or a part of the above three-dimensional structural coordinates or the above-mentioned computer storage medium. It is also a gist.

Furthermore, the present invention relates to a cytokine protein having a four-helix-bundle structure and a receptor thereof obtained by homology modeling based on the three-dimensional structural coordinates of the G_CSF and CRH-G-CSF-R complexes. The abstract is the three-dimensional structural coordinates of the complex. Furthermore, the present invention provides a homologous modeling based on a three-dimensional structural coordinate of the G-CSF and CRH-G-CSF-R complex, and a homologous modeling of a cytokine protein having a 41-helix 'bundle structure and its receptor complex. A method for obtaining the three-dimensional structural coordinates of the body is also a gist.

In the present specification, amino acids, peptides, and proteins are represented by using the following abbreviations adopted by the IUPAC-IUB Biochemical Nomenclature Committee (CBN). Unless otherwise specified, the sequences of peptides and amino acid residues of proteins are expressed from the left end to the right end such that the N-terminal is the C-terminal and the N-terminal is the first.

A or A 1 a: alanine residue, D or A sp aspartic acid residue, E or G 1 u: glutamic acid residue, F or P he phenylalanine residue, G or G 1 y: glycine residue, H Or H is a histidine residue,

I or I 1 e: isoloisin residue, K or Lys lysine residue,

L or Leu: leucine residue, M or met methionine residue,

N or Asn: asparagine residue, P or Pro proline residue,

Q or G 1 n: glutamine residue, R or Ar g arginine residue,

S or S er: serine residue, T or Th r threen residue,

V or Va 1: valine residue, W or T r p

Y or Tyr: tyrosine residue, C or Cys cysteine residue.

As used herein, "CRH-leptin receptor" refers to the region of the leptin receptor that binds to leptin. For example, in the case of a human leptin receptor, its amino acid sequence (protein amino acid sequence database Swiss Prot (LEPR HUMAN)), from the 424th glutamic acid to the 636th isoleucine, the start and end sites of the CRH-leptin receptor are not necessarily strict in the present invention, and the three-dimensional structure of the entire CRH-lebutin receptor It does not have a significant effect on Provided that its function is maintained, N-terminal and / or C-terminal shifted to any of several residues, or N-terminal and / or

Also included are those in which several amino acids are added to the Z or C terminus. Normally, it is considered that such a slight difference in the -7-fire structure does not greatly affect the three-dimensional structure of the entire CRH-lebutin receptor, and the function is maintained.

As used herein, the term “lebutin variant” refers to a variant of lebutin in which one or several amino acid residues of natural lebutin are substituted, deleted, inserted or chemically modified.

The terms “agonist J” and “antagonist” as used herein have their ordinary meaning. BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a ribbon diagram of the main chain of the structures of G—CSF and CRH—G—CSF—R, as viewed from a direction substantially perpendicular to the pseudo-twice symmetry axis of the molecule.

FIG. 1 is a ribbon diagram showing the main chain of the structures of G—C S F and CRH—G—C S F—R viewed from a direction substantially parallel to the pseudo-twice symmetry axis of the molecule.

FIG. 3 is a ribbon diagram of the main chain of the structure of leptin and the C RH-leptin receptor, viewed from a direction almost perpendicular to the pseudo-twice symmetry axis of the molecule.

FIG. 4 is a Ripon diagram of the main chain of the structure of leptin and the C R H-leptin receptor, as viewed from a direction substantially parallel to the pseudo-twice symmetry axis of the molecule. BEST MODE FOR CARRYING OUT THE INVENTION

1. Crystal of complex of G—CS F and CRH—G—CSF—R

G—C SF and CRH—G—C SF—R used in the present invention are derived from mammals, preferably mice, humans, and particularly preferably humans.

CRH—G—CSF—R is the area that connects to G—CSF in G—CSF—R. Say a minute. In the case of mouse-derived G-CSF-R, the region from the 97th tyrosine to the 309th alanine in its amino acid sequence (Fukunaga, R. et al., EMBOJ "10: 2855-2865 (1991)). In the case of mammalian G-CSF-R, it refers to the corresponding region. However, the start site and end site of CRH-G-CSF-R are not necessarily strict in the present invention, the CRH- G- CSF- R does not significantly affect the overall conformation. that the feature is retained as a condition, N shift-terminal and _/ / or number residues in either direction at the C-terminus Or the addition of several amino acids at the N-terminus and Z- or C-terminus Usually, such a slight difference in the primary structure is due to the fact that the CRH-G-CSF-R It is considered that the function is maintained without significantly affecting the three-dimensional structure. In the case of mouse-derived CRH-G-CSF-R, the amino acid sequence from the 95th alanine to the 309th araene is used.

The most commonly used method for elucidating the three-dimensional structure of a protein is an X-ray crystal structure analysis method. That is, a protein is crystallized, a monochromatic X-ray is applied to the crystal, and the three-dimensional structure of the protein is clarified based on the obtained X-ray diffraction image (Blundell, TL). And Johnson, LN, PROTEIN CRYSTALLOGRAPHY, 1-565, (1976) Academic Press, New York).

Crystallization is performed under certain conditions when the protein is changed from a solution state to a non-dissolved state by an operation such as adding a precipitant to the target protein solution or reducing the amount of solvent by evaporation or the like. Utilizes the property of precipitation as crystals. Crystallization requires a highly purified protein. Conditions for crystallization involve physical and chemical factors such as protein concentration, salt concentration, hydrogen ion concentration (pH), type of precipitant to be added, and temperature. In addition, there are many crystallization methods such as batch method, dialysis method and vapor diffusion method for adding the precipitant and adjusting the amount of solvent (Blundell, T.L. and Johnson, L.N., PROTEIN

CRYSTALLOGRAPHY, pp. 59-82, (1976) Acdemic Press, New York). In order to obtain protein crystals suitable for X-ray crystallography, For these proteins, it is necessary to obtain high-purity proteins and to study various factors in crystallization and optimization of crystallization techniques.

The crystal of the complex of human-derived G-CSF and mouse-derived CRH-G-CSF-R of the present invention is prepared as follows.

First, human-derived G-CSF and mouse-derived CRH-G-CSF-R are purified to high purity. Further, the purified proteins are mixed to form a complex. Further, the complex is purified to high purity so as to be suitable for crystallization. Purification methods include column chromatography (affinity, hydrophobicity, ion exchange, genole filtration, etc.), salting out, centrifugation, electrophoresis, and other methods commonly used by those skilled in the art to purify proteins. Can be used alone or in combination. In the purification step after the complex is formed, it is necessary to purify the complex while maintaining it, and a purification method that can adjust the salt concentration and hydrogen ion concentration to a state closer to the conditions in the living body It is desirable to use, for example, gel filtration mouth chromatography.

Next, a crystal of a complex of G-CSF and CRH-G-CSF-R is prepared. As a crystallization method, a crystallization method such as a batch method, a dialysis method, or a vapor diffusion method can be used. It is also necessary to determine physical and chemical factors such as protein concentration, salt concentration, hydrogen ion concentration (pH), type of precipitant added, and temperature.

In the crystallization of the complex of GC SF and CRH—G_C SF—R, it is essential to crystallize under the condition that the complex is maintained. For example, using the vapor diffusion method, using ammonium sulfate concentration of 1.0 to 1.2 M as a precipitant under conditions of pH = 7 to 8, protein concentration of 0.5 to 2 mg / ml, and temperature of 20 ° C. In this case, crystals of the complex of G-CSF and CRH-G-CSF-R are obtained. Furthermore, larger crystals suitable for X-ray crystallography can be obtained under the same conditions with the addition of 2 to 10% of 1,4-dioxane. However, since it is well known to those skilled in the art that the same protein can be crystallized under different conditions, the present invention is not limited to these conditions, and the same protein as that of the present invention may be used. Crystals of the complex of G-CSF and CRH-G-CSF-R that give the chemical constant are within the scope of the present invention. 2. Structural coordinates of the complex of G—CSF and CRH—G—CSF—R The structure of the complex crystal of G—CSF and CRH—G—CSF—R obtained in this way is known to those skilled in the art. Analyze using line-based crystal structure analysis technology.

The crystal of the complex of the human G—CSF shown in SEQ ID NO: 1 and the CRH—G—CSF—R derived from the mouse shown in SEQ ID NO: 2 belongs to the tetragonal space group I42. The unit cell has a size of 125 ± 1 OA in the a-axis and b-axis directions and 373 ± 1 OA in the c-axis direction. Furthermore, by the method of crystal structure analysis by X-ray diffraction using the crystal of the composite, the three-dimensional structural coordinates of the composite of G—CSF and CRH—G—CSF—R (each atom For the first time). Table 1 shows the obtained structural coordinates in accordance with the method of expressing three-dimensional structural coordinates of a protein generally used by those skilled in the art.

Three-dimensional locus obtained from crystals of the complex of G—CSF and CRH—G—CSF—R

CRYST 125.467 125.467 372.771 90.00 90.00 90.0014122

ATOM 1 N GLYA 5 42.132 17.880130.316 1.00133.67

ATOM 2 CA GLYA 5 42.499 19.310 130.545 1.00128.23

ATOM 3 C GLYA 5 42.600 20.009129.205 1.00124.12

ATOM 4 0 GLYA 5 42.468 19.336128.180 1.00126.65

ATOM 5 N PROA 6 42.826 21.337129.172 1.00116.53

ATOM 6 CA PROA 6 42.941 22.107127.925 1.00103.69

ATOM 7 C PROA 6 44.270 21.826127.220 1.00 87.76

ATOM 8 0 PROA 6 44.982 22.745126.807 1.00 87.46

ATOM 9 CB PROA 6 42.844 23.555128.416 1.00106.53

ATOM 10 CG PROA 6 43.539 23.495129.739 1.00114.75

ATOM 11 CD PEOA 6 42.974 22.220 130.346 1.00117.42

ATOM 12 N ALA A 7 44.589 20.543127.085 1.00 68.32 CO

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ATOM 188 CA ALAA 30 42.591 42.657 100.047 1.00 5.49

ATOM 189 C ALAA 30 43.174 43.827 99.273 1.00 7.85

ATOM 190 O ALA A 30 42.509 44.402 98.414 1.00 29.54

ATOM 191 CB ALAA 30 42.125 43.109 101.386 1.00 2.00

ATOM 192 N ALAA 31 44.414 44.178 99.587 1.00 12.61

ATOM 193 CA ALAA 31 45.108 45.262 98.901 1.00 14.83

ATOM 194 C ALAA 31 45.260 44.908 97.420 1.00 17.18

ATOM 195 O ALAA 31 44.995 45.732 96.549 1.00 20.51

ATOM 196 CB ALAA 31 46.465 45.487 99.519 1.00 2.00

ATOM 197 N LEU A 32 45.678 43.674 97.146 1.00 19.42

ATOM 198 CA LEU A 32 45.844 43.189 95.781 1.00 3.57

ATOM 199 C LEU A 32 44.498 43.263 95.056 1.00 17.23

ATOM 200 O LEU A 32 44.395 43.859 93.998 1.00 16.07

ATOM 201 CB LEU A 32 46.356 41.764 95.796 1.00 2.00

ATOM 202 CG LEU A 32 46.411 41.079 94.441 1.00 2.38

ATOM 203 CD 1 LEU A 32 47.283 41.871 93.559 1.00 2.00

ATOM 204 CD2 LEU A 32 46.916 39.647 94.532 1.00 2.00

ATOM 205 N GLN A 33 43.454 42.717 95.661 1.00 14.17

ATOM 206 CA GLN A 33 42.148 42.757 95.054 1.00 5.26

ATOM 207 C GLN A 33 41.635 44.170 94.842 1.00 4.24

ATOM 208 O GLN A 33 40.891 44.441 93.907 1.00 22.71

ATOM 209 CB GLN A 33 41.181 41.947 95.875 1.00 2.00

ATOM 210 CG GLN A 33 41.299 40.471 95.613 1.00 11.29

ATOM 211 CD GLN A ¾¾ 40 517 39.661 96.617 27 ί¾

ATOM 212 OEI GLN A 33 39.824 38.703 96.269 1.00 54.16

ATOM 213 NE2 GLN A 33 40.621 40.042 97.877 1.00 19.76

ATOM 214 N GLU A 34 42.043 45.082 95.693 1.00 6.32

ATOM 215 CA GLU A 34 41.620 46.453 95.533 1.00 11.86 ATOM 216 C GLU A 34 42.364 47.005 94.332 1.00 14.61

ATOM 217 O GLU A 34 41.770 47.567 93.420 1.00 23.83

ATOM 218 CB GLU A 34 41.977 47.276 96.753 1.00 18.27

ATOM 219 CG GLU A 34 41.130 48.525 96.916 1.00 59.53

ATOM 220 CD GLU A 34 41.219 49.484 95.729 1.00 79.47

ATOM 221 OEI GLU A 34 42.332 49.983 95.451 1.00 82.63

ATOM 222 OE2 GLU A 34 40.176 49.737 95.079 1.00 86.29

ATOM 223 N LYS A 35 43.667 46.818 94.309 1.00 5.50

ATOM 224 CA LYS A 35 44.458 47.310 93.197 1.00 8.29

ATOM 225 C LYS A 35 43.912 46.826 91.833 1.00 18.82

ATOM 226 O LYS A 35 43.666 47.632 90.942 1.00 21.49

ATOM 227 CB LYS A 35 45.903 46.867 93.371 1.00 11.50

ATOM 228 CG LYS A 35 46.914 47.649 92.575 1.00 27.07

ATOM 229 CD LYS A 35 47.132 49.047 93.140 1.00 41.60

ATOM 230 CE LYS A 35 48.180 49.802 92.322 1.00 51.41

ATOM 231 NZ LYS A 35 48.353 51.231 92.720 1.00 67.30

ATOM 232 N LEU A 36 43.700 45.521 91.684 1.00 17.04

ATOM 233 CA LEU A 36 43.181 44.950 90.447 1.00 2.00

ATOM 234 C LEU A 36 41.840 45.565 90.080 1.00 7.30

ATOM 235 O LEU A 36 41.539 45.755 88.908 1.00 27.03

ATOM 236 CB LEU A 36 43.005 43.445 90.582 1.00 2.00

ATOM 237 CG LEU A 36 44.268 42.605 90.665 1.00 2.00

ATOM 238 CD1 LEU A 36 43.969 41.292 91.277 1.00 7.99

ATOM 239 CD2 LEU A 36 44.815 42.390 89.325 1.00 2.00

Λ VI N CYS A 1 υυο Q 1 Λβ ΐ 1 on Ο.ΌΙ

ATOM 241 CA CYS A 37 39.743 46.459 90.729 1.00 13.52

ATOM 242 C CYS A 37 39.916 47.929 90.370 1.00 11.90

ATOM 243 O CYS A 37 39.259 48.432 89.482 1.00 25.18

ATOM 244 CB CYS A 37 38.741 46.292 91.860 1.00 5.69 ATOM 245 SG CYS A 37 37.206 47.274 91.689 1.00 48.92

ATOM 246 N ALAA 38 40.855 48.605 90.997 1.00 16.45

ATOM 247 CA ALAA 38 41.053 50.018 90.711 1.00 22.15

ATOM 248 C ALAA 38 41.743 50.234 89.383 1.00 28.29

ATOM 249 O ALAA 38 41.367 51.080 88.568 1.00 42.34

ATOM 250 CB ALA A 38 41.875 50.645 91.802 1.00 26.96

ATOM 251 N THR A 39 42.781 49.459 89.186 1.00 24.09

ATOM 252 CA THR A 39 43.599 49.548 88.010 1.00 19.84

ATOM 253 C THR A 39 43.006 48.922 86.745 1.00 20.80

ATOM 254 O THR A 39 43.226 49.428 85.654 1.00 39.12

ATOM 255 CB THR A 39 44.960 48.918 88.350 1.00 24.38

ATOM 256 OGl THR A 39 45.398 49.425 89.618 1.00 31.36

ATOM 257 CG2 HE A 39 46.006 49.236 87.296 1.00 26.80

ATOM 258 N TYE A 40 42.220 47.865 86.888 1.00 9.34

ATOM 259 CA TYK A 40 41.674 47.177 85.737 1.00 6.17

ATOM 260 C TYR A 40 40.190 46.889 85.826 1.00 17.01

ATOM 261 O TYE A 40 39.704 45.968 85.178 1.00 21.76

ATOM 262 CB TYE A 40 42.367 45.833 85.580 1.00 2.00

ATOM 263 CG TYE A 40 43.851 45.930 85.471 1.00 13.86

ATOM 264 CDI TYE A 40 44.442 46.850 84.624 1.00 17.74

ATOM 265 CD2 TYR A 40 44.669 45.099 86.208 1.00 9.73

ATOM 266 CEI TYE A 40 45.823 46.948 84.515 1.00 32.96

ATOM 267 CE2 TYR A 40 46.052 45.184 86.113 1.00 21.23

ATOM 268 CZ TYE A 40 46.630 46.120 85.265 1.00 28.30 Λ ΔΦΠΤ \ V / ΓI OH TYR A A (\

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ATOM 270 N LYS A 41 39.469 47.637 86.644 1.00 19.52

ATOM 271 CA LYS A 41 38.036 47.421 86.817 1.00 13.69

ATOM 272 C LYS A 41 37.566 45.960 86.786 1.00 8.72

ATOM 273 O LYS A 41 36.448 45.658 86.373 1.00 20.52 ATOM 274 CB LYS A 41 37.231 48.312 85.880 1.00 16.90

ATOM 275 CG LYS A 41 37.357 49.802 86.207 1.00 38.99

ATOM 276 CD LYS A 41 35.986 50.481 86.245 1.00 61.97

ATOM 277 CE LYS A 41 35.074 49.849 87.304 1.00 73.98

ATOM 278 NZ LYS A 41 33.673 50.381 87.273 1.00 90.30

ATOM 279 N LEU A 42 38.442 45.068 87.248 1.00 15.38

ATOM 280 CA LEU A 42 38.192 43.619 87.387 1.00 19.38

ATOM 281 C LEU A 42 37.804 43.466 88.872 1.00 20.54

ATOM 282 O LEU A 42 38.618 43.102 89.704 1.00 27.27

ATOM 283 CB LEU A 42 39.489 42.858 87.125 1.00 6.50

ATOM 284 CG LEU A 42 39.819 42.375 85.725 1.00 17.34

ATOM 285 CD 1 LEU A 42 41.279 42.027 85.626 1.00 25.39

ATOM 286 CD2 LEU A 42 38.971 41.164 85.442 1.00 21.04

ATOM 287 N CYS A 43 36.548 43.715 89.195 1.00 15.38

ATOM 288 CA CYS A 43 36.143 43.721 90.581 1.00 13.29

ATOM 289 C CYS A 43 35.354 42.579 91.184 1.00 26.70

ATOM 290 O CYS A 43 35.243 42.497 92.400 1.00 43.57

ATOM 291 CB CYS A 43 35.366 45.006 90.831 1.00 16.45

ATOM 292 SG CYS A 43 36.166 46.468 90.127 1.00 46.16

ATOM 293 N HIS A 44 34.789 41.708 90.365 1.00 31.16

ATOM 294 CA HIS A 44 33.955 40.638 90.903 1.00 25.40

ATOM 295 C HIS A 44 34.453 39.279 90.436 1.00 24.70

ATOM 296 O HIS A 44 34.165 38.860 89.318 1.00 33.30

ATOM 297 CB HIS A 44 32.478 40.836 90.464 1.00 28.77

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ATOM 299 NDl HIS A 44 32.585 43.252 89.686 1.00 63.77

ATOM 300 CD2 HIS A 44 30.995 42.873 91.133 1.00 48.07

ATOM 301 CEI HIS A 44 31.951 44.397 89.874 1.00 62.21

ATOM 302 NE2 HIS A 44 30.982 44.194 90.747 1.00 58.50 ATOM 303 N PRO A 45 35.164 38.545 91.301 1.00 20.62

ATOM 304 CA PRO A 45 35.694 37.220 90.950 1.00 17.21

ATOM 305 C PRO A 45 34.668 36.258 90.405 1.00 17.94

ATOM 306 O PRO A 45 34.999 35.378 89.626 1.00 17.47

ATOM 307 CB PRO A 45 36.265 36.706 92.277 1.00 15.61

ATOM 308 CG PRO A 45 35.534 37.463 93.304 1.00 21.64

ATOM 309 CD PRO A 45 35.456 38.855 92.704 1.00 19.87

ATOM 310 N GLU A 46 33.423 36.422 90.838 1.00 29.35

ATOM 311 CA GLU A 46 32.321 35.566 90.415 1.00 36.06

ATOM 312 C GLU A 46 32.235 35.564 88.906 1.00 38.35

ATOM 313 O GLU A 46 32.067 34.523 88.277 1.00 39.50

ATOM 314 CB GLU A 46 31.007 36.074 90.994 1.00 49.95

ATOM 315 CG GLU A 46 30.913 36.001 92.522 1.00 92.51

ATOM 316 CD GLU A 46 31.906 36.913 93.249 1.00 106.11

ATOM 317 OEI GLU A 46 31.993 38.118 92.899 1.00 109.39

ATOM 318 OE2 GLU A 46 32.594 36.413 94.174 1.00 115.01

ATOM 319 N GLU A 47 32.410 36.743 88.328 1.00 33.59

ATOM 320 CA GLU A 47 32.358 36.903 86.891 1.00 19.05

ATOM 321 C GLU A 47 33.416 36.043 86.231 1.00 18.53

ATOM 322 O GLU A 47 33.218 35.552 85.142 1.00 30.04

ATOM 323 CB GLU A 47 32.541 38.384 86.512 1.00 5.80

ATOM 324 CG GLU A 47 31.470 39.287 87.133 1.00 27.98

ATOM 325 CD GLU A 47 31.614 40.777 86.811 1.00 37.90

ATOM 326 OEI GLU A 47 32.728 41.261 86.486 1.00 34.28

ATOM 328 N LEU A 48 34.518 35.797 86.919 1.00 28.75

ATOM 329 CA LEU A 48 35.607 35.027 86.341 1.00 21.13

ATOM 330 C LEU A 48 35.562 33.558 86.686 1.00 20.94

ATOM 331 O LEU A 48 36.396 32.766 86.229 1.00 18.06 ATOM 332 CB LEU A 48 36.931 35.627 86.799 1.00 17.33

ATOM 333 CG LEU A 48 37.072 37.062 86.311 1.00 11.53

ATOM 334 GDI LEU A 48 38.391 37.683 86.745 1.00 14.76

ATOM 335 CD2 LEUA 48 36.959 37.018 84.807 1.00 2.00

ATOM 336 N VAL A 49 34.568 33.183 87.472 1.00 25.83

ATOM 337 CA VAL A 49 34.432 31.799 87.910 1.00 35.17

ATOM 338 C VAL A 49 34.852 30.712 86.912 1.00 26.48

ATOM 339 O VAL A 49 35.731 29.906 87.199 1.00 32.51

ATOM 340 CB VAL A 49 33.013 31.531 88.450 1.00 46.86

ATOM 341 CGI VAL A 49 32.695 30.034 88.421 1.00 41.99

ATOM 342 CG2 VAL A 49 32.905 32.081 89.887 1.00 57.06

ATOM 343 N LEU A 50 34.263 30.705 85.731 1.00 30.16

ATOM 344 CA LEU A 50 34.598 29.687 84.734 1.00 28.74

ATOM 345 C LEU A 50 36.053 29.587 84.296 1.00 36.05

ATOM 346 O LEU A 50 36.475 28.532 83.829 1.00 29.59

ATOM 347 CB LEU A 50 33.743 29.838 83.480 1.00 32.92

ATOM 348 CG LEU A 50 32.268 29.477 83.604 1.00 39.47

ATOM 349 GDI LEU A 50 31.599 29.592 82.249 1.00 35.23

ATOM 350 CD2 LEU A 50 32.138 28.072 84.123 1.00 28.10

ATOM 351 N LEU A 51 36.827 30.663 84.424 1.00 38.15

ATOM 352 CA LEU A 51 38.221 30.612 83.993 1.00 31.85

ATOM 353 C LEU A 51 39.126 29.804 84.913 1.00 28.13

ATOM 354 O LEU A 51 40.254 29.476 84.552 1.00 28.88

ATOM 355 CB LEU A 51 38.770 32.012 83.732 1.00 39.15 Λ ΔΤ 丄 Π U 丄 V ΟΌ ri T J-i Tl! PTUT r Δ O 丄 oo.u o οΔ.

