JPH06266810A - Method for specifying dihedral angle - Google Patents

Abstract

PURPOSE:To provide a method for modeling the structure of a protein by utiliz ing phi and psi maps in respect to a structural change due to the modification of an amino acid residual group in the protein. i CONSTITUTION:A main chain dihedral angle specifying method consists of a process for reproducing the coordinate data of a protein, a process for displaying the three-dimensional structure of the protein on the screen of a display device based upon the reproduced coordinate data, a process for selecting a required peptide from the displayed three-dimensional structure and specifying the position of an amino acide residual group to be modified, a process for specifying a dihedral angle between the modified amino acid residual group and a near-by amino acid residual group to be influenced by the modification of the residual group concerned on phi and psi maps, a process for displaying te range of phi and psi values determined from the array of amino acid residual groups constituting the peptide and disabled to be adopted on the maps, a process for specifying the phi and psi values of an amino acide residual group to be modified on the phi and psi maps and comparing them with the range of the phiand psi values, and a process for displaying the three-dimensional structure of the protein on the screen by using the modified dihedral angle.

Description

Detailed Description of the Invention

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a method for clarifying the change in steric structure that occurs when an amino acid residue constituting a protein is modified by designating an optimum value of the dihedral angle of the main chain.

Proteins such as enzymes and antibodies are being researched in the form of biosensors due to their high molecular discriminating power, and it is called protein engineering in which the structure is modified to add new functions and properties. The field is evolving.

A protein is composed of peptide chains in which amino acids are linked by peptide bonds, and each peptide chain is composed of a sequence of amino acid residues unique to each protein. Here, there are 20 kinds of amino acids that make up proteins, and in each case, the amino group (-NH ₂ ) is directly bonded to the α carbon (Cα) bonded to the carboxyl group (-COOH). It is an alpha amino acid.

[0004] Here, using genetic engineering techniques, it is possible in principle to modify an amino acid residue at any position into an amino acid residue of any kind, and insertion or deletion is also possible. Is.

Further, the three-dimensional structure of the protein is changed by the modification of the amino acid residue and has a new function. Thus, proteins have a close relationship between their three-dimensional structure and function, and therefore analysis of their three-dimensional structure is essential.

Here, to know the three-dimensional structure of the modified protein, an experimental method using X-ray diffraction or nuclear magnetic resonance (NMR) is known. However, there is already a lot of research on major proteins, and the Protein Data Bank
Since a database called (abbreviated as PDB) has been created and protein names, functions, coordinate data, literatures, etc. are described, it is possible to display a three-dimensional structure using computer graphics. A technique for modeling a three-dimensional structure that is modified based on a base has become possible.

Here, as a method of modeling, since the coordinates of amino acid residues constituting a protein are known, a hand-held position input device (pointing device) called a mouse is used. There is a method of changing the dihedral angle while displaying an image of the molecular structure in real time, and a method of directly specifying and inputting the atomic coordinates of the modified amino acid residue.

However, when the atomic coordinates of a huge molecule such as a protein are designated and input, the amount of data is huge and complicated. Therefore, instead of displaying the spatial coordinates, the dihedral angle of amino acid residues is designated to stereoscopically display the structure of the protein.

[0009]

2. Description of the Related Art In the proteins that actually exist,
The value of the dihedral angle is often a specific value or a value close to this.

Further, there are dihedral angles that cannot be taken due to steric hindrance that occurs when a bulky substituent exists in the same molecule, and dihedral angles that do not exist in actual proteins.

Regarding the dihedral angle of the main chain as in the present invention, a value in the vicinity of a typical dihedral angle forming a specific secondary structure such as α-helix or β-sheet is often taken. However, it has been unclear how much deviation from the typical dihedral angle occurs when the amino acid residue is modified using a conventional pointing device.

