JPH10287696A - Estimation of function of protein - Google Patents

Abstract

PROBLEM TO BE SOLVED: To obtain a database for estimation, etc., of functions of protein containing information about amino acid sequence of the protein in which one or more biological functions are known, by making the database include information on an importance score related to the expression of the biological functions of each amino acid residue constituting the amino acid sequence therein. SOLUTION: The database contains the information on the amino acid sequence of a protein capable of utilizing the information on the steric structure of the protein as information about the amino acid sequence of the protein in which one or more biological functions are known and is prepared by adding an importance score related to the expression of the biological functions about each amino acid residue constituting the amino acid sequence thereto to thereby determine the estimation value of the homology in consideration of the importance score related to the expression of the biological functions for the coincidence of the constituent amino acid sequence of the protein housed in the database for a polypeptide unknown about the biological functions. Thereby, the biological functions of the objective protein are estimated from the final estimation value for the whole proteins contained in the database.

Description

DETAILED DESCRIPTION OF THE INVENTION

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a method for estimating the function of a protein comprising an amino acid sequence based on information on the amino acid sequence. More specifically, based on amino acid sequence information, a method for efficiently estimating a biological function such as an enzymatic activity of a protein composed of the amino acid sequence using a specific database available on a computer. About.

[0002]

2. Description of the Related Art Proteins are indispensable substances for maintaining life activities in living organisms, and various proteins are present not only in animals and plants but also in microorganisms, and each has its own function and role. Proteins can be broadly classified by their functions into enzymes that catalyze chemical reactions, receptors that are signaling proteins, receptors that transmit signals, and proteins that bind and transport specific substances. Can be classified and each is further subdivided by various functions.
For example, enzymes catalyze a specific reaction, such as an enzyme that reduces a specific site of a specific substrate and an enzyme that hydrolyzes a protein.

[0003] A protein is mainly composed of 20 kinds of amino acids, and is a polypeptide molecule in which about 50 to 1000 amino acids are connected in a chain by peptide bonds in various orders. The order in which amino acids are connected (referred to as amino acid sequence or primary structure) differs for each protein, and as a result, each protein can express a different physiological function. That is, when a long polypeptide chain is folded to form a three-dimensional structure, it becomes possible to capture target molecules (enzyme substrate molecules, receptor substrate molecules, etc.),
A field suitable for the expression of a target biological action is provided, for example, the functional groups involved in the reaction are arranged in an appropriate positional relationship. Although it is easily presumed that a unique three-dimensional structure is determined from each amino acid sequence and a biological function is determined from the three-dimensional structure, the necessity of these relationships has not yet been well explained.

[0004] In the study of proteins, instead of the classical method of isolating and purifying a protein using an enzyme activity as an index, determining the molecular weight, the number of constituent amino acids, and the number of each amino acid, and then determining the amino acid sequence, a terminal method is used. After synthesizing the corresponding gene sequence by determining about 20 residues, a method of determining the entire amino acid sequence from the gene side by picking up the gene encoding the protein has come to be used. These studies have focused on proteins whose function is already known, but recently studies have often been performed in exactly the reverse order. The reason is that the analysis of the gene sequence has become so easy that the amino acid sequence of the protein that it should encode can be easily determined from the gene side without isolating the protein. .

[0005] As a result, the number of proteins whose amino acid sequences can be deduced without knowing their biological functions is rapidly increasing. Since the biological function of a protein is expressed based on its three-dimensional structure, attempts have been made to estimate the biological action by analyzing the three-dimensional structure of such a protein whose function is unknown by crystal analysis or nmr analysis. I have. However, such structural analysis is much larger than the biochemical usage,
And a sample of high purity is required. Also, the biological function is not immediately estimated from the three-dimensional structure, and even if the biological function is estimated, it is not necessarily important, so the investment efficiency of research is extremely low There is a problem. Therefore, development of a method for estimating the biological action of a protein having the amino acid sequence before determining the three-dimensional structure of the protein has been desired. If such a method is developed, it is expected to make a great contribution to protein research and gene research.