ATOM 357 CD 1 LEU A 51 37.139 32.379 81.804 1.00 51.53

ATOM 358 CD2 LEU A 51 38.872 34.077 82.336 1.00 48.78

ATOM 359 N GLYA 52 38.606 29.426 86.076 1.00 23.23

ATOM 360 CA GLY A 52 39.380 28.629 87.008 1.00 15.54 ATOM 361 C GLYA 52 39.655 27.257 86.425 1.00 31.04

ATOM 362 O GLYA 52 40.760 26.722 86.548 1.00 40.58

ATOM 363 N HIS A 53 38.634 26.667 85.810 1.00 25.79

ATOM 364 CA HIS A 53 38.788 25.358 85.211 1.00 17.29

ATOM 365 C HIS A 53 39.614 25.554 83.947 1.00 23.31

ATOM 366 O HIS A 53 40.591 24.856 83.719 1.00 28.12

ATOM 367 CB HIS A 53 37.426 24.759 84.867 1.00 14.91

ATOM 368 CG HIS A 53 36.637 24.299 86.052 1.00 21.66

ATOM 369 NDl HIS A 53 35.547 24.989 86.538 1.00 39.51

ATOM 370 CD2 HIS A 53 36.786 23.222 86.861 1.00 46.93

ATOM 371 CEl HIS A 53 35.065 24.365 87.600 1.00 42.29

ATOM 372 NE2 HIS A 53 35.799 23.289 87.817 1.00 53.46

ATOM 373 N SER A 54 39.252 26.564 83.166 1.00 28.83

ATOM 374 CA SER A 54 39.928 26.869 81.910 1.00 31.06

ATOM 375 C SEE A 54 41.426 27.090 82.083 1.00 38.63

ATOM 376 O SER A 54 42.221 26.650 81.254 1.00 53.06

ATOM 377 CB SERA 54 39.285 28.107 81.267 1.00 31.64

ATOM 378 OG SERA 54 39.910 28.496 80.049 1.00 53.46

ATOM 379 N LEU A 55 41.813 27.764 83.161 1.00 38.86

ATOM 380 CA LEU A 55 43.218 28.061 83.404 1.00 31.47

ATOM 381 C LEU A 55 43.897 27.032 84.247 1.00 32.20

ATOM 382 O LEU A 55 45.126 26.972 84.277 1.00 31.05

ATOM 383 CB LEU A 55 43.365 29.422 84.041 1.00 19.96

ATOM 384 CG LEU A 55 42.944 30.496 83.057 1.00 13.59

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ATOM 386 CD2 LEUA 55 43.931 30.543 81.926 1.00 16.66

ATOM 387 N GLYA 56 43.085 26.243 84.942 1.00 27.91

ATOM 388 CA GLYA 56 43.599 25.182 85.779 1.00 28.44

ATOM 389 C GLYA 56 43.994 25.615 87.162 1.00 34.24 ATOM 390 O GLYA 56 44.847 24.990 87.779 1.00 45.42

ATOM 391 N ILE A 57 43.373 26.680 87.649 1.00 30.04

ATOM 392 CA ILE A 57 43.658 27.191 88.981 1.00 25.34

ATOM 393 C ILE A 57 43.349 26.125 90.007 1.00 35.35

ATOM 394 0 ILE A 57 42.177 25.785 90.219 1.00 42.20

ATOM 395 CB ILE A 57 42.795 28.420 89.315 1.00 16.42

ATOM 396 CGI ILE A 57 43.420 29.660 88.721 1.00 18.49

ATOM 397 CG2 ILE A 57 42.681 28.615 90.810 1.00 10.15

ATOM 398 CD1 ILE A 57 43.855 29.467 87.298 1.00 42.53

ATOM 399 N PRO A 58 44.391 25.565 90.643 1.00 37.39

ATOM 400 CA PRO A 58 44.185 24.531 91.661 1.00 43.95

ATOM 401 C PRO A 58 43.362 25.000 92.884 1.00 48.88

ATOM 402 O PEO A 58 43.137 26.198 93.118 1.00 52.13

ATOM 403 CB PRO A 58 45.620 24.129 92.043 1.00 35.39

ATOM 404 CG PEO A 58 46.398 24.384 90.786 1.00 36.96

ATOM 405 CD PRO A 58 45.824 25.711 90.328 1.00 33.46

ATOM 406 N TRP A 59 42.866 24.026 93.629 1.00 56.58

ATOM 407 CA TEP A 59 42.089 24.297 94.814 1.00 61.02

ATOM 408 C TRP A 59 42.852 23.585 95.940 1.00 56.39

ATOM 409 O TRP A 59 43.514 22.562 95.710 1.00 53.30

ATOM 410 CB TRP A 59 40.639 23.779 94.619 1.00 76.54

ATOM 411 CG TEP A 59 40.194 22.653 95.535 1.00 88.89

ATOM 412 GDI TRP A 59 39.278 22.737 96.552 1.00 92.13

ATOM 413 CD2 TRP A 59 40.703 21.306 95.566 1.00 93.14

ATOM 415 CE2 TRP A 59 40.065 20.642 96.642 1.00 96.11

ATOM 416 CE3 TEP A 59 41.642 20.602 94.796 1.00 90.05

ATOM 417 CZ2 TRP A 59 40.342 19.305 96.970 1.00 91.47

ATOM 418 CZ3 TRP A 59 41.917 19.274 95.120 1.00 91.44 ΟΤΌ7 Π UΠU'Τ L VO V a.li VJ F

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99910 / I0df / X3d ATOM 593 C LEU A 85 50.009 27.436 96.085 1.00 9.56

ATOM 594 O LEU A 85 50.380 27.821 94.976 1.00 19.26

ATOM 595 CB LEU A 85 48.906 25.278 96.583 1.00 5.85

ATOM 596 CG LEU A 85 48.165 25.268 95.280 1.00 6.06

ATOM 597 CD 1 LEU A 85 48.972 24.466 94.270 1.00 15.37

ATOM 598 CD2 LEU A 85 46.825 24.645 95.553 1.00 10.87

ATOM 599 N TYR A 86 49.401 28.235 96.945 1.00 16.52

ATOM 600 CA TYE A 86 49.131 29.616 96.586 1.00 3.15

ATOM 601 C TYE A 86 50.420 30.374 96.478 1.00 2.62

ATOM 602 O TYE A 86 50.515 31.363 95.777 1.00 16.04

ATOM 603 CB TYR A 86 48.164 30.261 97.571 1.00 4.75

ATOM 604 CG TY A 86 46.762 29.665 97.517 1.00 7.88

ATOM 605 CDI TYK A 86 45.963 29.801 96.397 1.00 2.00

ATOM 606 CD2 TY A 86 46.255 28.943 98.582 1.00 2.90

ATOM 607 CEI TYR A 86 44.704 29.227 96.343 1.00 6.60

ATOM 608 CE2 TYK A 86 45.008 28.376 98.535 1.00 9.74

ATOM 609 CZ TYE A 86 44.233 28.513 97.419 1.00 9.30

ATOM 610 OH TYR A 86 42.989 27.906 97.400 1.00 24.47

ATOM 611 N GLN A 87 51.445 29.885 97.141 1.00 11.83

ATOM 612 CA GLN A 87 52.738 30.527 97.033 1.00 14.35

ATOM 613 C GLN A 87 53.186 30.332 95.581 1.00 21.56

ATOM 614 O GLN A 87 53.777 31.224 94.988 1.00 26.92

ATOM 615 CB GLN A 87 53.721 29.858 97.966 1.00 12.64

ATOM 616 CG GLN A 87 55.072 30.399 97.852 1.00 14.50

ATOM fii CD GLN A O 1 1 nn

ATOM 618 OEI GLN A 87 57.132 29.227 97.840 1.00 53.89

ATOM 619 NE2 GLN A 87 55.824 28.979 99.649 1.00 42.41

ATOM 620 N GLYA 88 52.881 29.165 95.015 1.00 19.53

ATOM 621 CA GLY A 88 53.236 28.875 93.636 1.00 11.97 ATOM 622C GLYA 88 52.368 29.606 92.627 1.00 15.68

ATOM 623 O GLYA 88 52.860 30.172 91.647 1.00 12.15

ATOM 624 N LEU A 89 51.061 29.607 92.843 1.00 13.61

ATOM 625 CA LEU A 89 50.178 30.303 91.919 1.00 2.25

ATOM 626 C LEU A 89 50.537 31.779 91.797 1.00 5.89

ATOM 627 O LEU A 89 50.624 32.305 90.705 1.00 11.26

ATOM 628 CB LEU A 89 48.723 30.135 92.341 1.00 6.44

ATOM 629 CG LEU A 89 48.188 28.708 92.244 1.00 6.00

ATOM 630 GDI LEU A 89 46.754 28.691 92.696 1.00 6.92

ATOM 631 CD2 LEUA 89 48.285 28.213 90.823 1.00 2.00

ATOM 632 N LEU A 90 50.772 32.441 92.921 1.00 8.29

ATOM 633 CA LEU A 90 51.127 33.852 92.912 1.00 2.00

ATOM 634 C LEU A 90 52.449 34.066 92.173 1.00 4.21

ATOM 635 O LEU A 90 52.668 35.104 91.566 1.00 15.58

ATOM 636 CB LEU A 90 51.208 34.403 94.346 1.00 2.00

ATOM 637 CG LEU A 90 49.945 34.308 95.217 1.00 2.00

ATOM 638 CD 1 LEU A 90 50.264 34.611 96.637 1.00 2.00

ATOM 639 CD2 LEUA 90 48.875 35.244 94.751 1.00 2.00

ATOM 640 N GLNA 91 53.342 33.091 92.234 1.00 10.18

ATOM 641 CA GLN A 91 54.615 33.216 91.547 1.00 19.84

ATOM 642 C GLNA 91 54.389 33.099 90.041 1.00 26.03

ATOM 643 O GLNA 91 55.013 33.802 89.255 1.00 33.17

ATOM 644 CB GLNA 91 55.606 32.134 92.004 1.00 38.30

ATOM 645 CG GLNA 91 56.382 32.439 93.287 1.00 71.50

ATOM V CD GLNA q 3i K Λ Λ Ά o οοο QQ ana 1.00 87.37

ATOM 647 OEI GLN A 91 58.261 31.029 92.754 1.00 100.53

ATOM 648 NE2 GLNA 91 57.447 30.896 94.839 1.00 92.49

ATOM 649 N ALAA 92 53.471 32.224 89.653 1.00 22.12

ATOM 650 CA ALAA 92 53.161 31.987 88.254 1.00 7.97 ATOM 651 C ALA A 92 52.625 33.188 87.540 1.00 4.50

ATOM 652 O ALAA 92 52.716 33.277 86.320 1.00 20.13

ATOM 653 CB ALA A 92 52.172 30.868 88.140 1.00 7.82

ATOM 654 N LEU A 93 52.027 34.103 88.292 1.00 11.36

ATOM 655 CA LEU A 93 51.433 35.314 87.722 1.00 3.76

ATOM 656 G LEU A 93 52.497 36.283 87.253 1.00 11.28

ATOM 657 O LEU A 93 52.188 37.408 86.873 1.00 18.09

ATOM 658 CB LEU A 93 50.534 36.016 88.753 1.00 2.00

ATOM 659 CG LEU A 93 49.233 35.347 89.162 1.00 6.58

ATOM 660 GDI LEU A 93 48.597 36.146 90.261 1.00 18.98

ATOM 661 CD2 LEU A 93 48.303 35.256 87.971 1.00 6.92

ATOM 662 N GLU A 94 53.755 35.882 87.372 1.00 17.10

ATOM 663 CA GLU A 94 54.878 36.707 86.971 1.00 13.56

ATOM 664 C GLU A 94 54.674 38.222 87.250 1.00 12.98

ATOM 665 O GLU A 94 54.886 39.076 86.380 1.00 24.86

ATOM 666 CB GLUA 94 55.248 36.376 85.527 1.00 15.50

ATOM 667 CG GLU A 94 55.785 34.946 85.367 1.00 59.66

ATOM 668 CD GLU A 94 55.327 34.252 84.080 1.00 87.89

ATOM 669 OEI GLU A 94 55.101 33.018 84.119 1.00 101.14

ATOM 670 OE2 GLU A 94 55.197 34.929 83.032 1.00 97.88

ATOM 671 N GLYA 95 54.209 38.528 88.470 1.00 13.88

ATOM 672 CA GLY A 95 54.007 39.905 88.914 1.00 2.00

ATOM 673 C GLYA 95 52.813 40.637 88.354 1.00 11.38

ATOM 674 O GLYA 95 52.521 41.764 88.763 1.00 6.35

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ATOM 676 CA ILE A 96 50.928 40.531 86.778 1.00 11.04

ATOM 677 C ILE A 96 51.334 41.703 85.874 1.00 18.54

ATOM 678 O ILE A 96 51.176 41.624 84.664 1.00 29.88

ATOM 679 CB ILE A 96 49.801 40.956 87.771 1.00 4.87 ATOM 680 CGI ILE A 96 49.292 39.754 88.554 1.00 2.00

ATOM 681 CG2 ILE A 96 48.604 41.493 87.008 1.00 2.00

ATOM 682 CD1 ILE A 96 48.092 40.109 89.430 1.00 4.14

ATOM 683 N SER A 97 51.860 42.778 86.450 1.00 21.02 ATOM 684 CA SER A 97 52.295 43.920 85.664 1.00 15.52

ATOM 685 C SER A 97 53.083 44.856 86.562 1.00 25.78

ATOM 686 O SER A 97 53.066 44.723 87.786 1.00 30.90

ATOM 687 CB SER A 97 51.084 44.653 85.098 1.00 16.03

ATOM 688 OG SER A 97 50.488 45.480 86.072 1.00 15.09 ATOM 689 N PRO A 98 53.810 45.803 85.969 1.00 34.26

ATOM 690 CA PRO A 98 54.593 46.751 86.766 1.00 35.39

ATOM 691 C PRO A 98 53.809 47.464 87.874 1.00 32.27

ATOM 692 O PRO A 98 54.311 47.645 88.990 1.00 34.22

ATOM 693 CB PRO A 98 55.107 47.708 85.703 1.00 25.12 ATOM 694 CG PRO A 98 55.452 46.718 84.593 1.00 38.70

ATOM 695 CD PRO A 98 54.217 45.844 84.550 1.00 37.21

ATOM 696 N GLU A 99 52.567 47.835 87.575 1.00 37.10

ATOM 697 CA GLU A 99 51.724 48.539 88.542 1.00 41.54

ATOM 698 C GLU A 99 51.409 47.650 89.739 1.00 32.94 ATOM 699 O GLU A 99 51.333 48.116 90.871 1.00 42.78

ATOM 700 CB GLU A 99 50.412 49.005 87.883 1.00 60.85

ATOM 701 CG GLU A 99 50.567 49.954 86.678 1.00 95.43

ATOM 702 CD GLU A 99 50.820 51.410 87.071 1.00 114.93

ATOM 703 OEI GLU A 99 50.017 51.972 87.854 1.00 126.83 ATOM 704 OE2 GLU A 99 51.814 51.996 86.581 1.00 119.04

ATOM 705 N LEU A 100 51.274 46.358 89.487 1.00 21.33

ATOM 706 CA LEU A 100 50.947 45.409 90.533 1.00 17.31

ATOM 707 C LEU A 100 52.069 44.608 91.147 1.00 11.87

ATOM 708 O LEU A 100 51.902 44.040 92.224 1.00 17.10

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ATOM 1000 CD PRO A 139 49.004 26.861 87.940 1.00 49.39

ATOM 1001 N ALA A 140 49.214 28.277 83.450 1.00 43.98

ATOM 1002 CA ALA A 140 49.901 28.999 82.400 1.00 42.85 ATOM 1003 C ALA A 140 49.924 30.525 82.453 1.00 45.34

ATOM 1004 O ALA A 140 51.001 31.122 82.457 1.00 44.52

ATOM 1005 CB ALA A 140 49.366 28.541 81.060 1.00 59.81

ATOM 1006 N PHE A 141 48.743 31.148 82.420 1.00 39.95

ATOM 1007 CA PHE A 141 48.611 32.613 82.414 1.00 34.95 ATOM 1008 C PHE A 141 49.445 33.167 81.266 1.00 39.66

ATOM 1009 O PHE A 141 50.458 33.819 81.488 1.00 44.82

ATOM 1010 CB PHE A 141 49.090 33.230 83.724 1.00 23.93

ATOM 1011 CG PHE A 141 48.519 32.580 84.953 1.00 26.19

ATOM 1012 CD1 PHE A 141 47.144 32.486 85.139 1.00 18.03 ATOM 1013 CD2 PHE A 141 49.360 32.068 85.937 1.00 29.80

ATOM 1014 CEl PHE A 141 46.618 31.894 86.286 1.00 17.32

ATOM 1015 CE2 PHE A 141 48.842 31.476 87.087 1.00 31.06

ATOM 1016 CZ PHE A 141 47.472 31.390 87.262 1.00 15.76

ATOM 1017 N ALA A 142 48.994 32.895 80.042 1.00 45.71 ATOM 1018 CA ALA A 142 49.667 33.293 7 & 801 1.00 42.47

ATOM 1019 C ALA A 142 49.542 34.742 78.300 1.00 38.39

ATOM 1020 O ALA A 142 50.328 35.177 77.461 1.00 52.80

ATOM 1021 CB ALA A 142 49.281 32.311 77.674 1.00 49.99

ATOM 1022 N SEE A 143 48.571 35.494 78.784 1.00 27.65 ATOM 1023 CA SER A 143 48.420 36.864 78.322 1.00 16.40

ATOM 1024 C SER A 143 48.240 37.809 79.483 1.00 18.30

ATOM 1025 O SER A 143 48.027 37.403 80.632 1.00 11.06

ATOM 1026 CB SEE A 143 47.186 36.990 77.446 1.00 23.64

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ATOM 1087 O GLYA151 43.936 37.038 91.919 1.00 15.43