For this reason, in some cases, even if the display has a proper structure, it actually has a dihedral angle value which is not so preferable. Further, when it is desired to re-specify a value that is slightly deviated from the typical dihedral angle, it is necessary to consider the angle at each time, and therefore the work is extremely complicated.

[0013]

[Problems to be Solved by the Invention] It has been attempted to replace a part of a plurality of amino acid residues constituting a peptide chain of a protein with another amino acid residue to improve the function of the protein. , The three-dimensional structure of proteins also changes, and there is a close relationship between the two.

Therefore, it is an object to put into practice a method of modeling a structure in which a dihedral angle is designated and easily modified.

[0015]

[Means for Solving the Problems] The above problems include a step of reproducing coordinate data of a protein required from a data bank in which protein data is registered, and a three-dimensional structure of the protein on the display device from the reproduced coordinate data. The process of displaying an image,
Selecting the required peptide from the three-dimensional structure displayed in the image and specifying the position of the amino acid residue to be modified,
The step of designating the dihedral angle between the amino acid residue to be modified and the neighboring amino acid residue that may be affected by the modification of this amino acid residue on the Φ and Ψ map, and the amino acid residue that constitutes the peptide The process of displaying on the map the range of Φ and Ψ values that cannot be taken, which is determined from the sequence of, and the Φ and Ψ values of the amino acid residue to be modified are specified on the Φ and Ψ map and taken. A step of comparing and examining the relationship with the range of values of Φ and Ψ that cannot be performed, and a step of designating the corrected values of Φ and Ψ on the Φ and Ψ map when the correction is appropriate,
For amino acid residues that may be affected by the modified amino acid residue, examine the relationship between the Φ and Ψ values of this amino acid residue and the modified amino acid residue, and if necessary, the Φ and Ψ values. And a redesignation of the protein, and a step of displaying the three-dimensional structure of the protein as an image using the modified dihedral angle value. You can

[0016]

In the present invention, the optimal structure can be easily selected visually by displaying the dihedral angles of the amino acid residues of the peptide containing the amino acid residue to be modified on the Φ and Ψ maps.

Here, Φ indicates the dihedral angle between the main chain nitrogen (N) atom and the α carbon (C), and Ψ is the dihedral angle between the main chain α carbon and the carbonyl carbon atom. Pointing to. The representative value of the dihedral angle is known for each amino acid residue that constitutes the peptide of the protein, and the structure of the protein has been clarified from this, but when the bulk of the substituents forming the amino acid residue is large, Causes a so-called steric hindrance by hindering the rotational movement of the dihedral angle of the main chain.

As described above, there are 20 kinds of amino acids that compose a protein. Now, consider the case where the protein has the following sequence of amino acid residues. 12345 35 3940 43 54 58 RPDFC ・ ・ ・ YGGCRANSS ・ ・ ・ ・ ・ TCGGA ・ ・ ・ (1) Here, Roman letters are one-letter symbols for amino acids, and numbers indicate the sequence order. , In this case the protein is 58
It consists of 4 amino acid residues.

R is arginine, P is proline and D
Represents aspartic acid, F represents phenylalanine, C represents cysteine, A represents alanine, and G represents glycine, and this protein may have a three-dimensional structure as shown in FIG. 4 by analysis using X-ray or NMR. Are known.

Now, regarding this protein consisting of 58 amino acid residues, among the peptides consisting of amino acid residues No. 35 to 43, arginine (R) No. 39 and alanine (A) No. 40 are selected. When substituting with other amino acid residues, the present invention performs energy calculation for the peptides No. 35 to 43, and first clarifies the regions that cannot be taken due to steric hindrance on the Φ and Ψ maps.

Further, α-helix and β-sheet are typical secondary structures of proteins, but it is known that the dihedral angle value of the main chain easily takes a value close to these dihedral angle values. Therefore, the dihedral angle values of the α helix and the β sheet are designated in advance on the Φ and Ψ maps for reference.