[0006] The three-dimensional structure and the biological function are closely related, and the three-dimensional structure information of a protein whose function is known not only explains the function mechanism but is useful for various purposes. The three-dimensional coordinates of the complex with the protein or ligand molecule are described in the Protein Data Bank (Brookhaven National La
boratories, USA) and is available worldwide. At present, the number of recorded structures is about 5,000, but it is about 400-500 in consideration of the difference in species and the independent proteins excluding mutants. Due to the spread of analysis techniques and advances in the isolation and purification of proteins, the number of proteins to be crystallized has been increasing at an accelerating rate, but at present there are overwhelmingly many proteins whose tertiary structure remains unclear.

[0007] Modeling can be used as a method for estimating the three-dimensional structure of a protein or the state of interaction with a ligand molecule without using crystal analysis or nmr analysis. If the three-dimensional structure of a similar protein with a high degree of homology in the amino acid sequence has already been analyzed, a three-dimensional structure based on the correspondence between the amino acid residues is constructed by performing modeling using that structure as a template. it can. This method is excellent because it does not require obtaining a sample and can be generally performed interactively on a computer graphics screen. For example, this is accomplished by substituting side chains for unmatched amino acids. Despite problems with side-chain conformation and problems with the backbone of inserted or deleted amino acids, the reliability of the deduced structure is determined by the high homology of the amino acid sequence, and the treatment is almost the same as the crystal structure. It is possible.

[0008] A method of aligning the amino acid sequences of two or more proteins so that the types of amino acids match as much as possible (alignment) is not only for the purpose of modeling, but also for the similarity between biological species and families. It is frequently used to examine differences. In the alignment method, conceptually, one sequence is shifted one residue at a time with respect to the other to find a corresponding position having the best amino acid matching score. Although the possibilities are endless, detailed considerations and repetitive operations are required, and extremely complicated work is required to obtain highly accurate results. For example, since there is often an insertion or deletion in one sequence, it is not possible to simply score the degree of amino acid identity in the entire sequence, and it is necessary to search for a partial sequence that partially matches well, It is also necessary to calculate a match score in a predetermined number of residues (window). In some cases, it is necessary to obtain a score based on homology between amino acids having similar properties instead of exact matches.

In general, when the homology is low, the alignment is not uniquely determined and there is a problem that ambiguity remains. However, a protein having a high similarity in amino acid sequence is selected from a group of proteins whose functions are known. Alignment is currently the easiest way to estimate the function of a protein whose amino acid sequence is the only clue, since it can be located. For these reasons, attempts have been made to partially automate the complicated operation of alignment using a computer. For example, FASTA (Pearson, WR and Lipman, D.
J., Proc. Natl. Acad. Sci. USA, 85, pp. 2444-2448,
1988) and BLAST (Altschul, SF et al., J. Mol. Bio
l., 215, pp. 403-410, 1990). Although these methods are suitable for quickly examining whether a short specific sequence is present in a long target sequence, they are suitable for comparing long sequences or having low homology and only fragmentary matches. When sequences that do not exist are to be searched, it is extremely difficult to determine similarity and extract similar parts, and the accuracy of determining homology is low. Therefore, these methods are insufficient for the purpose of alignment and for estimating the function of a protein, and the development of a more accurate and faster method has been required.

[0010]

SUMMARY OF THE INVENTION An object of the present invention is to provide a method for estimating a biological function of a protein comprising an amino acid sequence based on the information on the amino acid sequence. More specifically, when only amino acid sequence information is available, the homology with the amino acid sequence of a protein whose biological function is already known can be efficiently searched by a computer using a specific database. Another object of the present invention is to provide a method for accurately and rapidly searching for a biological function of a protein comprising the amino acid sequence.

[0011]

Means for Solving the Problems The present inventors have made intensive efforts to solve the above-mentioned problems, and as a result, using a database having the following characteristics, the function of a protein can be estimated from an amino acid sequence at an extremely high speed and with high accuracy. I found what I could do.