ATOM 1088 N VALA152 42.871 37.854 90.120 1.00 4.35

ATOM 1089 CA VALA152 41.615 38.009 90.824 1.00 2.06 ATOM 1090 C VALA152 41.106 36.691 91.367 1.00 5.21

ATOM 1091 O VALA152 40.554 36.631 92.469 1.00 15.36

ATOM 1092 CB VALA152 40.571 38.605 89.933 1.00 2.00

ATOM 1093 CGI VALA152 39.218 38.544 90.607 1.00 9.35

ATOM 1094 CG2VALA152 40.923 40.028 89.664 1.00 7.60 ATOM 1095 N LEU A 153 41.310 35.634 90.596 LOO 3.72

ATOM 1096 CA LEU A 153 40.889 34.304 91.003 1.00 3.58

ATOM 1097 C LEU A 153 41.728 33.761 92.133 1.00 7.42

ATOM 1098 O LEU A 153 41.188 33.323 93.151 1.00 17.63

ATOM 1099 CB LEU A 153 40.944 33.337 89.838 1.00 5.60 ATOM 1100 CG LEU A 153 39.783 33.577 88.903 1.00 15.20

ATOM 1101 CD1LEUA153 39.858 32.700 87.677 1.00 10.85

ATOM 1102 CD2LEUA153 38.539 33.333 89.691 1.00 7.86

ATOM 1103 N VALA154 43.041 33.754 91.947 LOO 10.83

ATOM 1104 CA VALA154 43.958 33.263 92.980 1.00 15.98 ATOM 1105 C VALA154 43.738 34.013 94.293 1.00 6.33

ATOM 1106 O VALA154 43.612 33.416 95.348 1.00 20.00

ATOM 1107 CB VALA154 45.431 33.374 92.546 1.00 12.42

ATOM 1108 CGI VAL A 154 46.325 32.955 93.660 1.00 3.98

ATOM 1109 CG2 VALA154 45.683 32.519 91.336 1.00 2.00 ATOM 1110 N ALA A 155 43.601 35.315 94.212 1.00 2.00

ATOM 1111 CA ALA A 155 43.347 36.088 95.397 1.00 2.00

ATOM 1112 C ALA A 155 42.043 35.662 96.036 1.00 5.28

ATOM 1113 O ALA A 155 41.923 35.628 97.253 1.00 20.59

ATOM 1114 CB ALA A 155 43.256 37.511 95.036 1.00 8.07 ATOM 1115 N SER A 156 41.050 35.366 95.213 1.00 8.01

ATOM 1116 CA SER A 156 39.749 34.985 95.721 1.00 2.28

ATOM 1117 C SER A 156 39.811 33.638 96.408 1.00 5.37

ATOM 1118 0 SER A 156 39.143 33.430 97.411 1.00 12.72 ATOM 1119 CB SER A 156 38.736 34.960 94.588 1.00 2.00

ATOM 1120 OG SER A 156 37.412 35.050 95.086 1.00 46.36

ATOM 1121 N HIS A 157 40.622 32.727 95.880 1.00 5.37

ATOM 1122 CA HIS A 157 40.747 31.392 96.455 1.00 5.03

ATOM 1123 C HIS A 157 41.569 31.433 97.719 1.00 9.12 ATOM 1124 0 HIS A 157 41.279 30.732 98.691 1.00 13.03

ATOM 1125 CB HIS A 157 41.398 30.421 95.481 1.00 3.02

ATOM 1126 CG HIS A 157 40.517 30.024 94.342 1.00 21.35

ATOM 1127 NDI HIS A 157 40.868 29.046 93.437 1.00 29.70

ATOM 1128 CD2 HIS A 157 39.314 30.497 93.941 1.00 19.82 ATOM 1129 CEl HIS A 157 39.921 28.939 92.523 1.00 27.64

ATOM 1130 NE2 HIS A 157 38.967 29.808 92.807 1.00 15.97

ATOM 1131 N LEU A 158 42.620 32.235 97.694 1.00 10.33

ATOM 1132 CA LEU A 158 43.475 32.385 98.851 1.00 5.20

ATOM 1133 C LEU A 158 42.602 32.883 99.965 1.00 2.00 ATOM 1134 O LEU A 158 42.634 32.365 101.052 1.00 13.61

ATOM 1135 CB LEU A 158 44.553 33.415 98.597 1.00 2.00

ATOM 1136 CG LEU A 158 45.522 33.581 99.751 1.00 5.32

ATOM 1137 CD1 LEU A 158 46.182 32.273 100.079 1.00 2.00

ATOM 1138 CD2 LEU A 158 46.560 34.558 99.326 1.00 9.58 ATOM 1139 N GLN A 159 41.785 33.872 99.662 1.00 4.25

ATOM 1140 CA GLN A 159 40.867 34.463 100.622 1.00 2.75

ATOM 1141 C GLN A 159 39.954 33.431 101.261 1.00 4.94

ATOM 1142 O GLN A 159 39.830 33.387 102.477 1.00 19.19

ATOM 1143 CB GLN A 159 40.003 35.519 99.932 1.00 28.14

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ZG'QZ 001 888 ^ 91682½ 9A6 SS SOI 0 dSV 90 898 HOXV

ZZ'L \ OOT m 9 6SI SIS SS SOT 0 dSV O 8 £ 98 HO V

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SI S OOT ^ 98291 Τ88Ί2 ^ OT 0 iiai VO 2Z9 MOJN 91

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ATOM 6070 OW WAT W 246 30.988 71.734 131.970 1.00 30.47

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ATOM 6073 OW WAT W 249 73.636 53.315 118.706 1.00 66.51

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ATOM 6076 OW WAT W 252 65.096 54.598 132.667 1.00 55.99

ATOM 6077 OW WAT W 253 39.331 13.455 135.759 1.00 57.18

ATOM 6078 OW WAT W 254 89.337 57.218 114.493 1.00 52.11

ATOM 6079 OW WAT W 255 63.958 21.368 127.030 1.00 52.06

ATOM 6080 OW WAT W 256 70.753 54.054 143.325 1.00 47.10

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END

In Table 1, the first line is the mathematical description of the crystal, showing the size of the unit cell (A unit in the order of the a-axis, b-axis, and c-axis), the angle formed by each axis, and the crystal system. . From the second line onwards, except for the last line, three-dimensional coordinates of each atom are described. ATOM in the first column indicates that this row is a row in atomic coordinates, the second column indicates the order of the atoms, the third column indicates the atom distinction in amino acid residues, etc., and the fourth column indicates the amino acid residue. The fifth column indicates the type of molecule (the same type indicates a single polypeptide chain), the fifth column indicates the number of the amino acid corresponding to SEQ ID NOS: 1 and 2, and the seventh column indicates the type of molecule. The 8th and 9th columns are the original Child coordinates (A units in the order of the a-axis, b-axis, and c-axis), the tenth column shows the occupancy of the atom (all 1.00 in the present invention), and the eleventh column shows the temperature factor of the atom. Is shown. The last row indicates that this is the last row in the table. The type of molecule is that A and C are each one molecule of G-CSF, B and D are each one molecule of CRH-G-CSF-R, and E and F are B and The linked sugar chain linked to D indicates the water molecule found in the crystal. In the fourth column, except for the amino acid residues, NAG represents N-acetyltyldarcosamine residue, and WAT represents a water molecule. This table is described in accordance with the format of Protein'Data @ Bank, which is a notation commonly used by those skilled in the art.

From the structural coordinates, one molecule of G—CSF (A) and one molecule of CRH—G—CSF—R (B) form a complex (A—B), and another molecule of G—CSF (C) It can be seen that another molecule (D) of CRH-G-CSF-R forms a complex (C-D). Furthermore, it can be seen that the complex (A-B) and the complex (C-D) 1 form an aggregate of two molecules of the complex around the axis of non-crystallographic symmetry. In the present specification, such an aggregate of the complex may be simply referred to as “complex”.

Based on the structural coordinates obtained from the crystal of the complex of G-CSF and CRH-G-CSF-R, the Ripon diagram is a notation method commonly used by those skilled in the art to understand the structure of proteins. Fig. 1 shows the structure viewed from the direction perpendicular to the non-crystallographic pseudo-two-fold symmetry axis, and Fig. 2 shows the structure viewed from a direction parallel to the coaxial axis. As can be seen from these figures, the complex crystal of G-CSF and CRH-G-CSF-R has the smallest unit without crystallographic symmetry, namely, the complex of two molecules in the asymmetric unit. Contains the body (-8 and .10). The complex of these two molecules is macroscopically related by a non-crystallographic quasi-double symmetry axis. The G-CSF part consists of four long a-helices, one short a-helix and the loop region connecting them. The CRH-G-CSF-R portion is roughly divided into two regions, each of which is composed of about 7) 3 sheets, and these regions are connected by loop regions. Hereinafter, these two regions are referred to as a BN domain near the N-terminus and a BC domain near the C-terminus. From these three-dimensional structures, G—CSF—R signals are received by G—CSF—R — It can be understood that CSF binds to G—CSF—R, that is, a complex of two molecules forms an association in the relative configuration shown in the figure.

Generally, the extracellular parts of G-CSF and G-CSF-R form a complex in solution with a stoichiometrically equivalent amount of substance, and the complex is a dimer or tetramer. (Horan, TP et al., J. Biochem. (Tokyo), 121: 370-375 (1997); Horan, TP et al., Biochemistry, 35: 4886-4896 (1996). ), Hiraoka, 0. et al., J. Biol. Chem., 270: 2592 8-25934 (1995); ffiraoka'O. Et al., FEBS Lett., 356: 255-260 (1994)). The aggregate formed by two molecules of G—CSF and two molecules of CRH—G—CSF—R disclosed in the present invention is considered to reflect these facts.

The amino acid residues M1 to L4 in the molecule A of G—CSF and the side chain portion of Q71 and L131, and the amino acid residues M1 to P6 in the molecule C of G—CSF and H53, W59, Amino acid residues from G120 to H126, K214 to A215 in molecule B of CRH—G—CSF-R, and side chain portions of K63 and R64, Al In the molecule D of CRH—G—CSF—R, the amino acid residues Al, 119-H126, K214-A215, and the side chains of K62, Κ63, R64, and Q127 are in the crystal. However, their positions are not fixed, and are excluded from consideration in X-ray crystallography.

Here, even in the structure of the crystal containing the mutant of G—CSF and the mutant of Z or G—CSF—R, those substantially matching the crystal structure according to the present invention are within the scope of the present invention. . Substantially identical means that the main part of the structure, specifically, the part that forms the secondary structure such as α-helix or / 3 sheet structure, or the temperature factor is lower than the other parts In the part, the structure where the mean square deviation of the main chain or C carbon part of the corresponding part is about 2 mm or less. In addition, the start site and end site of each sequence are not necessarily strictly defined in the present invention, and those in which another protein is bound to the N-terminal and / or C-terminal portion, the N-terminal and / or Substances that do not substantially change the recognition of G-CSF and G-CSF-R molecules, such as the addition of one or more amino acid residues at the C-terminus, are included in the present description. . Ma The scope of the present invention is not limited to those having a linked sugar chain, those having a sugar chain portion deleted, and the like that do not substantially change the recognition of G-CSF and G-CSF-R molecules. It is. Substantially identical in terms of molecular recognition refers to a structure in which the mean square deviation of the main chain or C carbon portion of the amino acid residue corresponding to molecular recognition is about 2 A or less.

The two molecules of the complex of G—C S F and C RH—G—C S F—R are microscopically different in their structure; For the two molecules of the complex (Molecules A and B, and Molecules and D), the part that has the secondary structure of each G—CSF, that is, the helix region of Molecules A and C has the best match. When one of the complex molecules is mathematically translated and rotated in a three-dimensional space, the orientations of molecule B and molecule D are different between the BN domain and the BC domain. That is, the complex of two molecules contained in a crystallographically independent unit has a slightly different positional relationship between G-CSF and CRH-G-CSF-R, and in the BN domain, An orientation difference of about 10 degrees and about 8 degrees in the BC domain is observed. In general, when a substance becomes a crystal, it goes to the state with the lowest free energy according to the laws of natural sciences, but in the crystalline state, the molecule has two crystallographically independent units having different structures. Indicates that the energy that is reduced in the crystalline state is larger than the energy that rises due to the difference in the structure. Furthermore, it becomes possible for the first time to identify the amino acid residues that interact with G-CSF and CRH-G-CSF-R from the structural coordinates revealed by the present invention. The interatomic distance between each residue is less than 4.2 A for atoms interacting with Hunder-Walders, and greater than 3.4 A for atoms interacting electrostatically. Table 2, Table 3, Table 4, and Table 5 show the followings as hydrogen bonds of 3.4A or less. For hydrogen bonds, those via water molecules are also shown. Table 2

The distance between each atom of the amino acid residue interacting with the molecule 8 of 0—〇3 and 01 1 ^ —0—〇3? —1 and the interaction, and the mode of interaction. G-CSF (molecule A) CRH-G-CSF-R (molecule B) Distance (A) Format

S13 0 L196 CD2 3.9 VDW

L16 CD1 S195 0 3.9 VDW

L16 CD1 S195 CB 3.4 VDW

L16 CB L196 CG 4.2 VDW

L16 CB L196 CD1 4.0 VDW

K17 0 Y78 CE1 4.2 VDW

K17 CB Y78 CD1 3.8 VDW

K17 CG Y78 GDI 4.0 VDW

K17 CG L196 CD2 4.1 VDW

K17 CD Y78 CD1 4.0 VDW

K17 CD D102 OD2 3.9 VDW

K17 CE D102 OD2 3.3 VDW

K17 CE D105 OD1 4.2 VDW

K17 NZ Y80 OH 3.9 VDW

K17 NZ Y80 CZ 4.2 VDW

K17 NZ Y80 CE1 3.9 VDW

K17 NZ D102 CB 4.2 VDW

K17 NZ D102 CG 3.9 VDW

K17 NZ D102 OD2 2.9 HYB

K17 NZ D105 OD1 4.4 ESI

K17 NZ D105 OD2 4.5 ESI

E20 0 Y143 CD2 4.0 VDW

E20 CB Y78 OH 4.2 VDW

E20 CG Y78 OH 3.5 VDW

E20 CG Y143 0 3.9 VDW

E20 CG Y143 CD2 3.8 VDW

E20 CG Y143 CE2 3.9 VDW

E20 CD Y78 CE1 4.2 VDW E20 CD Y78 OH 3.5 VDW

E20 CD Y143 CE2 4.1 VDW

E20 CD R193 NE 3.9 VDW

E20 CD E193 CZ 4.2 VDW

E20 CD R193 NH2 3.5 VDW

E20 OE1 M144 CA 4.2 VDW

E20 OE1 M144 CG 3.8 VDW

E20 OE1 E145 N 2.8 2.8 WMH WAT6

E20 OE1 R193 NE 3.2 HYB

E20 OE1 R193 CZ 3.8 VDW

E20 OE1 R193 NH2 3.4 HYB

E20 OE2 Y78 CE1 3.3 VDW

E20 OE2 Y78 CZ 3.4 VDW

E20 OE2 Y78 OH 2.7 HYB

E20 OE2 Y143 CE2 3.9 VDW

E20 OE2 R193 NE 3.7 VDW

E20 OE2 R193 CZ 3.7 VDW

E20 OE2 R193 NH2 2.9 HYB

Q21 CG Y78 CG 3.8 VDW

Q21 CG Y78 GDI 4.2 VDW

Q21 CG Y78 CD2 3.4 VDW

Q21 CG Y78 CE1 4.2 VDW

Q21 CG Y78 CE2 3.3 VDW

Q21 CG Y78 CZ 3.8 VDW

Q21 CD Y78 CB 3.9 VDW

Q21 CD Y78 CG 3.6 VDW

Q21 CD Y78 CD2 3.3 VDW

Q21 CD Y78 CE2 3.8 VDW

Q21 OE1 Y78 CB 3.6 VDW Q21 OE1 Y78 CG 3.7 VDW

Q21 OE1 Y78 CD2 3.8 VDW

Q21 NE2 Y78 CG 4.1 VDW

Q21 NE2 Y78 CD2 3.4 VDW

Q21 NE2 Y78 CE2 4.0 VDW

R23 C Y143 CB 4.2 VDW

R23 CB Y143 0 3.7 VDW

R23 CD Y143 0 3.5 VDW

R23 NHl Y143 0 3.3 HYB

R23 NHl E145 N 3.8 VDW

R23 NHl E145 N 3.4 2.8 WMH WAT6

R23 NHl E145 CB 4.0 VDW

R23 NH2 E145 CD 4.1 VDW

R23 NH2 E145 OE1 3.8 ESI

R23 NH2 E145 OE2 4.5 ESI

K24 N Y143 CB 3.9 VDW

K24 CA Y143 CB 3.8 VDW

24 CA Y143 CG 4.0 VDW

K24 CB Y143 CG 3.9 VDW

K24 CB Y143 CD2 3.8 VDW

K24 CG Y143 CD2 4.2 VDW

K24 CG Y143 CG 4.2 VDW

K24 CD Y143 CE2 4.2 VDW Belly NZ Y143 CZ 3.9 VDW

K24 NZ Y143 OH 4.1 VDW

K24 NZ Y143 CE1 3.8 VDW

L109 CB R72 CZ 4.2 VDW

L109 CB R72 NHl 4.0 VDW

DUO N R72 NHl 4.1 VDW DllO CG R72 NH1 3.7 VDW

DllO OD1 R72 NH1 3.2 HYB

DllO OD1 R72 NH1 3.3 3.3 WMH

DllO OD2 R72 NH1 4.0 ESI

D113 CA L76 GDI 4.0 VDW

D113 0 L76 CD1 4.1 VDW

D113 CB R72 NH2 4.2 VDW

D113 CB L76 cm 3.7 VDW

D113 CG R72 NH2 3.2 VDW

D113 CG L76 GDI 3.7 VDW

D113 OD1 R72 NH2 3.8 ESI

D113 OD1 L76 CD1 4.2 VDW

D113 OD2 E72 CZ 3.7 VDW

D113 OD2 R72 NH2 2.4 HYB

D113 OD2 L75 0 3.6 VDW

D113 OD2 L76 CA 3.7 VDW

D113 OD2 L76 C 4.2 VDW

D113 OD2 L76 CD1 3.7 VDW

D113 OD2 L77 N 3.6 VDW

T116 CG2 L76 GDI 4.2 VDW

T116 CG2 L76 CD2 4.1 VDW

T116 CB L76 GDI 4.1 VDW

T117 OG1 L77 0 3.4 VDW

T117 OG1 Y78 C 4.1 VDW

T117 OG1 Y78 0 3.7 VDW

T117 OG1 Y78 CB 3.9 VDW

Q120 CB Q79 OE1 4.1 VDW

Q120 CD L76 CD2 4.1 VDW

Q120 OE1 S45 0 3.3 3.0 WMH Q120 OE1 L76 CD2 3.7 VDW

Q120 OE1 Q79 CB 4.0 VDW

Q120 OE1 Q79 CG 3.2 VDW

Q120 OE1 Q79 CD 3.8 VDW

Q120 OE1 Q79 OE1 3.6 VDW

E123 CB R46 NH2 3.7 VDW

E123 OE1 R46 NH2 4.3 ESI

E124 N R46 NH2 3.9 VDW

E124 N R46 CZ 4.2 VDW

E124 OE1 R46 CB 4.2 VDW

E124 CA R46 NH1 4.0 VDW

E124 CA cz 4 2 VDW

E124 OE1 R46 CD 3.4 VDW

E124 CB R46 CZ 4.0 VDW

E124 CB R46 NH1 3.9 VDW

E124 CG R46 NH1 4.1 VDW Table 3

The distance between each atom of the amino acid residue interacting with the molecule A of G—CSF and the molecule D of CRH—G—CSF—R, the interaction, and the mode of interaction.

G-CSF (molecule A) CRH-G-CSF-R (molecule D) Distance (A) Format

G5 CA P168 CD 4.1 VDW

G5 CA K171 CE 3.9 VDW

P6 C Ή.166 O 3.6 VDW

P6 0 F165 O 4.0 VDW

P6 0 H166 O 3.3 VDW

P6 0 H166 CB 3.7 VDW

P6 0 H166 C 4.1 VDW P6 CD H166 0 4.2 VDW

P6 CD P168 CD 4.2 VDW

P6 CG H166 0 3.6 VDW

A7 N H166 0 4.0 VDW

A7 CA F165 0 3.3 VDW

A7 GA H166 0 4.2 VDW

A7 C F165 0 3.7 VDW

A7 CB V164 CGI 3.5 VDW

A7 CB F165 0 4.0 VDW

A7 CB L167 CD2 3.5 VDW

S8 N F165 N 4.2 VDW

S8 N F165 0 3.3 HYB

S8 C F165 N 3.9 VDW

S8 O V164 CA 3.7 VDW

S8 O V164 C 3.7 VDW

S8 0 F165 N 2.8 HYB

S8 O F165 CA 3.6 VDW

S8 0 F165 C 4.1 VDW

S8 0 F165 0 3.8 VDW

S8 O F165 CB 3.5 VDW

S8 0 F165 CG 3.8 VDW

S8 0 F165 GDI 3.3 VDW

S9 CA L163 0 3.7 VDW

S9 C F165 CD1 3.6 VDW

S9 c F165 CE1 3.8 VDW

S9 0 F165 GDI 3.7 VDW

S9 0 F165 CE1 3.3 VDW

L10 N F165 GDI 3.8 VDW

L10 N F165 CE1 4.1 VDW L10 CA F165 CD1 4.0 VDW

L10 CA F165 CE1 4.1 VDW

L10 G F165 GDI 3.6 VDW

L10 C F165 CE1 4.0 VDW

L10 0 F165 CB 4.2 VDW

L10 0 F165 cm 3.8 VDW

Pll N F165 CG 4.2 VDW

Pll N F165 cm 3.6 VDW

Pll N F165 CE1 3.7 VDW

Pll CA F165 CG 4.2 VDW

Pll CA F165 GDI 4.1 VDW

Pll C H166 NE2 4.0 VDW

Pll GG F165 CE1 3.7 VDW

Pll CG F165 CE2 4.1 VDW

Pll CG F165 CZ 3.6 VDW

Pll CD F165 CD1 4.2 VDW

Pll CD F165 CE1 3.7 VDW

Pll CD F165 CZ 4.2 VDW

Q12 N H166 CD2 3.9 VDW

Q12 N H166 NE2 3.1 HYB

Q12 N H166 CE1 4.1 VDW

Q12 CA H166 NE2 3.7 VDW

Q12 CB H166 CD2 4.2 VDW

Q12 CB H166 CE1 3.6 VDW

Q12 CB H166 NE2 3.2 VDW

L125 0 W161 0 3.8 VDW

L125 CD2 F165 CZ 3.6 VDW

L125 CD2 F165 CE1 3.7 VDW Table 4

The distance between each atom of the amino acid residue interacting with the molecule C of G—CSF and the molecule D of CRH—G—CSF—R, and the mode of interaction.