The dihedral angle value of the amino acid residue forming the peptide containing the amino acid residue before modification is also calculated from the coordinate data and designated in the Φ and Ψ maps. In the present invention, the dihedral angle value of the amino acid residue to be modified is designated in the Φ and Ψ maps, the validity is examined, and then the protein structure is determined from this value.

[0023]

[Example] Regarding the protein represented by the formula (1) above, No. 35
The present invention will be described for the case of modifying R of No. 39 and A of No. 40 to glycine (G) among peptides consisting of amino acid residues of ~ 43.

As described above, FIG. 4 shows the three-dimensional structure of the protein, the broken line in FIG. 3 shows the sequence of amino acid residues before modification, and the dihedral angle of R39 is the protein data bank ( It can be calculated from the coordinate data registered in PDB) and displayed on the map.

Here, as described above, C38 represents No. 38 cysteine, and N41 and N43 represent No. 41 and N.
o.43 is asparagine, and S42 is No.42 serine.

Next, FIGS. 1 and 2 show Φ and Ψ maps, and the broken line area in this figure is the area obtained by energy calculation and is clearly the area where steric hindrance occurs. The dihedral angle value of cannot be taken.

The values of the dihedral angles of the α-helix and β-sheet are shown by the circles centering on α and β, and No. 36
The dihedral angle values of amino acid residues of ~ 43 are calculated from the coordinate data registered in PDB and are shown by dots with No.

Further, in FIG. 2, the double circle 39 indicates the dihedral angle value of the conventional R (arginine). In FIG. 1, this R is changed to G (glycine) and the dihedral angle at the +39 position is changed. The figure shows the state in which the facet angle is taken, but this position is outside the region where steric hindrance occurs, and is close to the α helix.

The operation is the same when A40 is changed to G40. In addition, when the dihedral angle is significantly changed in this way, the amino acid residues (C38 and N41) adjacent to the amino acid residue to be modified are inevitably affected.
It is necessary to reexamine the dihedral angle value.

Next, when the dihedral angle value is determined in this way, a peptide structure in which amino acid residues are arranged can be obtained based on the value. The solid line in FIG. 3 is the structural diagram thus obtained.

[0031]

EFFECTS OF THE INVENTION When a protein having a complicated three-dimensional structure is modified by the practice of the present invention, amino acid residues are
By using the Φ and Ψ maps, the three-dimensional structure of the modified amino acid can be modeled by a relatively simple method.

[Brief description of drawings]

FIG. 1 is a map in which new Φ and Ψ values of modified amino acid residues are designated.

FIG. 2 is a map showing Φ and Ψ values of amino acid residues before modification.

FIG. 3 is a sequence diagram of amino acid residues before and after modification.

FIG. 4 is a three-dimensional structure of the protein according to the present invention.

Claims (1)

[Claims] 1. A step of reproducing coordinate data of a required protein from a data bank in which protein data is registered, a step of displaying a three-dimensional structure of the protein on a display device from the reproduced coordinate data, and an image. The step of selecting the required peptide from the displayed three-dimensional structure and designating the position of the amino acid residue to be modified, the amino acid residue to be modified, and the nearby amino acids that may be affected by the modification of the amino acid residue Step of designating dihedral angles with residues on the Φ and Ψ map, and step of displaying the range of Φ and Ψ values that cannot be taken on the map, determined from the sequence of amino acid residues that compose the peptide And a step of designating the Φ and Ψ values of the amino acid residue to be modified on the Φ and Ψ map, and comparing the relationship between the values of Φ and Ψ values that cannot be taken, and if correction is required, Repair of Φ and Ψ The step of designating a positive value on the Φ, Ψ map, and for amino acid residues that may be affected by the modified amino acid residue, the Φ, Ψ value of the amino acid residue and the modified amino acid residue value And the step of correcting the values of Φ and Ψ and re-designating the values if necessary, and displaying the three-dimensional structure of the protein as an image using the modified dihedral angle value. How to specify the dihedral angle of the main chain.