That is, the present invention includes information on the amino acid sequence of a protein of which one or more biological functions are known, and relates to the expression of the biological function for each amino acid residue constituting the amino acid sequence. It is intended to provide a database including information to which a score of importance is added.

This database can be used, for example, to estimate the function of a protein whose biological function is unknown based on the homology of amino acid sequences. In a preferred embodiment, the biological function is known. As the information on the amino acid sequence of the protein, using the amino acid sequence of the protein for which information on the three-dimensional structure such as the three-dimensional structure of the protein is available,
For each of the amino acid residues constituting the amino acid sequence, a score of importance relating to the binding between the protein and the ligand molecule or the expression of a biological function is added. These databases are typically stored on floppy disks, CD-ROMs,
It can be stored in various storage media such as a magnetic tape and an optical disk.

From another viewpoint of the present invention, the proteins in the above-mentioned database (which may be referred to as "template proteins" in this specification) and the polypeptides whose biological functions are unknown (in this specification, "proteins of interest") May be referred to as the same), an evaluation value of homology is determined in consideration of the score of the importance of the expression of the biological function with respect to the identity of each constituent amino acid, and the homology of the site having the higher importance is expressed. A method is provided for creating an aligned alignment.

[0015] In a preferred embodiment of this method, the protein in the database and the target protein are highly homologous by using a group sequence containing two or more consecutive amino acid residues which are highly important with respect to the expression of a biological function. The method includes a step of searching for a correspondence. In another preferred embodiment, a step of obtaining a final evaluation value of homology from the above-mentioned alignment for one protein in the database and the target protein, and a step of obtaining a target function regarding biological function from the final evaluation values of all proteins contained in the database. Estimating the protein most similar to the protein. With these methods, proteins with high homology at sites related to biological functions can be efficiently extracted even if the homology of the entire protein is low, and the function of the target protein can be quickly and accurately estimated. It has the feature of being able to.

[0016]

BEST MODE FOR CARRYING OUT THE INVENTION The database of the present invention contains information on the amino acid sequence of a protein of which one or more biological functions are known, and for each amino acid residue constituting the amino acid sequence, It is characterized by including information to which a score of importance relating to the expression of a target function is added. The protein to be stored has, for example, one or more biological functions such as an enzyme action and a receptor action,
Any amino acid sequence may be used as long as the entire amino acid sequence is known, and preferably, the three-dimensional structure of the protein or the three-dimensional structure of the ligand binding site has already been elucidated or estimated, or can be easily estimated. Preferably, there is. It is desirable that the database contain as much information as possible about the protein whose tertiary structure has been clarified. For example, the three-dimensional coordinates of a complex with a protein or ligand molecule can be obtained from the Protein Data Bank (Brookhaven N
ational Laboratories, USA)
Information on about 5000 proteins (about 400 to 500 when considered as independent proteins excluding differences in species and mutants) is available, and can be suitably used to create the database of the present invention.

In the database of the present invention, based on the amino acid sequence of a protein having a known biological function,
Each amino acid residue is characterized by adding a score of importance regarding the expression of the biological function.
Information to be stored for each protein includes, for example, protein name, species, organ / organ, subtype, type of function, and subclassification of function (for enzymes, for example, enzymatic action such as proteolytic action or reducing action). , Enzyme classification number (EC number), ligand molecules (enzyme substrate, receptor substrate, coenzyme, metal ion, etc.) involved in enzymatic reactions and biological functions, origin of three-dimensional structure (for example, X-ray crystallography, nmr
Analysis, information-based modeling of similar proteins with similar biological functions, etc.), primary citations, reference numbers from other databases, target site ligands,
And the entire amino acid sequence, but are not limited thereto, and appropriate information may be added or deleted.