G-CSF (molecule C) CEH-G-CSF-R (molecule D) Distance (A) Format

S13 0 L196 CD2 4.2 VDW

L16 C L196 cm 4.2 VDW

L16 GB L196 CD1 4.0 VDW

L16 GDI S195 CB 3.5 VDW

LL1166 CCDD11 SS119955 OOGG 44..22 VDW

K17 CB Y78 CD2 4.2 VDW

K17 CG L196 CD1 4.2 YDW

K17 CG L196 CD2 4.1 VDW

K17 CE L196 CD2 4.2 VDW

KK1177 NNZZ DD110022 OODD22 44..55 ESI

E20 O Y143 0 4.2 VDW

E20 0 Y143 CD2 3.9 VDW

E20 CG Y78 OH 3.8 VDW

E20 CG Y143 0 3.9 VDW

EE2200 CCGG YY114433 CCDD22 3 3.88 VDW

E20 CG Y143 CE2 3.9 VDW

E20 CD Y78 OH 3.8 VDW

E20 CD Y143 CE2 4.1 VDW

E20 CD R193 NH2 3.6 VDW

EE2200 CCDD RR119933 NNEE 33..77 VDW

E20 CD R193 CZ 4.1 VDW

E20 OE1 Y78 CE2 3.5 VDW

E20 OE1 Y78 CZ 3.7 VDW

E20 OE1 Y78 OH 3.0 HYB E20 OE1 Y143 CE2 4.1 VDW

E20 OE1 R193 CZ 3.6 VDW

E20 OE1 R193 NH2 2.8 HYB

E20 OE1 R193 NE 3.5 ESI

E20 OE2 M144 CA 4.1 VDW

E20 OE2 M144 CG 3.7 VDW

E20 OE2 R193 CG 4.0 VDW

E20 OE2 R193 CD 4.1 VDW

E20 OE2 R193 NH2 3.7 ESI

E20 OE2 R193 NE 3.1 HYB

E20 OE2 R193 CZ 3.8 VDW

Q21 CG Y78 CG 3.9 VDW

Q21 CG Y78 CD1 3.7 VDW

Q21 CG Y78 CD2 3.9 VDW

Q21 CG Y78 CE1 3.6 VDW

Q21 CG Y78 CE2 3.8 VDW

Q21 CG Y78 CZ 3.7 VDW

Q21 CD Y78 CB 4.0 VDW

Q21 CD Y78 CG 3.6 VDW

Q21 CD Y78 CD1 3.6 VDW

Q21 CD Y78 CD2 4.0 VDW

Q21 CD Y78 CE1 4.1 VDW

Q21 OE1 Y78 CB 3.9 VDW

Q21 OE1 Y78 CG 3.9 VDW

Q21 OE1 Y78 CD2 4.2 VDW

Q21 NE2 Y78 CB 4.0 VDW

Q21 NE2 Y78 CG 3.8 VDW

Q21 NE2 Y78 GDI 3.5 VDW

Q21 NE2 Y78 CE1 4.1 VDW R23 C Y143 CB 3.7 VDW

R23 0 Y143 CB 3.9 VDW

R23 CB Y143 CA 3.9 VDW

E23 CB Y143 C 4.0 VDW

R23 CB Y143 0 3.3 VDW

R23 CB Y143 CB 3.8 VDW

R23 CG Y143 0 3.9 VDW

K23 CD Y143 C 3.9 VDW

R23 CD Y143 0 3.1 VDW

R23 CD Y143 CA 4.2 VDW

R23 NE Y143 0 3.9 VDW

R23 NE E145 OE2 4.1 ESI

E23 CZ Y143 0 3.9 VDW

R23 cz E145 CB 4.1 VDW

R23 CZ E145 OE2 3.9 VDW

E23 cz E145 CD 4.1 VDW 23 NH1 Y143 0 3.2 HYB

R23 NH1 E145 N 3.6 VDW

R23 NH1 E145 CA 4.2 VDW

R23 NH1 E145 CB 3.6 VDW

R23 NH2 E145 CB 4.0 VDW

R23 NH2 E145 CD 3.7 VDW

R23 NH2 E145 OE1 3.5 ESI

R23 NH2 E145 OE2 3.9 ESI

K24 N Y143 CB 3.5 VDW

K24 N Y143 CG 4.0 VDW

K24 N Y143 CD2 4.1 VDW

K24 CA Y143 CB 3.6 VDW

K24 CA Y143 CG 3.8 VDW K24 CA Y143 CD2 4.0 VDW

K24 CB Y143 GE2 4.2 VDW

K24 CB Y143 CG 4.0 VDW

K24 CB Y143 CD2 3.8 VDW

K24 CG Y143 CG 4.2 VDW

K24 CG Y143 CD2 4.1 VDW

K24 CG Y143 CE2 4.2 VDW

K24 CD Y78 OH 3.7 VDW

K24 CD Y143 CE2 4.0 VDW

K24 CD Y143 CZ 4.1 VDW

K24 CD M104 CE 4.1 VDW

K24 CE M104 CE 3.8 VDW

K24 CE L77 cm 3.9 VDW

K24 NZ M104 CE 3.9 VDW

K24 NZ Y143 CE1 4.0 VDW

K24 NZ Y143 CZ 3.9 VDW

K24 NZ Y143 OH 3.8 VDW

L109 C R72 NHl 4.1 VDW

L109 c R72 NH2 4.2 VDW

L109 CB R72 CZ 3.6 VDW

L109 CB R72 NHl 3.6 VDW

L109 CB R72 NH2 3.6 VDW

L109 GDI R72 NE 4.1 VDW

L109 CD1 R72 CZ 4.1 VDW

L109 GDI K73 CA 4.1 VDW

DllO N R72 NHl 3.7 VDW

DllO CG R72 NHl 3.2 VDW

DllO CA R72 NHl 4.1 VDW

DllO CB R72 NHl 4.2 VDW ΟΛ L ε ao 8

9 ε 0 8 入 LTI

ΟΛ Z f D TOO, ΤΙΧ

Z f 0 LL1 TOO 2-IXX

ΟΛ 6 ε ao ZQO sua 92

8 ε νο Ζ Ί ZQO ετχα

6 Z Ν Mumm Ί ZQ.0 εχτα

L ε 0 LLI 2 (10 εττα

0 LLT. ZQ.0 ειια

ΟΛ 9L1 zao ετχα 02

ε ε 92/1 ZQO εχτα

ΟΛ νο 9 ム Ί zao ετχα 丛 OA 9 · 0 dLT zao εττα

(ΙΛ 0 SAT ZQO επα

3Λ.Η τ ε ZQ.0 ετχα 9Τ ΟΛ χαο 9 mm Ί ταο εχτα

isa S ム τ ταο ετχα

CEA O f Ν LLI 00 ειτα ΟΛ T 0 L T ΌΟ εττα

Z'2 ιαο 911 00 ειτα Οΐ

6 ε ΖίΈ. ΌΟετχα

6 ε 0 ao εττα

CL \ 9 ε χαο 92 Ί 90 ειια

NQA 0 ταο ετια

L ζ ε ε ιαο ZQO οττα

isa ε ΤΗΝ ZOO οττα

6 8 ταο ΙίΊ ιαο οπα

am ΙΗΝ ZLU ταο οιτα

丛 OA 6 ・ ε ζο ZLU ιαο οιια

6 Ζ T0 / I0df / X3d C6S99 / 10 OAV Q120 CD R46, NE 4.1 VDW

Q120 CD Q79 OE1 4.2 VDW

Q120 OE1 Q79 CG 3.8 VDW

Q120 OE1 Q79 CD 3.7 VDW

Q120 OE1 Q79 OE1 3.0 VDW

Q120 NE2 R46 NE 4.0 VDW

E123 OE1 R46 NH2 4.6 ESI Table 5

The distance between each atom of the amino acid residue interacting with the molecule C of G—CSF and the molecule B of CRH—G—CSF—R, and the mode of interaction.

G-CSF (molecule C) CRH-G-CSF-R (molecule B) Distance (A) Format

A7 N H166 0 3.4 VDW

A7 N H166 CB 4.2 VDW

A7 CA F165 C 4.2 VDW

A7 CA F165 0 3.0 VDW

A7 CA H166 C 3.9 VDW

A7 CA H166 0 3.3 VDW

A7 CA H166 CB 3.9 VDW

A7 C F165 0 3.5 VDW

A7 CB F165 0 3.3 VDW

A7 CB H166 C 4.0 VDW

A7 CB H166 0 3.4 VDW

A7 CB L167 CD2 3.9 VDW

S8 N F165 C 4.0 VDW

S8 N F165 0 3.0 HYB

S8 GA F165 0 4.2 VDW

S8 C F165 N 4.0 VDW τ ττ

6 ε 991 Η 0 IXd

ΛνθΛ 8 ε 99ΪΗ YD TTd

0 99TH 0 on

GLV 6 ε 99IH 0 on ΟΛ Vf 0 on

ΛνθΛ Z f 391 ^ 0 on ΟΛ Z f 0 o OZ

▲▲ T

ΛιΟΛ 6 ε 0 on ΟΛ I f 291 ^ vo on

Z'f Z "3 S9T> J N on

ΛνθΛ z ε 291 ^ 0 6S ST

ΛνΟΛ s ε 291 ^ 0 6S

A

8 ε 0 6S

9ε 9ld 0 6S

CL \ Z f 99ld vo 6S

Z'f 0 89TT vo 6S 01 A

9 ε 0 8S

ΟΛ 0 0 8S

mQA 2 £ 90 0 8S

QA 6 ε 0 0 8S

s ε νο 291 ^ 0 8S am Ν ΒΙΛ 0 8S

IAGA 8 ε 0 91 Α 0 8S

6ε Ψ9ΧΑ 0 8S T0 / I0df / X3d C6S99 / 10 OAV Pll CB F165 CE1 4.0 VDW

Pll CB F165 GDI 4.2 VDW

Pll CD F165 CD2 4.2 VDW

Pll CD F165 CE1 3.8 VDW

Pll CD F165 CZ 3.9 VDW

Q12 N H166 CD2 4.1 VDW

Q12 N H166 CE1 3.9 VDW

Q12 N H166 NE2 3.1 HYB

Q12 CA H166 NE2 4.0 VDW

Q12 CB H166 CE1 3.8 VDW

Q12 CB H166 NE2 3.7 VDW

L125 O L163 N 3.4 3.0 WMH

L125 CD2 F165 CE2 4.2 VDW

L125 CD2 F165 CZ 4.1 VDW

Table 2 shows G—CSF molecule A and CRH—G—CSF—R molecule B, Table 3 shows G—CSF molecule A and CRH—G—CSF—R molecule D, and Table 4 shows G—CSF Molecule C and CRH—G—CSF—R molecule D, Table 5 shows each atom of an amino acid residue interacting with G—CSF molecule C and CRH—G—CSF-R molecule B And the distance of their interaction, and the mode of interaction. From the structural coordinates shown in Table 1, the atomic distance between each residue between G—CSF (molecules A and C) and CRH—G—CSF—R (molecules B and D) is van der Waals Acting atoms of 4.2 A or less, electrostatically interacting atoms of greater than 3.4 A and 5.OA or less, and hydrogen bonds of 3.4 A or less Are shown in Table 2, Table 3, Table 4, and Table 5, respectively. Note that hydrogen bonds are also shown via water molecules. The first column is the amino acid residue of molecule A or C and its number, the second column is the atom of that amino acid residue, the third column is the amino acid residue of B or D and its number, The first column describes the atoms of the amino acid residue, the fifth column describes the distance between those atoms in A units, and the sixth column describes the mode of interaction. VDW indicates van der Waals interaction, ESI indicates electrostatic interaction, and HYB indicates hydrogen bonding. Furthermore, regarding hydrogen bonding via water molecules, the interatomic distance has two values, so the fifth column is further divided into two values, and the respective values are shown. The column shows the number of the water molecule involved.

First, in one molecule of CRH-G-CSF-R, each loop region of the domain divided into two recognizes one molecule of G-CSF on one side. As amino acid residues that characterize this recognition, 0-Rei_3 in side 313, L 16, K17, E20 , Q21, R23, K24, L 109, D110, D 113, T 1 16, T 1 17 S Q120 , E123, E124 (Table 2, Table 4), CRH—G—CSF—R side N20, S45, R46, R72, K73, L75, L76, L77, Y78, Q79, Y80, D 102, M104, D105, Y143,

Ml44, E145, R193, S195, L196 (Table 2, Table 4). That is, recognition of one molecule of G-CSF and one molecule of G-CSF-R (that is, formation of a complex) is characterized by the interaction of these amino acid residues and the amino acid residues in the vicinity thereof. Attached.

Next, two molecules of the complex are recognized and recognized (that is, the association of the complex) in a relationship macroscopically related by a non-crystallographic pseudo-two-fold symmetry axis. The amino acid residues that characterize this recognition are G5, P6, A7, S8, S9, L10, Pll, Q12, and L125 (Table 3, Table 5) on the G—CSF side. — G— CSF— On the R side, Wl 61, LI 63, VI 64, F 165, HI 66, L 167, P 168, and l 71 (Tables 3 and 5). That is, G—CSF

The complex consisting of one molecule and one molecule of CRH-G-CSF-R is further associated to form a dimer of the complex, and its recognition is based on these amino acid residues and the amino acids around them. Characterized by the interaction of acid residues.

The area surrounded by the complex dimer (ie, the aggregate) forms a space in which water molecules are present. This space is characterized by Y3 to L14, R46 to Y51, G92 to V106, E145 to E147, H166 to S169, S194 to G198, and the amino acid residues in the vicinity in CRH-G-CSF-R. ing.

The structural coordinates shown in Table 1 are based on the origin of the unit cell in the crystal in three-dimensional space. It is described as the origin in. In the case where the structural coordinates of the present invention are used for calculation by a computer, as a result of performing a mathematical movement operation such as translation, rotation, or symmetry in a three-dimensional space 変化 without changing the relative arrangement of each atom. The resulting new structural coordinates are also within the scope of the present invention.

3. Superposition of 3D structural coordinates of leptin and G—CSF

From the three-dimensional structural coordinates of the complex of G—CSF and CRH—G—CSF—R obtained as described above, homology modeling (Haruki Nakamura, Kenta Nakai, Introduction to Computers for Biotechnology, 186-204, Corona, 1995) can be used to determine the three-dimensional structural coordinates of the complex of leptin and the CRH-leptin receptor.

Lebutin used in the present invention is derived from mammals, preferably mice, rats, and humans, and particularly preferably humans. The three-dimensional structural coordinates of human leptin have been reported by Zhang et al. (Zhang, Υ · et al., Nature, 387: 206-209 (1997)). The three-dimensional structural coordinates of G-CSF are those of G-CSF derived from a mammal, preferably a mouse, a human, and particularly preferably a human. The three-dimensional structure coordinates of human G—CSF can be those of the complex of human G—CSF and mouse CRH—G—CSF—R in Table 1. Leptin and G-CSF both have a 4-helix 'bundle structure and are very similar in steric structure.

As a first step in homology modeling, a hypothetical leptin-CRH-G-CSF-R complex is formed by replacing leptin with G-CSF in the G-CSF ■ CRH-G-CSF-R complex. This is made possible by overlaying the three-dimensional structures of leptin and G—CSF in the G—CSF′CRHGCSF—R complex. In order to superimpose the three-dimensional structures, it is necessary to make correspondences between residues in advance by alignment. Sequence alignment cannot be used because leptin and G-CSF have no significant similarity at the amino acid sequence level. The term “sequence alignment” as used herein refers to an operation of associating the amino acid sequences of two or more different proteins so that the similarity is maximized. However, leptin and G—CSF are at a high level at the three-dimensional structure level. In order to show similarity, correspondence between residues can be determined by structural alignment. Structural alignment here is an operation that evaluates the similarity of relative positions in a three-dimensional structure, instead of amino acid sequence information, and finds a residue pair at a structurally corresponding position. Therefore, if a structural alignment is used, even if no sequence-level similarity is found, an alignment can be constructed if the three-dimensional structures are similar. As a computer program for this purpose, a program developed by this research institute (JP-A-10-185925) can be used, and a program suitable for the purpose is not limited to this.

Here, a structural alignment was created by the following procedure. In creating the structural alignment, the relative position of each residue in the protein 3D structure from the 3 carbons of the residue of interest to the 0 carbon of all other residues from the N-terminal to the C-terminal of the betattle And are represented as ordered sets. The 残基 -axis, X-axis and Υ are obtained by projecting the vector from the α-carbon to the main-chain oxygen and the X-axis and the α-carbon of the residue of interest to the plane perpendicular to the X-axis. On the local coordinate system with the vector product of the axes on the Ζ axis, the betattles for all other residues are represented. The similarity between residues is calculated as the similarity of this structural environment. The similarity between two structural environments is expressed as an alignment score when the ordered set of the two vectors is optimally juxtaposed by dynamic programming. The similarity between each vector in the calculation is

Is required. Here, a is an appropriate scaling factor, b is an element to avoid division by 0, and VI and V2 are two vectors to be compared. Dynamic programming for finding the similarity of structural environments is called lower dynamic programming. The dynamic planning method in this case means solving the following recurrence formula using the similarity between the above vectors.

D (i, j) = s (i, j) + Ma x {D (i−1, j − 1),

E (i-1, j-1), F (i-2, j-1)} E (i, j) = Max x (D (i, j)-a,

E (i, j-1) -β}

F (i, j) = Ma x (D (i, j) -a, F (i-1, j) one] 3}

s (i, j) represents the similarity between the two betatles mentioned above. i and j indicate that the i-th,; i-th vector in each structural environment is symmetric. D is a comparison matrix for dynamic programming, and E and F are auxiliary matrices for speedup. The size of the rows and columns in each matrix corresponds to the number of vectors that make up the structural environment to be compared. One considers the opening penalty of affine penalty in lower dynamic programming.

Indicates extension penalty.

Using the similarity between residues obtained by this method, the correspondence between residues, that is, alignment can be obtained by dynamic programming. Dynamic programming for finding the correspondence between residues is called upper dynamic programming. The recursion formulas solved are almost the same as those listed above, but the meaning of each element is different.

D (i, j) = s (i, j) + Max x (D (i-1, j-1),

E (i-1, j -2), F (i-one 2, j -1)}

E (i, j) = M ax (D (i, j) a x s e c,

E (i j — 1) —] 3 x s e c}

F (i, j) = Ma x {D (i j) — o; x se c,

F (i 1, j) — J3 x se c}

D is a comparison matrix for dynamic programming, and E and F are auxiliary matrices for speedup. The size of the rows and columns of each matrix corresponds to the number of residues that make up the compared proteins. s (i, j) is the similarity between residues i and j obtained by the lower dynamic programming. i and j indicate that the ith and jth residues of each protein are symmetric. a and / 3 represent the opening penalty and extension penalty of the afcne penalty in the dynamic g † method. sec is a factor that expresses the difficulty of insertion / deletion at residues in the secondary structure.

Structural alignment by this method is called double dynamic programming because dynamic programming is used in two different stages (Taylor, WR, et al., J. Mol. Biol. 2008, 1- 22 (1 989)).

Since this method requires a great deal of calculation time to create an alignment, a two-stage calculation as shown below can achieve high-speed alignment without reducing the accuracy of the alignment. (Toh, H., CABIOS, 13, 3787-396 (19997));

0-1 8 5 9 2 5). First, a distance cutoff is introduced, and only the residues within the cutoff distance from the residue of interest are used to approximately represent the structural environment of that residue. This is called the local environment. In addition, in this local environment, the number of residues located at the N-terminus and the number of residues located at the C-terminus from the residue of interest are stored. The similarity between two residues can be determined by applying low-level dynamic programming to this local environment. In the local environment, the lower dynamic programming itself can be calculated at high speed because its components are reduced. In addition, if a certain residue pair exists at a similar position, the number of residues constituting the local environment is expected to be similar. Conversely, if the number of constituent residues in the local environment is significantly different, the residue pairs are considered to be dissimilar in structural environment. Therefore, in the local environment, the number of residues located at the N-terminus and the number of residues located at the C-terminus from the residue of interest are compared with each other. If it is larger, the calculation of the lower dynamic programming is skipped and the similarity is set to 0.0. This approximation is called Δ Ν cutoff. With the introduction of these two approximations, alignment can be obtained at high speed, but the accuracy is reduced. However, since the obtained approximate alignment is very similar to the alignment created without introducing the approximation, the ε-suboptimal region of this approximate alignment was determined, and only for the residue pairs found in that region, By applying the double-dynamic method calculation without introducing approximation, it is possible to obtain structural alignment at high speed without reducing accuracy. The ε-suboptimal region was determined by the method of Vingron et al. (Vingron, M., et al., Protein Eng., 3, 565-569 (1990)). f is an index indicating the deviation from the score of juxtaposition. It is a parameter that determines the size of the suboptimal region. In this case, the unit is the standard deviation of the similarity between residues obtained when performing the approximate alignment.

Based on the obtained structural alignment, leptin and G—CSF • CRH—G—

The superposition of lebutin and G-CSF is performed by computer to minimize the square root of the mean square error between the main chain atoms of the corresponding residues of the G-CSF alignment width in the CSF-R complex. Can be done above. The computer program for this purpose is a program that performs molecular modeling commonly performed by those skilled in the art. Ram can be used. Programs suitable for this purpose are, for example, Insightll

(Molecular Simulation Inc), but is not limited to this. Deleting the G-CSF after leptin superposition creates a hypothetical leptin'CRH-G-CSF-R complex.

The computer used here is a computer on which these programs operate, and as a computer medium, the structural coordinates of a complex of leptin and CRH-lebutin receptor are read on the computer program. There is no particular limitation as long as it can do the job. For example, it may be an electrical temporary storage medium called a memory, or a semi-permanent storage medium such as a floppy disk, hard disk, optical disk, magneto-optical disk, or magnetic tape. In addition, the program is used by being introduced into a computer called a workstation usually supplied from Silicon Graphics, Sun Microsystems, or the like, but is not limited thereto. Three-dimensional structural coordinate modeling of the complex of lebutin and CRH-lebutin receptor

By homology modeling, the leptin-CRH-G-CSF-R complex obtained in step 3 was replaced with CRH-leptin receptor by leptin-CRH-leptin receptor. A body complex model can be created.

The CRH-lebutin receptor is of leptin from mammals, preferably mice, humans, particularly preferably humans. The amino acid sequence of the human leptin receptor has been reported by Tartaglia et al. (Tartaglia, LA et al., Cell, 83: 1263-1127 (1995)). The three-dimensional structural coordinates of CRH-G-CSF-R are those of leptin derived from mammals, preferably mouse and human, and particularly preferably human. The three-dimensional structural coordinates of CRH—G—CSF—R can be those of the complex of human G—CSF and mouse CRH—G—CSF—R in Table 1. For homology modeling, an alignment of the amino acid sequence of a protein with a known three-dimensional structure and the amino acid sequence of a protein with an unknown structure having a homologous amino acid sequence is required. CRH-leptin receptor and CRH-G-CSF-R Sequence alignments are available because they show significant homology at the bell. Amino acid sequence alignment of C RH-leptin receptor and CRH-G-CSF-R can be performed on a computer using the sequence alignment software C LUST ALW 1.4. The default values of CLUSTALW 1.4 and the like are suitable for the parameters of the alignment, and the association of amino acid residues, that is, the alignment, is performed using these parameters. The parameters and software used for this purpose are not limited to those described above. Since the three-dimensional structure information is not taken into account at all in the creation of the rooster alignment, there are parts that give inappropriate residue correspondences in homology modeling. These parts can be added with three-dimensional structure information by modifying them with a normal text editor.