[0018] The database of the present invention contains, in addition to the above-mentioned information, a score indicating the importance of the expression of the biological function for each amino acid residue constituting the amino acid sequence. The importance score is determined by giving a number or other symbol such as zero for no importance at all and 10 for extremely high importance, but is preferably related to importance. In general, the calculation is performed in consideration of two or more factors.
The database of the present invention further includes the presence or absence of a continuous amino acid residue sequence (1 to n) which contributes to the expression of a biological function (the score is not zero), a scoring method, a total score, a protein Information such as a scale factor for standardizing the total score and the like among them can be added, but the information to be added is not limited to these.
Appropriate information can be added or deleted. When a plurality of biological functions and a plurality of ligand molecules are known for one protein, it is preferable to store information on each of them.

Hereinafter, a specific method for giving a score of importance regarding the expression of the biological function for each amino acid residue constituting the amino acid sequence of the protein will be described. However, these descriptions are merely for illustrative purposes only. Shown,
It should not be construed as limiting in any way.
Further, the database of the present invention is not limited to those manufactured by these means. In the following description, an example in which the importance score is represented by a numerical value is described. For a case where there is no importance at all, zero is given, and as the importance becomes higher, a larger numerical value is given. It should also be understood that the method of attachment is not limited to such a method.

(A) When crystal analysis of a protein complex containing a low-molecular-weight ligand molecule has been performed: a protein stored in a protein data bank, which is a protein complex such as an enzyme substrate, a receptor substrate, or an inhibitor. When the three-dimensional structure of a complex with a ligand molecule having a molecular weight has been analyzed, the distance of each amino acid residue from the ligand molecule is determined, and a score of importance according to the distance is given to each amino acid residue. be able to. The low-molecular-weight ligand molecule may be any of pharmacologically active organic compounds, enzyme substrates, metal ions, and the like. For example, amino acid residues within 10 ° of any atom of a ligand molecule (for example, Ca atom serving as a ligand or one atom of a side chain in a ligand molecule) are 1,8 ° or 2,6 °. , 10Å, a score such as 0 can be given.

(B) When the crystal analysis is performed on the protein alone: Even for the protein analyzed without the ligand molecule, the structural region related to the biological function (enzyme activity, etc.) has been obtained from various experiments. If is estimated,
It is possible to give a numerical value corresponding to the distance as described in (a) above to the amino acid residue in the vicinity. Even if there is no correspondence between the biological function and the three-dimensional structure, if the biological function is clear, draw the three-dimensional structure of the protein on a computer graphics screen and rotate By searching for, amino acid residues related to biological functions can be extracted.

(C) Structural conservation region: For proteins having the same biological function, if analysis results of two or more types of three-dimensional structures such as proteins of different subtypes or heterologous species having different amino acid sequences can be used, By superimposing the structures described above, regions that are three-dimensionally conserved can be extracted, and a high numerical value can be given to the amino acid residues contained in those regions.

(D) Modeling: When the three-dimensional structure of a protein has not been analyzed, a modeling structure constructed based on the three-dimensional structure of a related protein that is known to have substantially the same biological action is used. Based on this, it is possible to give a score of importance. For example, it is known that the reliability of the modeling structure is high when the homology of the amino acid sequence is high when the receptor subtype or isozyme, a protein belonging to the same family, or a protein of the same function of a different species are high. How to give a score of importance may be performed, for example, in the same manner as each of the above methods.

(E) Biochemical experiment or genetic experiment: For example, an amino acid residue presumed to be important for the expression of a biological function from a biochemical experiment or a genetic amino acid conversion experiment ( Amino acid residues presumed to be essential for the expression of a biological function such as an enzymatic action from point mutation or the like can be given a high degree of importance. For example, in an enzymatic reaction, it is possible to give a large numerical value to an amino acid residue that plays a catalytic role, in addition to the evaluation from the viewpoint of binding to a ligand molecule.

(F) Protein which is a high molecular ligand molecule: Generally, a protein whose binding to a low molecular weight ligand molecule is essential for its function has an inner hole for stably binding to the ligand molecule. I have. On the other hand, for example, a protein to which a high molecular weight ligand molecule such as a protein binds to a receptor protein on the molecular surface without having a remarkable inner hole, and the receptor protein also does not have a remarkable inner hole. Sometimes.
For example, when the ligand itself is a macromolecule ligand such as a cytokine, a large value may be given to amino acid residues in the epitope region estimated using a monoclonal antibody.