Here, the three-dimensional structure information refers to information such as a secondary structure and a disulfide bond. Based on the obtained sequence alignment of CRH-leptin receptor and CRH-G-CSF-R, CRH-G-CSF-R of leptin'CRH-G-CSF-R complex was converted to CRH-lebutin receptor. Can be changed in stages. First, according to the sequence alignment, a portion of the G—C S F—R in which the amino acid residue is different from the leptin receptor is replaced with an amino acid of the leptin receptor. As a program for this purpose, Biopolymer of InsightII Ver97.2. Then, under the condition that the motion of the main chain is restricted by the harmonic function, the energy of the side chain is minimized for the region including the substituted amino acid and its surrounding two residues. A suitable computer program for this purpose is the protein simulation tool PRESTO Ver.3. The force field used at this time can be AMBER C966, and minimization can be performed using the conjugated gradient method. The calculation is performed in a vacuum, the electrostatic interaction is calculated with a distance cut-off of 15 A, and it is desirable to set the permittivity to be proportional to the distance in consideration of the screening effect. The parameters, calculation methods or software used for this purpose are not limited to those described above.

Amino acid insertion and deletion introduction of the CRH-lebutin receptor can be performed by using the Biopolymer function of Insightll Ver 97.2. These 揷 For the insertion and deletion regions, it is desirable to minimize the energy using PRESTO Ver. 3 including the two surrounding residues. The force field used at this time can use AMBER C96, and the minimum field can use conjugated gradient method. The calculations are performed in vacuum, the electrostatic interaction is calculated with a 15 A distance cutoff, and the permittivity can be set to be proportional to the distance, taking into account the scuttling effect. The parameters, calculation methods or software used for this purpose are not limited to those described above.

It is desirable to minimize energy in PRESTO Ver. 3 for all the atoms including leptin and CRH-leptin receptor thus obtained. The program suitable for the purpose is not limited to this, and other molecular simulation programs can be used. The force field used at this time can be AMBER C966, and minimization can be performed using the conjugated gradient method. The calculations are performed in vacuum, the electrostatic interaction is calculated with a 15 A distance cutoff, and the dielectric constant can be set to be proportional to the distance, taking into account the screening effect. The parameters, calculation methods or software used for this purpose are not limited to those described above.

Further chemical or biochemical information can be added to each atom of the leptin-CRH-leptin receptor obtained here. Specifically, Arg20 of leptin is a residue that has been suggested to be involved in receptor binding

(Verploegen, S.A.B.W., et al., FEBS Lett. 405: 237-240 (19997)). In the leptin'CRH-leptin receptor model obtained here, Arg20 was present in the vicinity of the receptor, but its side chain was in a direction in which direct receptor interaction was not observed. Therefore, if the side chain of Arg20 is manually operated on the computer so as to face the receptor, and then energy minimization is performed, the energy is reduced to 5.0 kcallfi from the model before the calculation, Was obtained. The manual operation performed here is

It is desirable to use the biopolymer function of Insight II Ver. 9 7.2 to manipulate the three-dimensional structure of lebutin-CRH-lebutin receptor visualized on a computer screen. The method is not limited. Programs suitable for this purpose are not limited to these, and other molecular modeling programs may be used. A program can also be used. Energy can be minimized with PRESTO Ver. The program suitable for the purpose is not limited to this, and other molecular simulation programs can be used. The force field used at this time can be AMBER C966, and minimization can be performed using the conjugated gradient method. The calculation is performed in a vacuum, the electrostatic interaction is calculated with a distance cut-off of 15 A, and it is desirable to set the permittivity to be proportional to the distance in consideration of the screening effect. The parameters, calculation methods or software used for this purpose are not limited to those described above.

The computer used here is a computer on which these computer programs operate, and as a medium for the computer, the structural coordinates of a complex of leptin and CRH-lebutin receptor are read on the computer program. There is no particular limitation as long as it can do the job. For example, it may be an electrical temporary storage medium called a memory, or a semi-permanent storage medium such as a floppy disk, hard disk, optical disk, magneto-optical disk, or magnetic tape. The program is used by being introduced into a computer called a workstation usually supplied from Silicon Graphics, Sun Microsystems, or the like, but is not limited thereto.

Three-dimensional structure of the thus obtained complex of human-derived levulin having the amino acid sequence shown in SEQ ID NO: 3 and human-derived CRH-leptin receptor having the amino acid sequence shown in SEQ ID NO: 4 The coordinates are shown in Table 6 according to the method of expressing the three-dimensional structural coordinates of a protein commonly used by those skilled in the art. Table 6

Three-dimensional structural coordinates of the complex of leptin and CRH—leptin receptor

ATOM I N ILE A 3 51.156 28.495 124.107 14.01 -0.42

ATOM 2 H ILE A 3 51.146 27.868 124.908 1.01 0.27

ATOM 3 CA ILE A 3 50.230 28.253 122.993 12.01 -0.06

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ATOM 1197 CB VAL A 89 56.993 28.557 116.146 12.01 0.30 ATOM 1198 HB VAL A 89 56.227 29.268 115.847 1.01 -0.03

ATOM 1199 CGI VAL A 89 57.184 28.605 117.671 12.01 -0.32

ATOM 1200 1HG1 VAL A 89 57.851 27.808 117.998 1.01 0.08

ATOM 1201 2HG1 VAL A 89 57.610 29.563 117.961 1.01 0.08

ATOM 1202 3HG1 VAL A 89 56.222 28.507 118.175 1.01 0.08 ATOM 1203 CG2 VAL A 89 58.332 28.959 115.505 12.01 -0.32

ATOM 1204 1HG2 VAL A 89 58.253 28.958 114.420 1.01 0.08

ATOM 1205 2HG2 VAL A 89 58.597 29.968 115.820 1.01 0.08

ATOM 1206 3HG2 VAL A 89 59.120 28.269 115.809 1.01 0.08

ATOM 1207 C VAL A 89 55.373 26.617 116.489 12.01 0.60 ATOM 1208 O VAL A 89 55.594 25.851 117.422 16.00 -0.57

ATOM 1209 N LEU A 90 54.123 26.941 116.129 14.01 -0.42

ATOM 1210 H LEU A 90 53.998 27.643 115.399 1.01 0.27

ATOM 1211 CA LEU A 90 52.925 26.317 116.712 12.01 -0.05

ATOM 1212 HA LEU A 90 52.920 26.565 117.774 1.01 0.09 ATOM 1213 CB LEU A 90 51.645 26.903 116.074 12.01 -0.11

ATOM 1214 HB2 LEU A 90 51.864 27.912 115.729 1.01 0.05

ATOM 1215 HB3 LEU A 90 51.365 26.319 115.197 1.01 0.05

ATOM 1216 CG LEU A 90 50.437 27.016 117.030 12.01 0.35

ATOM 1217 HG LEU A 90 50.722 27.616 117.893 1.01 -0.04 ATOM 1218 CD 1 LEU A 90 49.293 27.736 116.308 12.01 -0.41

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ATOM 1220 2HD1 LEU A 90 48.447 27.855 116.983 1.01 0.10

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ATOM 1495 O SEE, A 109 43.629 26.154 87.851 16.00 -0.57

ATOM 1496 N LEU A 110 45.477 26.813 88.953 14.01 -0.42

ATOM 1497 H LEU A 110 46.483 26.706 88.987 1.01 0.27 ATOM 1498 CA LEU A 110 44.835 27.762 89.862 12.01 -0.05

ATOM 1499 HA LEU A 110 43.948 27.282 90.270 1.01 0.09

ATOM 1500 CB LEU A 110 45.786 28.125 91.019 12.01 -0.11

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ATOM 1502 HB3 LEU A 110 45.518 29.113 91.396 1.01 0.05 ATOM 1503 CG LEU A 110 45.752 27.147 92.212 12.01 0.35

ATOM 1504 HG LEU A 110 46.528 27.462 92.910 1.01 -0.04

ATOM 1505 CD1 LEU A 110 44.415 27.201 92.956 12.01 -0.41

ATOM 1506 IHDI LEU A IIO 43.615 26.776 92.351 1.01 0.10

ATOM 1507 2HD1 LEU A 110 44.494 26.626 93.878 1.01 0.10 ATOM 1508 3HD1 LEU A 110 44.170 28.235 93.194 1.01 0.10

ATOM 1509 CD2 LEU A 110 46.030 25.691 91.831 12.01 -0.41

ATOM 1510 1HD2 LEU A 110 46.950 25.633 91.252 1.01 0.10

ATOM 1511 2HD2 LEU A 110 46.134 25.086 92.731 1.01 0.10

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ATOM 1543 C VAL A 113 40.148 30.853 89.87312.01 0.60

ATOM 1544 0 VAL A 113 39.692 31.213 90.96416.00 -0.57

ATOM 1545 N LEU A 114 40.948 31.633 89.13914.01 -0.42 ATOM 1546 H LEU A 114 41.263 31.243 88.255 1.01 0.27

ATOM 1547 CA LEU A 114 41.489 32.944 89.49512.01 -0.05

ATOM 1548 HA LEU A 114 41.073 33.260 90.449 1.01 0.09

ATOM 1549 CB LEU A 114 43.020 32.841 89.63912.01 -0.11

ATOM 1550 HB2LEUA114 43.364 31.917 89.187 1.01 0.05 ATOM 1551 HB3LEUA114 43.488 33.642 89.074 1.01 0.05

ATOM 1552 CG LEU A 114 43.546 32.910 91.08312.01 0.35

ATOM 1553 HG LEU A 114 43.295 33.882 91.507 1.01 -0.04

ATOM 1554 GDI LEU A 114 42.993 31.821 92.00912.01 -0.41

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END

In Table 6, the three-dimensional coordinates of each atom are described, except for the line beginning with TER. Lines beginning with TER specify the end of each subunit structure. ATOM in the first column indicates that this row is a row in atomic coordinates, 2nd row in the IJ column indicates the order of the atoms, 3rd row indicates the distinction between atoms in amino acid residues, etc. The fifth column indicates the type of molecule (the same type indicates a single polypeptide chain), the sixth column indicates the number of the amino acid corresponding to SEQ ID NOS: 1 and 2, and the like. Columns 7, 8, and 9 show the coordinates of the atom (A units in the X-, Y-, and Z-axis directions), column 10 shows the mass of the atom, and column 11 shows the atom's mass. It shows the partial charge of an atom. END in the last row indicates that this is the last row in the table. The type of molecule indicates that A and C are each one molecule of leptin, and B and D are each one molecule of CRH-leptin receptor. This table is described according to the format of Protein 'Data Bank, which is a notation generally used by those skilled in the art. From the structural coordinates, one molecule of lebutin (A) and one molecule of CRH-lebutin receptor (B) form a complex (A_B), and another molecule of lebutin (C) and CRH-leptin receptor One other molecule (D) forms a complex (CD). Furthermore, the complex (A-B) and the complex (C-D) form an aggregate of two molecules of the complex around the quasi-two-fold symmetry axis. In the present specification, such an association of a complex may be simply referred to as a “complex”.

Based on the structural coordinates of the complex of lebutin and CRH-lebutin receptor, a tube diagram, which is a notation commonly used by those skilled in the art to understand the structure of a protein, is used to simulate this structure. Figure 3 shows a view from a direction perpendicular to the two-fold symmetry axis, and Figure 4 shows a view from a direction parallel to the coaxial axis.

As can be understood from these figures, the complex crystal of leptin and CRH-lebutin receptor has a minimum unit having no crystallographic symmetry, ie, a complex of two molecules (asymmetric unit). A-B and C-D) are included. The complex of these two molecules is macroscopically related by a non-crystallographic quasi-double symmetry axis. The part of levtin consists of four long helices, one short α-helix and the loop region connecting them. The CRH-leptin receptor is roughly divided into two regions, each of which consists of about seven zero-sheets, and these regions are connected by loop regions. Hereinafter, these two regions are referred to as Ν domain near the Ν end, and BC domain near the C terminus. From these three-dimensional structures, the leptin signal is received by the leptin receptor because leptin binds to the leptin receptor, that is, a complex of two molecules forms an association in the relative configuration shown in the figure. Can be understood.

In general, lebutin and the extracellular portion of the lebutin receptor form a complex in solution with stoichiometrically equivalent amounts of substance, and the complex may exist as a dimer or tetramer. (Devos, R. et al., J. Biol. Chem., 272: 18304-118310 (1997)). The three-dimensional structure of the aggregate formed by the two molecules of leptin and the two molecules of the CRH-leptin receptor obtained in the present invention does not contradict these facts.

The amino acid residues VI to P2 in the leptin molecules A and C and S25 No structure has been identified for the amino acid residues from G38 to G38, and the amino acid residues from T548 to I549 in the molecules B and D of the CRH-leptin receptor are identified in the three-dimensional structure of the G-CSF complex. The positions of the corresponding residues (G214-H220) are not fixed and have been excluded from consideration in modeling the lebutin complex. In addition, since the structure of A95 of molecule D of CRH-G-CSF-R has not been determined, the corresponding residue E424 of molecule D of CRH-leptin receptor in the model is also excluded from the model.

Furthermore, it becomes possible for the first time to identify amino acid residues that interact with leptin and the CRH-lebutin receptor from the structural coordinates revealed by the present invention. A pair of hydrophobic residues with a geometrical center-to-center distance of 7.5 A in the side chain is considered to have hydrophobic interaction, and the distance between the oxygen and nitrogen atoms of the residue pair is Tables 7 and 8 show that those with 3.4 A or less have polar interaction or hydrogen bond. In the hydrogen bonding, those via water molecules are not considered in the model. Reflecting the pseudo-symmetry of the structure of G-CSF / CRH-G-CSF-R, which became type 铸, pseudo-symmetry was also observed in the model, but considering the accuracy problem of the model itself, Residue interactions commonly observed in the major interface (between A and B, between C and D) and in the minor '~ ^ T interface (between A and D, between C and B) Only shown. The major interface referred to here is the main binding surface where leptin and leptin receptor are bound one-to-one, that is, between leptin molecule A and leptin receptor molecule B, or between leptin molecule C and leptin receptor D molecule. The bonding surface of In addition, the minor interface is a complex of lebutin-lebutin receptor that further forms a dimer, and the binding surface where each lebutin molecule binds to the partner lebutin receptor molecule, that is, lebutin molecule A and lebutin It refers to the binding between receptor molecules D or between lebutin molecule C and lebutin receptor molecule B. Table 7

Amino acid residue pairs interacting at the major interface between the leptin molecule and the CRH-leptin receptor molecule, and the type of interaction Leptin CRH-leptin receptor type of interaction

D85 (side chain) R468 (side chain) Extreme interaction

R20 (side chain) V562 (backbone) Hydrogen bond

E15 (Main chain) Hydrogen bond

D8 (side chain) N567 (side chain) Hydrogen bond

D9 (side chain) R615 (side chain) Polar interaction

K5 (side chain) L616 (backbone) Hydrogen bond

F92 (side chain) L471 (side chain) hydrophobic interaction

V89 (side chain) L471 (side chain) hydrophobic interaction

L13 (side chain) L506 (side chain) hydrophobic interaction

L86 (side chain) L506 (side chain) Hydrophobic interaction Table 8

Amino acid residue pairs interacting at the minor interface between the leptin molecule and the CRH-leptin receptor molecule, and the type of interaction Leptin CRH-leptin receptor Interaction type

13 (Main chain) D617 (Side chain) Hydrogen bond

K5 (Main chain) D617 (Side chain) Hydrogen bond

13 (Side chain) V588 (Side chain) Hydrophobic interaction Table 7 shows the amino acid residue pairs interacting with the leptin molecule at the major interface of the CRH-leptin receptor molecule and the type of interaction. Is shown. Table 8 shows the amino acid residue pairs that interact at the minor interface between the leptin molecule and the CRH-leptin receptor molecule, and the type of interaction. The first column shows the amino acid residues of molecule A or molecule C and their numbers, the second column shows the amino acid residues of molecule B or D and their numbers, and the third column shows the type of interaction. Has been described.

First, one molecule of the CRH-leptin receptor recognizes one molecule of lebutin at the major interface. Amino acid residues that characterize this recognition On the leptin side, they are D85, R20, K15, D8, D9, K5, F92, V89, L13, L86, and CRH—on the leptin receptor side, R468, V556, E565, N567, R615, L616. , L471 and L506 (Table 7). That is, recognition of one molecule of lebutin (ie, complex formation) is characterized by the interaction of these amino acid residues and the amino acid residues in the vicinity thereof. Next, macroscopically, the two molecules of the complex are recognized (that is, associated with the complex) in a relationship related by a pseudo-twice axis of symmetry. The amino acid residues that characterize this recognition interact at the minor interface, 13 and K5 on the leptin side, and D617 and V588 on the CRH-leptin receptor side (Table 8). . That is, a complex consisting of one molecule of leptin and one molecule of CRH-leptin receptor is further associated to form a dimer of the complex, and its recognition is based on these amino acid residues, and It is characterized by the interaction of nearby amino acid residues. The number of residues forming the minor interface is smaller than that of G-CSF and CR H—G—CSF—R, but CRH-G—CSF—R forms a ligand-induced dimer. This is thought to be because dimer formation occurs in the leptin receptor irrespective of ligand binding. Therefore, the role of the minor interface may be involved in stabilization of the associated complex, not dimer formation.

The above structural coordinates were obtained for a complex of leptin and the CRH_leptin receptor. However, with respect to leptin binding, the CRH-leptin receptor is considered an equivalent of the leptin receptor, and the structure coordinates obtained above are substantially retained in the complex of leptin and leptin receptor it is conceivable that. Therefore, it is possible to elucidate the actual state of binding between lebutin and the lebutin receptor using the structural coordinates obtained above, and to identify, search, evaluate, or identify a mutant of lebutin or an agonist or antagonist of the lebutin receptor. Can be designed. Further, using the structural coordinates obtained above, the three-dimensional structural coordinates of a complex of a protein and a protein having homology in the amino acid sequence with the leptin and leptin receptor or similarity in the three-dimensional structure are obtained. , Can be obtained by homology modeling. 5. Use of Structural Coordinates of Complex to Produce Lebutin Mutant The present invention includes using the structural coordinates obtained as described above to determine the activity of a lebutin receptor as an agonist or antagonist. And a method for identifying, searching for, or designing a mutant of lebutin.

By inputting to a computer or a storage medium of a computer running the computer program that expresses the three-dimensional structure coordinates of the complex of leptin and CRH-lebutin receptor according to the present invention, the leptin and CRH-lebutin receptor can be used. This makes it possible to express in detail the mode of dimensional chemical interaction.

Further, the structural coordinates of the complex of lebutin and CRH-lebutin receptor according to the present invention are input to a computer or a storage medium on which a computer program that expresses the three-dimensional structural coordinates of a molecule operates, and are visually examined. And / or calculating the energy yields a lebutin that has properties such as higher bioactivity, higher biological stability, and better physical properties such as thermodynamic stability than the original lebutin. In order to obtain a mutant having an activity as an agonist or a mutant having an activity as a lebutin antagonist, which has a binding activity to a lebutin receptor but suppresses the biological activity of the original lebutin, 3 For the first time, rational design in dimensional space is possible.

The storage medium of the computer is not particularly limited as long as the structure coordinates of the complex of leptin and the CRH-leptin receptor can be derived on the computer program. For example, an electrical temporary storage medium called a memory or a semi-permanent storage medium such as a floppy disk, hard disk, optical disk, magneto-optical disk, or magnetic tape may be used.

Many computer programs for expressing the three-dimensional structural coordinates of protein molecules are commercially available, but these programs are generally used for inputting the three-dimensional structural coordinates of molecules, and for visually expressing and expressing the coordinates on a computer screen. And a means for measuring the distance and bond angle between atoms in a molecule, and a means for additionally correcting the coordinates.

Furthermore, it is also possible to use a program created to provide a means for calculating the structural energy of a molecule based on the coordinates of the molecule and a means for calculating the free energy in consideration of a solvent molecule such as a water molecule. It is. Molecular simulation Insight II, a computer program available from Yon

QUANTA is an example of a program suitable for this purpose. The present invention is not limited to these programs.

The program is usually supplied from Silicon Graphics, Sun Microsystems, or the like, and is used by being introduced into a computer called a workstation. However, the present invention is not limited to these.

Those skilled in the art can use a computer adapted to operate a program suitable for the purpose to obtain the structure coordinates of the complex of lebutin and the CRH-leptin receptor of the present invention using the computer or its computer. By introducing it into a storage medium, for the first time, it is possible to understand the binding mode of the complex of leptin and the leptin receptor in a state in which each atom in the three-dimensional space is represented by the position of each atom. Since it becomes possible for the first time to design a three-dimensional and rational lebutin mutant in order to obtain a mutant having activity as an agonist or a mutant having activity as an antagonist as described above. is there. One of the typical methods for designing leptin mutants is to input the three-dimensional structural coordinates of the leptin and CRH-leptin receptor complex of the present invention into a computer or its storage medium, and use an appropriate program. This is a method in which the three-dimensional structure of a protein is displayed on a computer screen and visually examined.

First, for the complex of lebutin and the CRH-lebutin receptor, the interacting amino acid residues and the amino acid residues in the vicinity thereof are displayed on a computer screen. Then, mutation or chemical modification of one or more amino acid residues, such as substitution, deletion and insertion, or chemical modification is performed on the amino acid residue on the lectin side, and the resulting change in the interaction is evaluated. Observe on the computer screen. At this time, when displaying the three-dimensional structure of the protein on the computer screen, use a display that can use Crystal Eyes glasses supplied by Silicon Graphics, or use it frequently by those skilled in the art. Stereoscopic vision

By using a method called the (Stereo view) that simultaneously displays two screens corresponding to the fields of view of the right and left eyes, it is easier to understand the 3D space, but it is not always necessary to use the 3D space display However, visual examination is possible. In addition, local mutations such as mutations such as substitution, deletion, or insertion of amino acid residues, or chemical modification. Structural coordinates are obtained by determining the spatial position of each atom so as to maintain the validity of the chemical bond. At this time, the computer may display an appropriate group of conformation candidates, and the computer may select one of them, or the computer may calculate a structure that reduces the energy state. From among them, we will find mutations or chemical modifications of lebutin that produce more favorable binding between CRH and lebutin receptor.