One of the methods exemplified above, or 2
By using a combination of more than one kind, and further adding an appropriate technique as needed, for each amino acid residue constituting the amino acid sequence of a protein having a known biological function, the expression of the biological function Of the amino acid sequence to which the importance score has been added. The relationship between amino acid residues and expression of biological functions is described in, for example,
It goes without saying that various criteria can be used for scoring, such as those in which the relationship is fully demonstrated by the method (a) and others in which the relationship can be estimated to some extent.

For example, amino acid sequences to which a score of importance is added for as many proteins as possible, such as proteins having a known crystal structure and proteins which are presumed to have a similar tertiary structure in terms of biological functions. Information can be collected and stored in a computer-usable predetermined format to build the database of the present invention. At this time, a score may be added to each protein according to an appropriate different standard according to the amount and quality of information of each protein. However, it may be necessary to add to the database a scoring method and a scale factor for normalizing the total score between proteins. The above information can be manually input according to a certain method, but generally, it is more efficient to use a predetermined program on a computer graphics screen.

In the method of the present invention, using the above database, the homology calculated from the score of the importance of amino acid residues between the template protein whose information is stored in the database and the target protein whose biological function is unknown. Alignment is made so that the evaluation value of is maximized, and then a similar alignment is made for two or more template proteins contained in the database, preferably for all template proteins, and then the evaluation value of homology between the template proteins is made. And a template protein having the highest evaluation value can be selected. The template protein selected in this manner has a high degree of similarity in the three-dimensional structure to the target protein, and can be estimated to be a protein having substantially the same biological function.

The above method is generally performed by extracting information on the template protein from the database of the present invention one by one and performing an alignment operation on the amino acid sequence of the target protein. If the amino acid sequence information of the target protein is directly available, the information may be input and used.If only the information of the gene sequence encoding the target protein is available, the target nucleic acid sequence information may be used. It is necessary to translate and use the information on the amino acid sequence of the protein.

As an example of a preferred method of the present invention, a group sequence containing two or more consecutive amino acid residues (consecutive non-score amino acid residues) contributing to biological function in the amino acid sequence of the template protein , A method of searching for a highly homologous correspondence between a template protein and a target protein can be mentioned. However,
The alignment operation is not limited to this method and may be performed by any method available to those skilled in the art.

In the above method using the group arrangement,
While shifting the group sequence by one residue with respect to the amino acid sequence of the target protein, an evaluation value of homology can be obtained for each group, and then, if necessary, factors such as the order and length of connection of the group sequences are determined. In consideration of this, it is possible to determine the correspondence between each group sequence and the amino acid sequence of the target protein so that the total evaluation value of all the group sequences is the best. This procedure was performed for all template proteins in the database, and one with a high total score
Alternatively, two or more proteins can be extracted. The target protein is likely to have substantially the same biological function as the template protein extracted in this manner.

As the evaluation value of homology, for example, when the group sequence in the template protein and the corresponding amino acid residue in the target protein sequence match, the importance score is transferred to the matching amino acid residue. It is simply easy to sum. Of course, in order to create an alignment with emphasis on matching amino acids with high importance scores, each importance score may be further processed and used with one or more functions. When creating an alignment of the target protein and all template proteins contained in the database, all the homology evaluation values may be compared between different alignments.
In general, a scale factor for normalizing the importance score is used so that the degree of homology with the target protein can be compared based on the total value of the importance scores even between template proteins having different sizes. It is desirable to calculate for each template protein and store it in a database. At the stage where the alignment work between the target protein and each template protein is completed and the homology score has been calculated, the final score is obtained by multiplying the homology score of each template protein by the corresponding scale factor to obtain a final score between the template proteins. The homology of the two can be determined. .

In the same type of proteins existing in different species, for example, aspartic acid and glutamic acid having a carboxyl group in common but differing in the length of a side chain by one carbon atom are the same as those in the amino acid sequence. May play the same role in different locations. In such a case, it is appropriate to consider these amino acid residues to be coincident when judging the coincidence of the amino acid residues.
Also, amino acid residues such as leucine and isoleucine and valine have similar properties from the viewpoint of hydrophobicity, although they differ in shape and size (bulk). Therefore, when quantifying the homology of amino acid sequences, it is desirable to use a correspondence table in which the similarity of amino acid residues is graded so as to reflect the presence of such similar amino acid residues. Any kind of similarity of amino acid residues may be used. For example, PAM250 (Dayhoff, MO, et al., Atlas et al.)
f Protein Sequence and Structure, Dayhoff, MO E
d., Vol. 5, Suppl. 3, pp. 345-352, NBRF, Washington,
1978) and BLOSUM (Henikoff, S. and Henikoff, JG,
Proc. Natl. Acad. Sci. USA, 89, pp. 10915-10919, 19
92) are available.

[0034]

[Table 1]

An example of the method of the present invention is shown above as a conceptual diagram. Further, the method of the present invention may be, for example, a method including the following steps. However, the method of the present invention is not limited to these methods. In addition to the steps employed in these methods, one or more appropriate steps can be added as necessary, It should be understood that one or more steps may be omitted. It goes without saying that all such modified or modified methods are included in the scope of the present invention.

(1) a step of retrieving the amino acid sequence of the target protein; (2) a step of retrieving one template sequence from the database; (3) a partial sequence a having a score of importance greater than a certain value from the amino acid sequence of the template protein , B, c, d, e, ---, n, ----
(For example, the length of each subsequence is 1a, 1b, 1c, 1d, 1e ---, 1n, ----); (4) Subsequence a is the target sequence Calculating the homology evaluation value S (a) i while shifting one amino acid residue at a time (adding the importance score of the matched amino acid residue as the homology evaluation value); ) Position subsequence b at the (1 + 1a) th position of the target sequence
The homology evaluation value S (b) is shifted by one amino acid residue at a time.
i is calculated (the score of the importance of the amino acid residue that matches is added as the evaluation value of homology); (6) Similarly, the homology of c, d, e,- (7) taking into account the order of a, b, c, d, e, ---, n, --- and the number of amino acid residues, A step of determining the corresponding position of the partial sequence so that the homology SS of all partial sequences is maximized; (8) a step of applying SS to a scale factor to obtain SSS; and (9) a step of determining all template proteins in the database as described above. Performing a procedure to obtain an SSS; and (10) extracting a protein having a high SSS

[0037]

EXAMPLES The present invention will be described more specifically with reference to the following examples, but the scope of the present invention is not limited to the following examples. Example 1: Creation of database Dihydrofolate reductase (DHFR-EC) derived from Escherichia coli with known biological function and three-dimensional structure, trypsin (TRYP) derived from bovine, ribonuclease A (RNAS) derived from bovine, derived from whale A database consisting of four proteins of myoglobin (MYGL) was created. Each crystal structure is described in the Protein Data Bank (Brookhaven National Laborato
ries, USA). When any of the constituent atoms of the amino acid residue is within 4 ° of any of the atoms of the ligand molecule (inhibitor or coenzyme) bound to the protein, it is within the range of 2, 4 to 10 ° 1 and 0 in other cases, amino acid sequence information in which a score of importance for expression of each biological function was added to each amino acid residue constituting each amino acid sequence was prepared. FIG. 1 shows the amino acid sequence of each protein and the results of scoring.

Example 2: Estimation of Biological Function Using human-derived dihydrofolate reductase (DHFR-HM) as a target protein, the biological function of the target protein is estimated by the method of the present invention using the above database. did. Although DHFR-HM is a protein whose biological function and tertiary structure are known, analysis was performed assuming that the biological function and tertiary structure were unknown. For each amino acid sequence of the template protein in the database, a partial sequence having a score value of 1 or more is extracted, and the homology evaluation value S is calculated while shifting one residue at a time with respect to the amino acid sequence of the target protein. The highest alignment position was determined.