In other words, to design a levbutin mutant having activity as an agonist, amino acid residues that interact with the CRH-levbutin receptor to form a complex, as shown in Tables 7 and 8, ie, D85, R20 , K15, D8, D9, K5, F92, V89, L13, L86 amino acid residues and their neighboring regions, and / or amino acid residues forming aggregates, i.e., 13 and K5 amino acid residues In the group and its neighboring region, a mutation is introduced so as to more strongly bind to the amino acid residue in the region on the side of the CRH-lebutin receptor corresponding to the interaction. As used herein, the term "neighboring region" refers to a region that is involved in a polar interaction, a hydrophobic interaction, a hydrogen bond, or the like with the amino acid residue, specifically, a region within about 5 A. The same applies to other parts of this specification.

Furthermore, even when a mutant lebutin having an activity as an agonist is designed by introducing a mutation into a site other than the above, the present invention is within the scope of the present invention as long as the structural coordinates in the present invention are used.

At this time, non-covalent interactions to be considered include electrostatic interactions, hydrophobic interactions, van der Waals interactions, hydrogen bonds, etc. Can do body design. For example, in the vicinity of the side chain of an amino acid residue having a negative charge in the side chain such as glutamic acid and aspartic acid on the CRH-lebutin receptor side, lysine, arginine, and histidine are present in the adjacent amino acid residues of lebutin. Amino acid residues that have a positive charge on the side chain such as lysine, argyen, and histidine on the CRH-leptin receptor side, such that the side chain of a positively charged amino acid residue is arranged. Is mutated so that the side chain of a negatively charged amino acid residue such as glutamic acid or aspartic acid in the adjacent amino acid residue of leptin is located near the side chain of leptin. Also, Allaen, Serine and threonine are used in leptin in the part where the side chain moiety such as leucine, isoleucine, valine, proline, pheninolealanine, tryptophan and methionine interacts mainly with highly hydrophobic amino acid residues. , Tyrosine, asparagine, glutamine, and other hydrophilic amino acid residues such as asparaginic acid, glutamic acid, lysine, anoreginin, and histidine, where the presence of charged amino acid residues are found. Replace with hydrophobic amino acid residues to enhance hydrophobic interactions. In addition, the corresponding amino acid residue is mutated in the side chain portion of the amino acid residue such as serine and tyrosine to form a new hydrogen bond. In the above mutations, care must be taken to ensure that the Fundelwaals interaction is as large as possible in the side chain and main chain of the amino acid residue, and that steric hindrance does not occur between the atoms. In addition, it is necessary to consider a mutation that will not create a new void due to the mutation, and in a region where a void already exists, fill the void as much as possible. In this way, the final mutant design is performed by comprehensively considering the electrostatic interaction, the hydrophobic interaction, the van der Noireals interaction, the hydrogen bond, and other factors visually on the computer screen. It can be performed.

In order to design a lebutin mutant having activity as an antagonist, first, an amino acid residue that interacts with the CRH-levbutin receptor to form a complex shown in Tables 7 and 8, ie, D 85, R 20, K 15, D 8, D 9, K 5, F 92, V 89, L 13, L 86 and amino acid residues in the vicinity thereof, and Z or aggregate A mutation is introduced into the amino acid residue that forms the amino acid residue, that is, the amino acid residue at 13 and K5 and the vicinity thereof. Then, the mutant lebutin binds to the CRH-lebutin receptor, whereby the relative positions of the two original lebutin and CRH-leptin receptor molecules in the three-dimensional space are not maintained, or The mutant leptin and CRH-leptin receptor cannot interact with each other in either the complex-forming region or the complex-forming region, and as a result, have an activity as an antagonist against natural type leptin Such a mutant is selected.

Furthermore, even when a mutant lebutin having an activity as an antagonist is designed by introducing a mutation into a site other than the above, the use of the structural coordinates in the present invention is limited. This is the scope of this effort.

In this case, the non-covalent interactions to be considered are the same as those of the lebutin mutant having activity as an agonist, and these electrostatic interactions, hydrophobic interactions, van der Waals interactions, The final variants can be designed by considering the hydrogen bond and other factors visually and comprehensively on a computer screen. The second method of the design is to evaluate the binding to the CRH-lebutin receptor by performing an energy calculation with a computer to design the above mutant. The energy calculation can be achieved by using a computer program for performing a molecular force field calculation generally performed by those skilled in the art. Programs suitable for this purpose include, but are not limited to, the AMBER force field and CVFF in Insight's DISCOVER module optimized for proteins. Furthermore, the first method and the second method of design are not strictly distinguished, and the respective methods may be used in combination. In other words, for those that are expected to be more desirable mutants by visual examination, the energy is actually calculated using the second method, its validity is evaluated, and the process is repeated. In this way, we will design even better mutants.

As described above, the creation of mutants, which had been performed by trial and error without theoretical support in the three-dimensional structure, is now possible by using the structural coordinates of the present invention, It can be performed based on a simple analysis.

The structural coordinates of the amino acid residue on the CRH-lebutin receptor side used in the first and second design methods are the structural coordinates of the human-derived CRH-leptin receptor in Table 6 shown in the specification of the present invention. However, based on this, other species with high homology to each amino acid sequence

In addition, the coordinates of amino acid residues involved in these interactions, or amino acid residues in the vicinity thereof, if necessary, can be selected from Table 6 and used. In the design, the structural coordinates of the leptin and the CRH-lebutin receptor are usually fixed and used in a three-dimensional space, but are not necessarily fixed. The two molecules of the receptor that exist in the symmetry unit translate and rotate in a three-dimensional space, as one lump, and further, at the amino acid residues in each lump, By moving the chemical covalent bond to the extent that it is not cleaved, the energy of the bond to the lebutin mutant can be calculated. In a calculation in such a three-dimensional space, structural coordinates that have changed with translation, rotation, or movement are within the scope of the present invention. Variants designed according to the present invention can be prepared by a number of methods. For example, based on the present invention, at a site identified as having a higher biological activity by mutation, the site of the oligonucleotide encoding the corresponding amino acid residue is replaced with an oligonucleotide corresponding to the mutant. Is chemically synthesized and replaced with a natural oligonucleotide by using a sequence-specific oligonucleotide cleavage enzyme (restriction enzyme) to obtain the mutation designed based on the present invention. You can get the DNA that encodes the body. The above mutant DNA can be obtained by incorporating the obtained mutant DNA into an appropriate expression vector, introducing it into an appropriate host, and producing it as a recombinant protein. Such a preparation method is generally performed by those skilled in the art. (For example, Saigo I, Sano Yumiko, CURRENT PROTOCOLS Compact Edition, Molecular Biology Experiment Protocol, I, II, III, Maruzen Co., Ltd .: Original, Ausubel, FM, etc., Short Protocols in Molecular Biology, Third Edition, John Wiley & Sons, Inc., New York).

Chemical modification of the amino acid residues of proteins is also commonly performed by those skilled in the art (for example, Hirs, CHW and Timasheff, S, N., eds, (1977)). Methods in Enzymology, 47, 407-498, Academic

Press, New York.) ₀

6. Use of the Structural Coordinates of the Complex to Create an Agonist for the Lebutin Receptor

The present invention provides a lebutin receptor comprising using the structure coordinates obtained as described above. It provides a way to identify, search, evaluate or design agonists for the body.

The steric structure of the complex of lebutin and the CRH-lebutin receptor has revealed in detail the amino acid residues of the receptor involved in the lebutin binding and the positions of the atoms therein. By using the results of this steric structure, compounds that bind to the receptor binding site can be efficiently selected on a computer (The

Practice of Medicinal Chemistry, Part II, Chapter 11, "Electronic screening: Lead finding from database mining", p.167-178, Edited by Camille G.

See Wermut, 1996, Academic Press, 42-28 Oval Road, LONDON. This document forms part of the present specification). As a specific procedure, there is the following method. First, by calculating the contact surface area when the compound binds to the receptor binding site and selecting a compound that maximizes the value, a compound that fits formally to the binding site can be selected. Further, a compound that maximizes the chemical bond between the receptor binding site and the compound binding site is selected. When examining chemical bonds, for example, whether the atoms are in contact with each other at a position where hydrogen bonding is possible between the acceptor atom and the compound, the force or the atom with the opposite potential in terms of electrostatic interaction, or Confirm that the hydrophobic groups are in contact with each other, score them, and select a compound with a high score. By performing these operations, it is possible to efficiently select a compound that strongly binds to the receptor binding site from a very large group of compounds. Further, by performing a visual method for examining the details in detail while directly confirming the binding state to the receptor on a computer screen, a compound having a stronger binding ability can be selected. Details of each operation are shown below.

All or a part of the structural coordinates of the complex of lebutin and CRH-lebutin receptor provided by the present invention can be transferred to a computer operated by a computer program for expressing the three-dimensional structural coordinates of a molecule or a storage medium of the computer. By inputting, CRH binds to one lebutin receptor, and the arrangement of two molecules of CRH-lebutin receptor in the complex of lebutin and CRH-leptin receptor is substantially identical to the arrangement in three-dimensional space. Given, it is possible to identify, search, evaluate or design compounds with a biological activity equivalent to or better than lebutin. Those skilled in the art generally refer to such compounds as agonists (agonists). Compounds can be either natural products or synthetic compounds It may be either a high molecular compound or a low molecular compound.

The computer used in designing the active drug is preferably, for example, a workstation Indigo 2 supplied by Silicon Graphics, Inc. Power is not limited to this, but an appropriate program runs. Any computer that is tuned to do so may be used. There are no particular restrictions on computer storage media. The program used for the design can be achieved, for example, by using the computer II program Insight II marketed by Molecular Simulation. In particular, the "LUDI" module, an Insight II module specially created for this purpose, can be more easily identified, searched, evaluated or evaluated by using a program called "DOCK" alone or in combination. Can be designed. However, the present invention is not limited to these programs and methods.

There are two conceptual stages in the design of an active drug. The first step is to find the starting compound for drug design, called the lead compound by those skilled in the art. The next step is the process of optimizing a lead compound, starting with the lead compound and finding compounds with better properties, such as better activity, better pharmacokinetics, less toxicity and side effects.

The step of finding a lead compound using the structural coordinates of the complex of lebutin and CRH-lebutin receptor provided by the present invention may be performed, for example, by using a database in a computer in which the structures of a plurality of compounds are input. The method of calculating the interaction between the compound in the database and the CRH-lebutin receptor on the three-dimensional structure and the size of the steric hindrance sequentially, and searching for the compound that stably binds to the CRH-lebutin receptor from the database Or by means of sorting by visual means. It is desirable that the three-dimensional structure coordinates of the compound structure database be determined and input. However, in the case of low-molecular-weight compounds, many three-dimensional databases, such as the experimental database, "Cambridge Crystal Database '\

As the "Brookhaven Protein Database '\" or the theoretical database, Molecular Design's "MACCS Drug Report file", "Available Chemical Directory'\" Compounds of Medical Chemistry ", or Chemical Abstracts can be used. For compounds whose three-dimensional structure coordinates are unknown, "CONCORD", Using programs such as "COKINA", "WIZARD / COBRA", "AIMB", and "CHEM-X BUILDER", it is easy to calculate the three-dimensional structure coordinates from a two-dimensional structure on a computer.

There is also a method of designing a compound capable of binding to the receptor binding site directly on a computer. In this case, depending on a program such as “LUDI”, “CLIX” and “CAVEAT”, a protein molecule may be used. Given the three-dimensional structural coordinates of the interacting amino acid residues in, some automatically output lead compounds and can be applied to the CR H-leptin receptor.

Specifically, in a method based on energy evaluation by a computer using a three-dimensional database, the binding energy at a binding site between a compound and a receptor is calculated by a computer, and the result is scored for evaluation. First, the computer changes the conformation of the compound in the three-dimensional database to the leptin binding site of the CR H-leptin receptor on a computer so that the three-dimensional and electronic elements are optimized. While applying. As an index of a three-dimensional element and an electronic element, an energy value using a molecular force field is representative. The energy of the lowest energy applied to the leptin-binding site of the CRH-leptin receptor is assessed as the compound's score. Editor operations such as moving molecules and changing dihedral angles can be linked to molecular mechanics calculations on a computer, automatically changing the conformation of the compound or the position of the CR H-leptin receptor at the leptin binding site. Nevertheless, a program that has the function of seeking a stable compound-lebutin receptor complex structure is optimal. Molecular mechanics calculations can also be performed using only the partial structure of the compound and the leptin-binding site of the CRH-levbutin receptor.

First, in order to evaluate compounds in a large amount of database, as a first step, before performing precise molecular mechanics calculations, calculate the contact surface area between the compound and the receptor and narrow down by three-dimensional elements, or Chemical properties such as charge and hydrogen bond can be qualitatively or quantitatively evaluated and selected using a simple force field. Qualitative means that the compound has a negative charge, such as a carboxyl group, a nitro group, or a halogen, so that there is no steric hindrance between the compound and the CRH-lebutin receptor, and no large voids are created. Or the functional group that is easily polarized negatively is CRH-lebutin receptor Like lysine, anoreginin, and histidine, amino acids, amino groups, imino groups, guanidyl groups, and other functional groups that tend to be positively charged, interact with glutamic acid, a CRH-leptin receptor, Hydrophobic moieties such as fatty chains and aromatic rings are linked to leucine, isoleucine, palin, arayun, proline, huelualanin, tributofan, and methionine to interact with negatively charged amino acid residues such as aspartic acid. Hydroxyl, amide, amino, daranidyl, and lipoxyl groups can be hydrogen-bonded to the main chain and side chain of CRH-lebutin receptor to interact with hydrophobic amino acid residues Evaluate whether or not. As a second step, in order to perform a quantitative evaluation on the selected compound, it is necessary to determine the energy for binding by the above-mentioned precise molecular mechanics calculation, and to obtain a candidate for an agonist with a quantitative value. it can. There are sales programs specialized for that purpose, such as Insight II and 'DOCK', etc. Insight II can use multiple force fields such as AMBER specialized for biomolecules or CVFF applied to general organic molecules. In addition, modules such as "LUDr ',""Affinity", and "MCSS" are prepared as calculation tools for agonist design.

In the visual method, first, two molecules of the CRH-leptin receptor in the aggregate are displayed on a computer screen according to the structural coordinates of the present invention. At this time, a three-dimensional display such as the above-described crystal eye may be displayed on the screen of the computer, but visual examination is possible without necessarily using the three-dimensional display. Next, the computer attempted to bind to the CRH-leptin receptor in the database, taking into account the chemical interaction shown above, and strongly bound to the CRH-leptin receptor. And evaluate whether it is possible to do so.

In addition, there is no strict distinction between studies that consider energy and visual studies, and it is also useful to use a combination of these methods as appropriate.

The next step, the method for optimizing a lead compound using the structural coordinates of a complex of leptin and CRH-leptin receptor provided by the present invention, is a lead compound that binds to a CRH-lebutin receptor in advance. Is found by the above method or separately experimentally, and the Reedy conjugate is used as a more excellent molecule, for example, a compound having higher biological activity as an active agent, absorption efficiency and pharmacokinetics. Molecule with excellent structure It is used for the purpose of optimizing. As a technique for experimentally finding a lead compound, for example, in the case of a low-molecular compound, it may be selected from a series of compounds obtained from the above-described three-dimensional database or the like, or a culture of a microorganism or the like. It may be selected from the liquid. Further, a compound found in the design of an antagonist described below may be used. In short, only by clarifying the chemical bonding between the lead compound and the CRH-lebutin receptor, it was possible to directly find the suboptimal interaction site in the interaction between the lead compound and the CRH-lebutin receptor, It is possible to newly design a compound having an optimal functional group at that site, and a more optimized compound can be designed.

In the case of visual examination by computer, first, a computer program that expresses the three-dimensional structural coordinates of the lead compound and the structural coordinates of the CRH-lebutin receptor provided by the present invention and the three-dimensional structural coordinates of the molecule operates. Computer, or a computer storage medium, and display a complex model of the lead compound and CRH-levbutin receptor on the computer screen. At this time, a three-dimensional display such as the above-mentioned crystal eye may be used on the computer screen, but visual examination is possible without necessarily using the three-dimensional display. Designing compounds that can lead to more favorable pharmacokinetics while maintaining or maintaining the interaction of the lead compound with the CRH-leptin receptor more favorably. It is.

In the method based on energy evaluation using a computer, the binding energy between a new compound designed from a lead compound and the CRH-lebutin receptor is determined using molecular force field calculations, and the validity of the design is determined. . In addition, there is a method in which solvent molecules and the like are added to the model, the free energy is obtained by using molecular dynamics, and the compound is guided to a compound that can be stably bonded. The force field used for molecular force field calculation can be the force field of AMBER optimized for proteins, or CVFF suitable for general organic compounds, in the "DISCOVER" module of the program Insight II.

In addition, the visual examination and the method based on energy evaluation may be used in an appropriate combination.

The structure of the amino acid residue on the CRH-lebutin receptor side used in the above method The structural coordinates may be the structural coordinates of the human-derived CRH-lebutin receptor shown in Table 6 in the specification of the present specification, or may be the structural coordinates calculated based on this. When designing as a drug for human use, it is more preferable to use the structural coordinates of human-derived CRH-lebutin receptor. Also, it is not necessary to use the coordinates of all of these receptor portions for the structural coordinates of the CRH-lebutin receptor used. For agonists, the regions corresponding to the leptin-CRH-leptin receptor-interacting regions shown in Tables 7 and 8 are important, and the amino acid residues involved in these interactions and, if necessary, It is also possible to select and use the coordinates of the amino acid residue in the vicinity from Table 7 or Table 11. That is, the coordinates of these amino acid residues are selected, and one molecule of the compound is designed to bind simultaneously to the two sites of the CRH-leptin receptor to which one leptin molecule binds. By doing so, an agonist of lebutin is obtained that maintains the relative arrangement of the two CRH-levbutin receptor molecules in the conjugate.

An agent designed by the above method can be obtained by using a generally used chemical synthesis method according to the compound. It is also preferable to conduct a biological study on these chemically synthesized compounds. In addition, a superior drug can be obtained by successively feeding back the results of biological examination in the above-mentioned process of drug design and complementing both tasks.

7. Use of Structural Coordinates of Complex for Creating Antagonist for Lebutin Receptor The present invention identifies, searches, and evaluates an antagonist for lebutin receptor, including using the structural coordinates obtained as described above. Or provide a design method.

Structural analysis of the complex between lebutin and the CRH-lebutin receptor revealed in detail the amino acid residues of the receptor involved in the leptin binding and the positions of the atoms therein. By using the results of this steric segregation, the compounds that bind to the receptor binding site can be efficiently selected on a computer (The Practice of Medicinal Chemistry, Part II, Chapter 11, "Electronic screening: Lead finding from database mining ", p.167-178, Edited by Canaille G. Wermuth, 1996, Academic Press, 42-28 Oval Road, LONDON). The specific procedure is as follows. First, by calculating the contact surface area when the compound binds to the receptor binding site and selecting a compound that maximizes the value, a compound that fits the binding site in shape can be selected. Further, a compound that maximizes the chemical bond between the receptor binding site and the compound binding site is selected. When looking at chemical bonds, for example, make sure that the atoms are in contact with each other at a position where hydrogen bonding is possible between the acceptor atom and the compound. Confirm that the atomic groups are in contact with each other, score them, and select the compound with the highest score. By performing these operations, it is possible to efficiently select a compound that strongly binds to the receptor binding site from a very large group of compounds. Further, by performing a visual method for examining the details in detail while directly confirming the binding state with the receptor on a computer screen, it becomes possible to select a compound having a stronger binding ability. The details of each operation are shown below.

All or a part of the structural coordinates of the complex of lebutin and CRH-lebutin receptor provided by the present invention can be transferred to a computer that runs a computer that expresses three-dimensional structural coordinates of a molecule or a storage medium of the computer. By inputting, it becomes possible for the first time to identify, search, evaluate or design compounds that bind to leptin and Z or CRH-leptin receptor and inhibit leptin biological activity. Those skilled in the art generally refer to such compounds as antagonists. The compound may be a natural compound or a synthetic compound, and may be a high molecular compound or a low molecular compound.

As antagonists for the lebutin receptor,

(1) binds to lebutin and inhibits complex formation,

(2) binds to lebutin receptor and inhibits complex formation;

(3) Ability to bind to lebutin and Z or lebutin receptor to form a complex or an aggregate.

And so on.

The computer used to design the antagonist is, like the agonist, There is no particular limitation as long as the computer is tuned to run the program. There is no particular limitation on the computer storage medium. The program used for the design can be achieved by using, for example, Insight II, a computer program commercially available from Molecular Simulation. In particular, by using a program called "LUDI" or "DOCK", which is a module of Insight II specially created for the purpose, alone or in combination, it is easier to identify, search, evaluate or design. can do. However, the present invention is not limited to these programs and methods.

There are conceptually two stages in the design of an antagonist, as in the case of agonists. The first step is to find the lead compound, and the second step is the lead optimization process.

The step of finding the lead compound of the antagonist using the structural coordinates of the complex of lebutin and CRH-lebutin receptor provided by the present invention is performed, for example, by using a database in a computer in which the structures of a plurality of compounds are input. The three-dimensional interaction between the compound in the database and leptin and Z or CRH-lebutin receptor on the three-dimensional structure, and the magnitude of the steric hindrance are calculated sequentially, and the leptin and Z or CRH-lebutin receptor are stably calculated. This can be achieved by searching for a compound to be bound in a database or by a visual method. It is desirable that the three-dimensional structure coordinates are determined and entered in the compound structure database. However, in the case of low-molecular-weight compounds, many three-dimensional databases such as "Cambridge Crvstal Dataoase" and " Brook aven Protein Database ", as well as file", "Available Chemical Directory '\" Compounds of Medical Chemistry' \ or Chemical Abstracts ", etc. Also, for conjugation compounds whose 3D structural coordinates are unknown, refer to" CONCORD ", "CORINA '\" WIZARD / COBRA ",

Using programs such as "AIMB" and "CHEM-X BUILDER", it is easy to derive 3D structural coordinates from 2D structures by calculation on a computer.

There is also a method of designing a compound capable of binding to the receptor binding site directly on a computer. In this case, a compound such as ": LUDI", "CLIX", or "CAVEAT" is used. Some programs automatically output candidates for lead compounds when given the three-dimensional structural coordinates of interacting amino acid residues in a protein molecule. Is also possible.

Specifically, in a method based on energy evaluation by a computer using a three-dimensional database, the binding energy at a binding site between a compound and a receptor is calculated by a computer, and the result is scored for evaluation. First, the computer changes the conformation of the compound in the 3D database to the leptin-binding site of the CRH-leptin receptor in a timely manner so that the three-dimensional and electronic elements are optimized. While applying. As an index of a three-dimensional element and an electronic element, an energy value using a molecular force field is representative. The energy value of the lowest energy applied to the leptin binding site of the CRH-leptin receptor is assessed as the compound's score. Editor operations such as molecular movement and dihedral angle modification can be linked to molecular mechanics calculations on a computer, and the position of the compound at the leptin binding site of the conformation or CRH-leptin receptor can be automatically determined. A program that has the function of seeking a complex structure of a compound that is stable while it is changing is most suitable. Molecular mechanics calculations can also be performed using only the partial structure of the compound and the leptin-binding site of the CRH-levbutin receptor.

First, in order to evaluate compounds in a large amount of database, as a first step, before performing precise molecular mechanics calculations, calculate the contact surface area between the compound and the receptor and narrow down by three-dimensional elements, or Chemical properties such as charge and hydrogen bond can be qualitatively or quantitatively evaluated and selected using a simple force field. Qualitative means that the compound has a negative charge, such as a carboxyl group, a -tro group, or a halogen, so that there is no steric hindrance between the compound and the CRH-lebutin receptor, and no large voids are created. Positive charge such as amino group, imino group, guanidyl group, etc., so that a functional group that is easily polarized negatively or negatively interacts with a positively charged amino acid residue such as lysine, anoreginin, and histidine of the CRH-levbutin receptor. Hydrophobic moieties such as fatty chains and aromatic rings are linked to leucine, isoleucine, and valine so that functional groups that are likely to take on interact with negatively charged amino acids such as glutamic acid and aspartic acid in the CRH-leptin receptor. , Alanine, proline, phenylalanine, Hydroxyl, amide, amino, granidyl, and lipoxyl groups can hydrogen bond with the main chain and side chains of the CRH-levbutin receptor to interact with hydrophobic amino acid residues such as tryptophan and methionine Evaluate whether it can be arranged in such a way. As a second step, in order to perform a quantitative evaluation on the selected compound, it is necessary to obtain the energy for binding by the precise molecular mechanics calculation described above, and to obtain a candidate for the antagonist using a quantitative value. it can. There are Insight II and "DOCK" as sales programs specialized for that purpose. Insight II can use multiple force fields such as AMBER specialized for biomolecules or CVFF applied to general organic molecules. In addition, modules such as 'LUDI', 'Affinity', and 'MCSS' are provided as calculation tools for antagonist design.

In the visual method, first, two molecules of the CRH-leptin receptor in the aggregate are displayed on a computer screen according to the structural coordinates of the present invention. At this time, a three-dimensional display such as the above-mentioned crystal eye may be displayed on the screen of the computer, but visual examination is possible without necessarily using the three-dimensional display. Next, the computer attempts to bind the compound in the database to the CRH-leptin receptor, taking into account the chemical interaction shown above, and it is found that the compound binds strongly to the CRH-leptin receptor. We evaluate whether it is possible one by one.

In the next step, a method for optimizing a lead compound using the structural coordinates of a complex of lebutin and CRH-lebutin receptor provided by the present invention, a method for previously optimizing leptin and Z or CRH-lebutin receptor is used. When the lead compound to be bound is found by the above method or separately by experiment, the compound can be used as a more excellent molecule, for example, a compound having higher biological activity as an antagonist, or as a pharmaceutical. It is used to optimize the molecule to have a structure that is advantageous when considering absorption efficiency and pharmacokinetics. The method for experimentally finding a lead compound is the same as that for an agonist, but may be a compound found in the above-mentioned designing of an agonist. In short, it is only by clarifying the chemical bonding between the lead compound and leptin and Z or CRH-lebutin receptor that the phase between the lebutin and Z or CRH-lebutin receptor and the lead compound is determined. It is possible to directly find an interaction site that is not optimal in the interaction, and to newly design a compound having an optimal functional group at that site, so that a more optimized compound can be designed.

In the case of visual examination using a computer, first, the three-dimensional structural coordinates of the lead compound and the structural coordinates of the leptin and / or CRH-lebutin receptor provided by the present invention are represented by a computer that represents the three-dimensional structural coordinates of the molecule. Then, input to the computer on which the program runs or the storage medium of the computer, and display the complex model of leptin and / or CRH-leptin receptor and the lead compound on the computer screen. At this time, three-dimensional display such as the above-mentioned crystal eye may be used on the computer screen, but visual examination is possible without necessarily using three-dimensional space display. Then, the lead compound binds to leptin and / or CRH-leptin receptor, and the interaction between leptin and CRH-leptin receptor is inhibited. The ability to change to a compound with excellent kinetics is a rational design of the compound. Attempts to bind compounds in the database with leptin and Z or CRH-leptin receptor molecules, taking into account chemical interactions on a computer, and the compound is a complex of leptin and CRH-leptin receptor It will be evaluated sequentially whether it can work to inhibit the formation of chromosomes. At least one site at which the antagonist binds to leptin and / or CRH-lebutin receptor coincides with the amino acid residue that binds to leptin at the CRH-lebutin receptor or the amino acid residue adjacent to it. It is desirable that the binding of leptin and CRH-leptin receptor is sterically inhibited by binding of the antagonist to leptin and ZH or CRH-leptin receptor, and a complex of leptin and CRH-leptin receptor can be formed. Select compounds that are: Furthermore, it is not necessary to simultaneously bind to two molecules of leptin, two molecules of CRH-leptin receptor, or a complex of one molecule of leptin and one molecule of CRH-leptin receptor. -It is preferred to screen for compounds that bind to the lebutin receptor. The chemical interactions to be considered are the same as those for finding a lead compound. Finally, a new compound having more favorable properties as an antagonist is designed from the lead compound. In the method based on computer energy evaluation, using molecular force field calculation, Determine the binding energy of the new compound designed from the lead compound to lebutin and Z or CRH-leptin receptor, and judge the validity of the design. In addition, there is a method in which solvent molecules and the like are added to the model, the free energy is determined by using molecular dynamics, and the compound is guided to a compound that can be stably bonded. The force field used for molecular force field calculation is optimized for proteins in the "DISCOVER" module of the program InsighUI

AMBER's force field or CVFF applied to general organic molecules can be used. Also, the visual examination and the energy evaluation method may be appropriately combined and used. In the above method, the structural coordinates of the amino acid residues on the leptin and / or CRH-leptin receptor side used are the human leptin and the human CRH-leptin receptor shown in Table 6 shown in the specification of the present invention. The structural coordinates may be used, or they may be calculated based on the structural coordinates. When designing as a drug for human use, it is more desirable to use the structural coordinates of human leptin and CRH-leptin receptor. In addition, since the design of an antagonist means designing a compound that binds to leptin and Z or CRH-leptin receptor, the structural coordinates of leptin or CRH-leptin receptor are shown in Tables 7 and 8. The amino acid residues corresponding to the interacting portion between leptin and the CRH-leptin receptor and the region of the amino acid residues in the vicinity are important, and the coordinates of these residues are shown in Table 7 and Table 11 It is also possible to select from and use them. That is, by selecting the coordinates of the portion corresponding to these amino acid residues and designing the compound so as to inhibit the normal binding of leptin to the CRH-lebutin receptor, it is possible to prevent the biological activity of leptin from being exerted. And an antagonist is obtained.

The antagonist designed by the above method can be obtained by using a generally used chemical synthesis method according to the compound. It is preferable to conduct a biological study on these chemically synthesized compounds. In addition, by sequentially feeding back the results of the biological examination in the above-described antagonist design process and proceeding while complementing both operations, a better antagonist can be obtained.

8. Three-dimensional structural coordinate modeling of the complex between protein and its receptor G-CSF and G-CSF-R have homology (more than 20% homology) in amino acid sequence or conformational similarity when G-CSF and G-CSF-R have similarity in amino acid sequence. From the three-dimensional structural coordinates of the complex between CSF and CRH- (Ϊ, ') CSF-R, the three-dimensional structural coordinates of the complex between the other protein and its receptor can be obtained. The protein is preferably a protein having a four α-helix structure called a 4-helix ′ bundle structure, and the receptor of the protein is preferably a single-transmembrane receptor. Such proteins and their receptors include G-CSF and its receptor, or leptin and its receptor, interleukin-16, leukemia cell inhibitory factor, ciliary neurotrophic factor, GM-GSF , Growth hormone, interferon-1 (¾, 0, γ, interleukin-1 J3, etc., and site force-in receptors. In particular, interleukin-16, leukemia cell inhibitory factor, hairy Somatic neurotrophic factors are classified as long-chain helical site force infamilies, among cytokines with a four-helix-bundle structure. The amino acid sequence of the receptor for these cytokins is also highly homologous to G-CSF and lebutin, especially interleukin. Down one 6, leukemia inhibitory factor, homology receptor Amino acid sequence of the ciliary neurotrophic factor particularly high.

These proteins and receptors are from mammals, preferably mice, rats, humans, especially preferably humans.

The three-dimensional structural coordinate modeling of the complex between these four-helix-pandle-structured protein and its receptor was performed by the same method as that described in Example 5 for the three-dimensional structure of the protein and G-CSF. It becomes possible by superimposing. Specifically, by replacing the target protein having a four-helix bundle structure with G-CSF ■ G-CSF in the CRHG-CSF-R complex, the hypothetical protein and CRH- Create G-CSF-R complex.

In order to superimpose the three-dimensional structures, it is necessary to perform correspondence between residues in advance by alignment. Here, when the protein has a sequence homologous to the amino acid sequence of G-CSF, sequence alignment can be performed on a computer. The term sequence alignment as used herein refers to two or more different proteins. This is an operation that associates residues in the amino acid sequence of white matter so that the similarity is maximized. The default value of CLUSTA LW 1.4 is suitable as a parameter for sequence alignment, and amino acid residue association, that is, alignment can be performed using these parameters. The sequence alignment does not take into account any three-dimensional structure information at the time of its creation, and there are parts where inappropriate residue correspondences are given in homology modeling. The three-dimensional structure information can be added to these parts by modifying them with a normal text editor.

Here, the three-dimensional structure information refers to information such as a secondary structure and a disulfide bond. Based on the obtained sequence alignment of the protein receptor and G-CSF, G-CSF of the protein-CRH-G-CSF-R complex can be changed stepwise to the protein. First, according to the sequence alignment, a portion of the G-CSF having an amino acid residue different from that of the protein is substituted with an amino acid of the protein. A suitable program for this is Biopolymer of Insight II Ver 97.2. Then, under the condition that the motion of the main chain is restricted by the harmonic function, the energy of the side chain is minimized for the region containing the substituted amino acid and its surrounding two residues. Computer ■ A protein simulation tool such as PRESTO Ver. 3 is suitable for this purpose. The force field used at this time can use AMBERC96, and minimization can use the conjugated gradient method. The calculation is performed in a vacuum, the electrostatic interaction is calculated with a distance cut-off of 15 A, and it is desirable to set the permittivity to be proportional to the distance in consideration of the screening effect.

The introduction of amino acids and the introduction of deletions of the protein were confirmed by Insight II Ver 97.2.

It can be performed by using a Biopolymer function or the like. For these inserted and deleted regions, it is desirable to perform energy minimization using PRESTO Ver. 3 including the two residues around the region. The force field used at this time can be AMBER C96, and the minimization can be performed using the conjugated gradient method. The calculations are performed in a vacuum, the electrostatic interaction is calculated with a distance cutoff of 15 A, and the dielectric constant can be set to be proportional to the distance, taking into account the screening effect. It is desirable to minimize energy in PRESTO Ver. 3 for all atoms including the protein and C RH—G—CSF—R obtained in this way. The program suitable for the purpose is not limited to this, and other molecular simulation programs can be used. The force field used at this time can be AMBER C966, and minimization can be performed using the conjugated gradient method. The calculations are performed in a vacuum, the electrostatic interaction is calculated with a 15 A distance cut-off, and the dielectric constant can be set to be proportional to the distance, taking into account the screening effect.

Chemical or biochemical information can be further added to each atom of the protein 'CRH-G-CSF-R thus obtained. The manual operation performed here is performed by manipulating the three-dimensional structure of the protein ■ CRH-G-CSF-R visualized on a computer screen using the Biopolymer function of Insight II Ver. 97.2. It is desirable, but not particularly limited to visualization. The program suitable for the purpose is not limited to this, and other molecular modeling programs can be used. Energy can be minimized with PRESTO Ver. The program suitable for the purpose is not limited to this, and other molecular simulation programs can be used. The force field used at this time can be AMBER C966, and minimization can be performed using the conjugated gradient method. The calculation is performed in a vacuum, the electrostatic interaction is calculated with a distance cutoff of 15 A, and it is desirable to set the permittivity to be proportional to the distance in consideration of the screening effect.

The computer used here is a computer on which these computer programs are operated, and as the storage medium of the computer, the structural coordinates of the complex of the protein and CRH—the protein receptor are read on the computer program. There is no particular limitation as long as it can do the job. For example, it may be an electrical temporary storage medium called a memory, or a semi-permanent storage medium such as a floppy disk, hard disk, optical disk, magneto-optical disk, or magnetic tape. In addition, the program is used by being introduced into a computer called a workstation usually supplied from Silicon Graphics, Sun Microsystems, or the like, but is not limited thereto.

In addition, when performing three-dimensional structure superposition, If no significant homology is found between the protein and the amino acid sequence level of G-CSF in performing the association, sequence alignment cannot be used. The term “sequence alignment” as used herein refers to an operation of associating the amino acid sequences of two or more different proteins so that the similarity is maximized. However, both the protein and the G-CSF have a homologous structure of a four-helix-and-pandle structure. In this case, the amino acid residues can be associated with each other by structural alignment. Structural alignment here is an operation that evaluates the similarity of relative positions in the body structure and finds pairs of residues at structurally corresponding positions instead of amino acid sequence information. . Therefore, if structural alignment is used, even if no sequence-level similarity is found, alignment can be established if the three-dimensional structures are similar. As a computer program for this purpose, a program developed in this laboratory (Japanese Patent Laid-Open No. 10-185925) can be used, but a program suitable for the purpose is not limited to this. is not.

Here, a structural alignment was created by the following procedure. In constructing the structural alignment, the relative position of each residue in the protein three-dimensional structure is determined from the N-terminal to the C-terminal of the betattle from the J3 carbon of the residue of interest to the i3 carbon of all other residues. It is represented as a set ordered. The projection of the vector from the carbon of interest to the main chain oxygen and the X axis, and the vector from the α carbon to the carbon onto the plane perpendicular to the X axis are plotted on the Υ, X and 軸 axes. On the local coordinate system with the vector product as the Ζ axis, the betattle for all other residues is represented. The similarity between residues is calculated as the similarity in this structural environment. The similarity between two structural environments is expressed as an alignment score when an ordered set of the two vectors is optimally juxtaposed by dynamic programming. The similarity between each vector in the calculation is

a / (IV 1 -V 2 I ² + b)

Is required. Here, a is an appropriate scaling factor, b is an element to avoid division by 0, and VI and V2 are two vectors to be compared. Dynamic programming for finding the similarity of structural environments is called lower dynamic programming. The dynamic planning method in this case means solving the following recurrence formula using the similarity between the above-mentioned betatles. D (i, j) = s (i, j) + Ma x {D (i-1, j — l),

E (i−1, j−1 2), F (i−1, j−1)}

E (i, j) = Ma x (D (i, j) -a,

E (i, j-1) -β}

F (i, j) = Max (D (i, j)-a,

F (i-one, j)-β}

s (i, j) represents the similarity between the two vectors mentioned above. i and j indicate that the i-th and j-th vectors of each structural environment are symmetric. D is a comparison matrix for dynamic programming, and E and F are auxiliary matrices for fast programming. The row and column size of each row corresponds to the number of vectors that make up the structural environment to be compared. α and] 3 are the opening penalty of affine penalty in lower dynamic programming

Indicates extension penalty.

Using the similarity between residues obtained by this method, the correspondence between residues, that is, alignment can be obtained by dynamic programming. Dynamic programming for finding the correspondence between residues is called upper dynamic programming. The recurrence formulas that can be solved are almost the same as those listed above, but the meaning of each element is different.

D (i, j) = s (i, j) + Ma x {D (i — 1, j-1),

E (i-1, j-2), F (i-2, j-1)}

E (i, j) = M ax {D (i, j) — <¾ x se c,

EE ((i1. J-l) -j3 x se c}

F (i, j) = Ma x {D (i j) — a x se c,

F (i 1, j — i3 x se c}

D is a comparison matrix for dynamic programming, and E and F are auxiliary matrices for speedup. The size of the rows and columns of each matrix corresponds to the number of residues that make up the compared proteins. s (i, j) is the similarity between residues i and j obtained by the lower dynamic programming. i and j indicate that the ith and jth residues of each protein are symmetric. a and / 3 represent the opening penalty and extension penalty of the affine penalty in dynamic programming. _sec is a factor that expresses the difficulty of insertion_deletion at residues in the secondary structure. Structural alignment by this method is called double dynamic programming because dynamic programming is used in two different stages (Taylor, WR, et al., J. Mol. Biol., 208: 1—22 (1989)).

Since this method requires a great deal of calculation time to create an alignment, the following two-step calculation can achieve high speed without reducing the accuracy of the alignment (Toh, H, .CABIOS, 13 : 387-396 (1997); JP-A-10-185925). First, a distance cutoff is introduced, and only the residues within the cutoff distance from the residue of interest are used to approximately represent the structural environment of that residue. This is called the local environment. In addition, in this local environment, the number of residues located at the N-terminal and the number of residues located at the C-terminal from the residue of interest are stored. The similarity between two residues is determined by applying lower dynamic programming to this local environment. In the local environment, the lower dynamic programming itself can be calculated at high speed because its components are reduced. If a certain residue pair exists at a similar position, the number of residues constituting the local environment is expected to be similar. Conversely, if the number of constituent residues in the local environment is significantly different, it is considered that the residue pair is not similar in structural environment. Therefore, 內 in the local environment, the number of residues located at the N-terminus from the residue of interest and the number of residues located at the C-terminus are compared. If it is larger, the calculation of the lower dynamic programming is skipped and the similarity is set to 0.0. This approximation is called the ΔΝ cutoff. With the introduction of these two approximations, it is possible to obtain the alignment at high speed, but the accuracy is reduced. Since the approximate alignment obtained is very similar to the alignment created without introducing the approximation, the ε-suboptimal region of this approximate alignment is determined, and the residue pair found in that region is determined. Only for, it is possible to obtain the structural alignment at high speed without reducing accuracy by applying the calculation of the double dynamic method without introducing approximation. The ε-suboptimal region is described by Vingron et al. (Vingron, M-, et al., Protein Eng., 3: 5

65-569 (1990)). ε is an index indicating the deviation from the optimal juxtaposition score, and is a parameter for determining the size of the suboptimal region. In this case, the unit is the standard deviation of the similarity between residues obtained when performing the approximate alignment. Based on the obtained structural alignment, the root mean square error between the protein and the main chain atom of the G-CSF residue in the G—CSF · CRH-G-CSF—R complex was minimized. The superimposition of the protein and G-CSF can be performed on a computer. As a computer program for this purpose, a program for performing molecular modeling generally performed by those skilled in the art can be used. Suitable programs for this purpose include, but are not limited to, Insight II (Molecular Simulation Inc). By superimposing the proteins and then deleting the G-CSF, a hypothetical protein 'CRH-G-CSF-R complex can be formed.

The computer used here is a computer on which these computer programs are operated, and as the storage medium of the computer, the structural coordinates of the complex of the protein and CRH—the protein receptor are read on the computer program. There is no particular limitation as long as it can do the job. For example, it may be an electrical temporary storage medium called a memory, or a semi-permanent storage medium such as a floppy disk, hard disk, optical disk, magneto-optical disk, or magnetic tape.

The program is installed in a computer called a workstation usually supplied by Silicon Graphics, Sun Microsystems, or the like, and is used, but is not limited thereto.

The obtained protein and CRH-G-CSF-R complex of CRH-G-CSF-R complex are replaced with the protein receptor by homologous modeling, whereby the protein and the protein-binding portion of the protein receptor are substituted. (CRH-protein receptor) complex model can be created.

For homology modeling, an amino acid sequence of a protein having a known tertiary structure and an alignment of an amino acid sequence of a protein of unknown structure having a homologous amino acid sequence are required. Both CRH-protein receptor and CRH-G-CSF-R are single-transmembrane receptors, and the protein binding domain is called the CH domain, which has high homology to the amino acid sequence and can be used for sequence alignment. is there. Therefore, sequence alignment between the protein receptor and CRH-G-CSF-R can be performed.

This sequence alignment is performed on a computer, and the parameters of the sequence alignment are The default value of CLUS TA LW 1.4 is suitable for the meter, and the correspondence of the amino acid residues, that is, the alignment is performed using these parameters. The sequence alignment does not take into account any three-dimensional structural information in its creation, and there are portions that give inappropriate residue correspondences in homology modeling. The three-dimensional structure information can be added to those parts by modifying them with a normal text editor.