The evaluation value S is calculated using a correspondence table BLOSUM62 relating to the similarity of amino acids, and an evaluation value of similarity according to a set of amino acid residues between the partial sequence and the amino acid sequence of the target protein is obtained from the table. And a method of integrating the product of the score of each residue of the partial sequence and the evaluation value of the similarity over the length of the partial sequence. The homology SS of all partial sequences was calculated as the sum of the maximum evaluation value S obtained for each partial sequence. To correct the difference in the length of the sequences used for the homology determination, the reciprocal of the sum of the scores of all partial sequences is used as a scale factor, and the scale factor is multiplied by the value of SS to obtain a final evaluation value SSS. Calculated. As a result, as shown in Table 1, when DHFR-EC, TRYP, RNAS, and MYGL were used as template proteins, DHFR-EC gave the highest evaluation value SSS, and the target protein (DHFR-HM) was DHFR-EC. It is a protein similar to and has been presumed to have dihydrofolate reductase activity. FIG. 2 shows the alignment of DHFR-HM and DHFR-EC.

[0040]

[Table 2] 評 価 Protein evaluation value SSS ──────────── DHFR-EC 1.82 TRYP 1.09 RNAS 1.22 MYGL 0.61 ──────── ────

[0041]

The database of the present invention is useful for estimating the biological function of a protein comprising the amino acid sequence on the basis of the information on the amino acid sequence. This is useful because the biological function of a protein composed of an amino acid sequence can be accurately and rapidly searched by utilizing the method.

[Brief description of the drawings]

FIG. 1 shows the amino acid sequences of amino acid sequences constituting the amino acid sequences of four types of proteins whose biological functions and three-dimensional structures are known, to which an importance score relating to the expression of each biological function is added. It is a figure showing information. Symbols in the figure are dihydrofolate reductase (DHFR-EC) derived from E. coli and trypsin (TRY
P), bovine ribonuclease A (RNAS), and whale-derived myoglobin (MYGL).
Indicated by letter notation.

FIG. 2 is a diagram showing an alignment between a target protein (DHFR-HM) and DHFR-EC extracted as a template protein that gives the highest evaluation value SSS to the target protein. The symbols in the figure indicate human-derived dihydrofolate reductase (DHFR-HM) and Escherichia coli-derived dihydrofolate reductase (DHFR-EC), respectively. Is the amino acid sequence of DHFR-HM, the third row is DHFR-E
The fourth row of the partial sequence of the amino acid sequence of C shows the amino acid number of the partial sequence of the amino acid sequence of DHFR-EC.

Continued on the front page (72) Inventor Masazumi Imamura 4-39 Asumigaoka Midori-ku, Chiba-shi, Chiba

Claims (8)

[Claims] Claims 1. An amino acid sequence of a protein having one or more known biological functions, and information on the amino acid sequence of the protein. A database containing information with added scores. 2. The database according to claim 1, which is used for estimating the function of a protein whose biological function is unknown based on the homology of amino acid sequences. 3. The method according to claim 1, wherein the information on the amino acid sequence of the protein whose biological function is known is prepared using the amino acid sequence of the protein for which information on the three-dimensional structure of the protein can be used. Database. 4. The database according to claim 1, wherein the database is stored in a storage medium. 5. For a protein and a polypeptide whose biological function is unknown stored in the database according to any one of claims 1 to 3, the biological function of the polypeptide is determined by matching the respective constituent amino acids. A method of obtaining an evaluation value of homology in consideration of a score of importance regarding expression, and creating an alignment indicating homology of the site of high importance. 6. Using a group sequence containing two or more consecutive amino acid residues which are highly important for the expression of a biological function, searching for a highly homologous correspondence between the protein and the target protein in the database. The method of claim 5, comprising a step. 7. The method according to claim 5, further comprising the step of obtaining a final evaluation value of homology from the alignment for one protein and a target protein in the database. 8. The method according to claim 7, further comprising a step of estimating a protein most similar to the target protein in biological function from the final evaluation value of all proteins contained in the database.