Here, the three-dimensional structure information refers to information such as a secondary structure and a disulfide bond. Based on the obtained sequence alignment of CRH—the protein receptor and C RH—G—CSF—R, the C RH—G—CSF-R of the protein′C RH—G—CSF—R complex was converted to C RH -Can be stepwise changed to the protein receptor. First, according to the sequence alignment, a portion of the G-CSF-R in which an amino acid residue differs from that of the protein receptor is substituted with an amino acid of the protein receptor. For this purpose, Biopolymer of Insight II Ver 97.2 is suitable. Then, under the condition that the motion of the main chain is restricted by the harmonic function, the energy of the side chain is minimized for the region including the substituted amino acid and its surrounding two residues. As a computer program for this purpose, a protein simulation tool such as PRESTO Vei. 3 is suitable. The force field used at this time is AMBER C 9

6. For minimization, conjugated gradient method can be used. The calculation is performed in a vacuum, the electrostatic interaction is calculated with a distance cutoff of 15 A, and it is desirable to set the permittivity to be proportional to the distance in consideration of the screening effect.

C RH—Introduction of amino acid insertion and deletion of the protein receptor was performed using Insight II Ver 9

This can be done by using the Biopolymer function in 7.2. For these inserted and deleted regions, it is desirable to minimize the energy using PRESTO Ver. 3 including the two residues around the region. The force field used at this time can be AMBER C96, and the minimization can be performed using the conjugated gradient method. The calculations are performed in a vacuum, the electrostatic interaction is calculated with a distance force cutoff of 15 A, and the dielectric constant can be set to be proportional to the distance, taking into account the screening effect. It is desirable to minimize energy in PRESTO Ver.3 for all atoms including the protein and CRH-protein receptor thus obtained. The eyes A suitable program is not limited to this, and other molecular simulation programs can also be used. The force field used at this time can use AMBER C966, and the minimum force field can use the conjugated gradient method. The calculations are performed in vacuum, the electrostatic interaction is calculated with a 15 A distance cutoff, and the dielectric constant can be set to be proportional to the distance, taking into account the screening effect.

Chemical or biochemical information can be added to each atom of the protein 'CRH-protein receptor thus obtained. The manual operation performed here is performed by manipulating the three-dimensional structure of the protein {CRH—the protein receptor visualized on a computer screen using the Biopolymer function of Insight II Ver. 97.2. It is desirable, but not particularly limited to the visualization method. The program suitable for the purpose is not limited to this, and other molecular modeling programs can be used. Energy can be minimized with PRESTO Ver. The program suitable for the purpose is not limited to this, and other molecular simulation programs can be used. The force field used at this time can be AMBER C966, and minimization can be performed using the conjugated gradient method. The calculation is performed in a vacuum, the electrostatic interaction is calculated with a distance cutoff of 15 A, and it is desirable to set the permittivity to be proportional to the distance in consideration of the screening effect.

The computer used here is a computer on which these computer programs operate, and as a storage medium for the computer, the structural coordinates of a complex of leptin and a CRH-lebutin receptor are stored on the computer program. There is no particular limitation as long as it can be guided. For example, it may be an electrical temporary storage medium called a memory, or a semi-permanent storage medium such as a floppy disk, hard disk, optical disk, magneto-optical disk, or magnetic tape. In addition, the program is used by being introduced into a computer called a workstation usually supplied from Silicon Graphics Co., Ltd. or Sun Microphone Co., Ltd., but is not limited thereto.

Using any of the three-dimensional structural coordinates of the complex of the protein and its receptor obtained in this manner, the same method as described for lebutin in 5 to 7 can be used to obtain a mutant, Identify, search, evaluate or design drugs and antagonists. Example

EXAMPLES Hereinafter, the present invention will be described in more detail with reference to examples. The present invention is not limited to these examples. The scope of the present invention should be defined by the contents described in the detailed description of the invention rather than by the specific embodiments shown in the examples. ': Seo

Example 1

Preparation of complex of G—CSF and CRH—G—CSF—R

Mouse-derived CRH-G-CSF-R (SEQ ID NO: 2) was prepared by the method described in Japanese Patent Application No. 6-280655 (JP-A-8-140678). Furthermore, in order to be suitable for crystallization, CRH-G is used for ion-exchange column chromatography (Mono-SHR10 / 10 (Mono-SHR10 / 10), Pharmacia) due to its electrical properties. — The CSF—R fraction was purified. Human-derived G-CSF (SEQ ID NO: 1) was produced by Kirin Brewery Co., Ltd. as a recombinant protein produced by E. coli.

In order to form a complex of G—CSF and CRH—G—CSF—R, the obtained protein concentrations of G—CSF and CRH—G—CSF—R were determined by measuring the absorbance of ultraviolet light, respectively. The stoichiometric amount calculated from the above, or G-CSF was mixed in excess. The sample was added to a mobile phase containing 0.1 M sodium chloride, 0.01 M 2- (N-monorefolino) ethanesnolefonic acid (2- (N-

Gel filtration chromatography using a buffer solution of Morpolino) ethansulfonic acid) (Hiroad Superdettas 200 HR 26/60 (HiLoad

Superdex 200 HR 26/60), fractionated by Pharmacia) to obtain a highly purified complex of G—CSF and CRH—G—CSF—R. Example 2

Preparation of crystal of G-CSF and CRH-G-CSF-R complex

Crystals of the complex of G-CSF and CRH-G-CSF-R were obtained using the vapor diffusion technique described below. G—CSF and CRH—G— purified to high purity in Example 1 複合 The complex with 3-1 was converted to a device using Centrifugal filtration membrane (Centricon-10)

(Centricon-10), Grace Japan Co., Ltd.) to adjust the protein concentration to 0.5 to 2 mg / ml. This protein solution contains 1 to 10 μl of crystallization solution and contains 1.0 to 1.2% of ammonium sulfate. 0.1M of ρΗ = 7 to 8 M- 2-hydroxyethinoleviperazine 1 一, 12-ethane Sulfonic acid (Ν— 2—

Hydoroxyethylpiperazine-N'-2-ethanesulfonic acid) Relative ί The solution was mixed with an equal amount of calories and placed on a glass plate treated with a silicon treatment agent (Sigma coat, Sigma) to make the surface hydrophobic. The glass plate on which this sample was placed was placed in an airtight storage container containing a crystallization solution of 1 to 5 ml, and allowed to stand at 20 ° C. After standing for about 3 days to 1 month, prism-shaped crystals having a size of about 20 μm × 20 μπιΧ150 μμη were obtained in the sample solution. By adding 2 to 10% of 1,4-dioxane to the crystallization solution, larger crystals having a size of up to about 60 / imx6O ^ mX600Xια were obtained. Example 3

Crystal structure of G-CSF and CRH-G-CSF-R complex

The crystals obtained in Example 2 were immersed in a crystallization solution to which 50% sucrose was added, and then placed under a 100 ° nitrogen stream and rapidly frozen. X-ray diffraction data were collected using a vibration method in a 100 Κ nitrogen stream. Further, the crystal obtained in Example 2 was immersed in a crystal solution containing lmM ethylmercurithiolate (ethylmercrithiosaHcylate) for 6 hours to obtain a homomorph-substituted crystal containing mercury atoms in the crystal. The crystals were immersed in a crystallization solution containing 50% sucrose, then placed under a stream of nitrogen at 100 K, and rapidly frozen. X-ray diffraction data were collected using the vibration method in a 100K nitrogen stream. Furthermore, an E. coli strain prepared to express G-CSF was cultured in a medium containing selenomethionine to obtain G-CSF in which methionine residues were replaced with selenomethionine residues. Using the G-CSF substituted for the selenomethionine residue, the compound of G—CSF and CRH—G—CSF—R in which the methionine residue was substituted for the selenomethionine residue was prepared according to the method described in Example 2. A body crystal was obtained. The crystals were immersed in a crystallization solution containing 50% sucrose, and then placed under a 100 K nitrogen stream. Quick frozen. X-ray diffraction data were collected using the vibration method in a 10 OK nitrogen stream. From each of the obtained diffraction images, the diffraction intensity was quantified using DENZOZSCALEPACK (Mac Science) to determine the crystal structure factor. At this stage, the crystal has a tetragonal space group symmetry, I 4 i 22, and the unit cell of the crystal can have dimensions of a = b = 125 ± 10 A and c = 373 ± 1 OA. Indicated.

Next, the following analysis was performed using a series of programs called CCP 4. The Fourier transform is calculated using the difference between the diffraction intensities obtained from the isomorphous substitution crystal of mercury and the crystal of the natural type, and the mercury atom in real space that satisfies this is calculated from the obtained difference Patterson diagram. Was determined in the unit cell. Using the obtained mercury coordinates, the phase of the natural type crystal structure factor is determined, and the phase difference and the absolute value of the selenomethione-substituted crystal and the natural type crystal structure factor are subjected to Fourier synthesis to obtain a difference electron. A density map was created and the atomic coordinates of selenium were determined. In addition, we used three crystal structure factors, natural type, mercury-substituted and selenium-substituted, to calculate the refinement so as to determine the positions of the atoms of mercury and selenium more accurately. Using the phase of the natural type crystal structure factor calculated from the obtained positions of the mercury and selenium atoms, the electron density diagram of the crystal of the complex of G-CSF and CRH-G-CSF-R in real space was obtained. Obtained. Furthermore, smoothing of the electron density in the solvent region and calculation of the averaging of the electron density using non-crystallographic symmetry were performed, and G-— was plotted on the electron density diagram using QUANTA (Molecular Simulation). 3 Binding 1 ^ ー 0—. The site corresponding to the amino acid residue in the complex of 3? -1 was identified.

Next, the position of the site corresponding to the amino acid residue was refined using X-PLOR (Molecular Simulation), and the amino acid residue was identified using QUANTA. By repeating this operation, one of two molecules of G-CSF (molecule A) consisting of 175 amino acid residues (molecule A) has amino acid residues M1 to L4, P129 to G136 and the side chain of Q71, and On the other hand, in (molecule C), the structural coordinates of the amino acid residues M1 to A7, Q68 to L70 and the amino acid residue excluding the side chain of Q71, CRH—G—CSF—R In one of the molecules (molecule B) V123-S125, the amino acid residues from K214 to A215 and the side chains of K63, R64, HI26, and in the other (molecule D) A1-G2, H33 ~ P35, G Structural coordinates of the amino acid residues from 120 to S 125, K214 to A215 and the amino acid residues excluding the side chains of K62, R64, 1119, Ql27, and M213, and one residue of N-acetyl darcosamine residue, 182 water molecules were identified.

At this stage, the R factor, which is regarded as an index of the accuracy of the structure coordinates by those skilled in the art, is as follows: When a structure factor obtained from a diffraction image having a Bragg reflection angle of 6 A to 2.8 A is used, R = l 9 It was 5%. Furthermore, the R factor (factor called Free-: R factor by those skilled in the art) calculated from the structural factors that were not separately included in the refinement calculation at the refinement stage was R = 28.3%. . Furthermore, the root-mean-square errors of the bond distance and bond angle between each atom from the ideal state were 0.012A and 2.0 degrees, respectively. Example 4

Refinement of the structural coordinates of the complex of G—CSF and CRH—G—CSF—R

The structure coordinates of the complex of G-CSF and CRH-G-CSF-R obtained in Example 3 were further refined. Using the crystal structure factor and the structure coordinates obtained in Example 3,

REFMAC (in the program group of CCP 4) and X—; Repeated calculation using POLR and modification of model using QUANTA to obtain two molecules of G—CSF consisting of 175 amino acid residues. In one of them (molecule A), the amino acid residues M1 to L4 in molecule A of G—CSF and the side chain portion of Q71 and L131, and the amino acids M1 to P6 in molecule C of G—CSF Residues and H53, W59, Q68,

L70, the side chain part of Q71, the amino acid residues from G120 to H126, K214 to A215 in the molecule B of CRH—G—CSF—R and the side chain part of K63, R64, and In the molecule D of CRH—G—CSF—R, the structural coordinates of the amino acid residues Al, I119 to H126, and K214 to A215, and the amino acid residues excluding the side chains of K62, K63, R64, and Q127, Two N-acetyldarcosamine residues and 260 water molecules were identified. At this stage, the R factor, which is regarded as an index of the accuracy of the structural coordinates by those skilled in the art, is R = 22 when using a structural factor obtained from a diffraction image having a Plug reflection angle of 25A to 2.8A. 2%. R factor calculated from structural factors that were not separately included in the refinement calculation at the refinement stage (Factor referred to in the art as the Free R factor) was R = 29.8%. Furthermore, the root-mean-square errors of the bond distance and bond angle between the atoms from the ideal state were 0.014 and 1.9 degrees, respectively.

The obtained structural coordinates are shown in Table 1 according to the format of Protein'Data Bank, a notation commonly used by those skilled in the art. Example 5

Superposition of 3D structure of human leptin and 3D structure of G—C.SF

The three-dimensional structural coordinates of human leptin (SEQ ID NO: 3) were reported by Zhang et al. (Zhang, Y. et al., Nature, 387: 206-209 (1997)).

As the three-dimensional structural coordinates of G—CSF, those of G—CSF of the G—CSF ■ CRH—G—CSF—R complex obtained in Example 3 were used. In superimposing the two three-dimensional structures, correspondences between residues were made in advance by structural alignment. As a computer program for this purpose, the affine penalty, the vector environment of the structural environment, and the weighting of the gap in the secondary structure were used in the program developed by this research institute (JP-A-10-185925). The improved program was used. The computer used was SUN 7/300 u. The calculation conditions at this time are as follows. In lower dynamic programming, 50.0 and 2.0 were used for a and b in the equation for evaluating the similarity between vectors. The opening penalty () of the affine penalty of the lower dynamic programming was 5.0, and the extension penalty (/ 3) was 0.0. The penalty at the N-terminal and C-terminal boundaries was set to 0.0 for both a and j3. The opening penalty (α) of the affine penalty in the upper dynamic programming is 500.0,

extension penalty (] 3) was set to 0.0. The factor of difficulty in the occurrence of the insertion Z deletion in the secondary structure was set at 500.0. The penalty at the N-terminal and C-terminal boundaries was set to 0.0 for both α and] 3. The cutoff distance was 10. θΑ and ΔΝ was 10. f, which is the width of f-suboptimal region, adopted 3.0 SD.

Next, based on the obtained structural alignment, the square root of the mean square error between leptin and the main chain atom of the G-CSF residue in the G-CSF-CRH-G-CSF-R complex was minimized. Leptin and G—CSF are superimposed so that — By removing CSF, a hypothetical leptin'CRH-G-CSF-R complex was created. As a computer program for this, Insight II (Molecular Simulation Inc) was used on the SGI workstation Indy. Example 6

3D structural modeling of the complex between human leptin and CRH-human leptin receptor Amino acid sequence alignment of human CRH-lebutin receptor (SEQ ID NO: 4) and rat CRH-G-CSF-R (SEQ ID NO: 2) On a computer. Sequence alignments were performed on a workstation SUN 7 300 u using the program CLUSTALW 1.4. The alignment parameters used were the default values of CLUSTALW 1.4.

The obtained sequence alignment was modified into a form suitable for modeling based on the structural information of G-CSF-R. The alignment was modified on the above workstation SUN7Z300u with the UNIX standard editor, vi. First, since the ninth] 3 strand of G-CSF-R corresponded to the gap, the position of the gap was shifted to a nearby loop region, and the] 3 strand in question was the residue of the leptin receptor. Modified to correspond to Second, an alignment was created in which Cysl62 involved in the disulfide bond of G-CSPVR was shifted by one residue to Cys498 of the leptin receptor. Was modified so that those Cys residues were juxtaposed. Third, Ala Γ76 of G-CSF-R was associated with the gap, but this was a residue that forms a] 3 strand, so Met Γ75 was shifted by one residue to correspond to the gap, The gap was moved to the end of the strand.

Amino acid substitutions for homology modeling were performed on the SGI Workstation Indy using Insight II Ver 97.2 Biopolymer. The energy minimization of the side chain of the substituted residue and its surrounding residues was performed by the protein simulation tool PRESTO Ver.3 using 2CPU on the SGI parallel computer origin 2000.

Amino acid insertion and deletion for homology modeling It was performed using Biopolymer of Insight II Ver 97.2 on Indy. Subsequently, the energy minimization of the side chains of the inserted / deleted residues and the peripheral residues was performed by a protein simulation tool PRESTO Ver. 3 on a SGI parallel computer origin 200 using two CPUs.

Finally, the energy minimization including all atoms in the model was performed by the protein simulation tool PRESTO Ver. 3 using two CPUs on the SGI parallel computer origin 2000.

Manual changes in the direction of the Arg20 side chain of the model were performed on the SGI workstation Indy using Insight II Ver 97.2 Biopolymer. The subsequent energy minimization was performed by the protein simulation tool PRESTO Ver.3 on the SGI parallel computer origin 2000 using two CPUs.

Table 6 shows the three-dimensional structural coordinates of the complex of leptin and CRH-leptin thus obtained.

Claims

The scope of the claims

1, Three-dimensional structural coordinates of the complex formed by the region that binds leptin and leptin in the leptin receptor (CRH-leptin receptor).

2. The three-dimensional structural coordinates according to claim 1, wherein the lebutin and the CRH-levbutin receptor are derived from a mammal.

3. The method according to claim 2, wherein the lebutin comprises a human-derived amino acid sequence represented by Rooster sequence number 3, and the CRH-levbutin receptor comprises a human-derived amino acid sequence represented by SEQ ID NO: 4. Dimensional structure coordinates.

4. The three-dimensional structural coordinates according to claim 3, wherein the three-dimensional structural coordinates are those shown in Table 6.

5. The three-dimensional structural coordinates according to claims 1 to 4, used for identifying, searching, evaluating or designing a mutant, agonist or antagonist of lebutin.

6. Store all or part of the three-dimensional structural coordinates according to claim 5, which is used to identify, search, evaluate or design a mutant, agonist or antagonist of lebutin. Storage media for computers.

7. All or part of the three-dimensional structural coordinates described in claims 1 to 5, or claim for identifying, searching, evaluating, or designing a mutant, agonist, or antagonist of lebutin. Use of a storage medium for a computer according to paragraph 6 above.

8. A lebutin characterized by using all or a part of the three-dimensional structural coordinates according to claims 1 to 5, or the computer storage medium according to claim 6. A method for identifying, searching, evaluating, or designing a mutant of lebutin having an activity as an agonist and having one or several amino acid residues substituted, deleted, inserted, or chemically modified.

9. Lebutin characterized by using all or a part of the three-dimensional structural coordinates described in claims 1 to 5 or the computer storage medium described in claim 6. A method for identifying, searching, evaluating, or designing a mutant of lebutin having activity as an antagonist, in which one or several amino acid residues have been substituted, deleted, inserted, or chemically modified.

10. The mutant is the amino acid residue of I3, K5, D85, R20, K15, D8, D9, K5, F92, V89, L13, L86 and its leptin in human leptin shown in SEQ ID NO: 3. 10. The method according to claim 8, wherein one or more amino acid residues are substituted, deleted, inserted, or chemically modified in the vicinity of the amino acid residue.

1 1. In human leptin shown in SEQ ID NO: 3, amino acid residues of I3, K5, D85, R20, K15, D8, D9, K5, F92, V89, L13, L86 and amino acids near the amino acids A lebutin variant in which one or more amino acid residues are substituted, deleted, inserted, or chemically modified at the residue.

12. The action of lebutin, characterized by using all or a part of the three-dimensional structural coordinates described in claims 1 to 5, or the storage medium for a computer described in claim 6. How to identify, search, evaluate or design a drug.

13. Among the three-dimensional structural coordinates listed in Table 6, the amino acid residues of C RH—leptin receptor D617, V588, R468, V562, E565, N567, R615, L616, L471, and L506 13. The method according to claim 12, wherein the three-dimensional structural coordinates of the part and the part corresponding to the amino acid residue in the vicinity thereof are used.

14. The agonist is bound to the CRH-lebutin receptor, and the resulting spatial arrangement of the CRH-lebutin receptor is defined by the three-dimensional structural coordinates according to claim 4. 14. The method according to claim 12 or 13, wherein the spatial arrangement of CRH-leptin receptor in a complex of a complex of CRH-lebutin receptor and lebutin is substantially the same.

15. A compound which is an agent acting on leptin, which is obtained by using the method for drug design according to claims 12 to 14.

16. The compound according to claim 15, wherein the agonist of lebutin is a natural compound or a synthetic compound.

17. An antagonist of lebutin, characterized by using all or a part of the three-dimensional structural coordinates described in claims 1 to 5, or the storage medium for a computer described in claim 6. How to identify, search, evaluate or design a drug.

18. An antagonist binds to lebutin and inhibits binding of lebutin to the levulin receptor 18. The method according to claim 17, which is a compound that inhibits.

19. The method according to claim 17, wherein the antagonist is a compound that binds to CRH-lebutin receptor and inhibits the binding of potent leptin to the leptin receptor.

20. The method according to claim 17, wherein the antagonist is a compound that binds to a complex of lebutin and a lebutin receptor and inhibits the normal binding of lebutin and a lebutin receptor.

21. A compound that is a leptin antagonist, obtained using the method according to any one of claims 17 to 20.

22. antagonists natural compound of Rebuchin, or synthetic compound, Compound ranging ^second one of claims claims.

23. A method for obtaining the three-dimensional structure coordinates of a complex of a protein and its receptor by homology modeling using the three-dimensional structure coordinates of the G—CSF and CRH—G—CSF—R complexes.

24. The method according to claim 23, wherein the protein is a cytokine.

25. The method according to claim 24, wherein the protein is a cytokine having a four-helix bundle structure.

26. 4—Helix. The method of claim 25, wherein the cytokine having a bundle structure is a cytokinin belonging to the ganglion helicopterin family.

27. The method according to claim 26, wherein the cytokinin belonging to the long chain helical cytokinin family is interleukin-16, a leukemia cell inhibitory factor, or a ciliary neurotrophic factor.

28. The method of claims 23-27, wherein the receptor for the protein is a single transmembrane.

29. Three-dimensional structural coordinates of a complex of a protein and its receptor, obtained by the method according to claims 23 to 28.

30. A storage medium for a computer which stores all or a part of the 37 fire origin structural coordinates according to claim 29.

31. Identify, search, evaluate or design protein variants, agonists, or antagonists 30. Use of all or part of the three-dimensional structure coordinates according to claim 29 or a computer storage medium according to claim 30.