Method of anticipating interaction between proteins

A prediction method and protein technology, applied in the field of prediction of protein-protein interactions, can solve problems such as lack of information on protein-protein interactions

Inactive Publication Date: 2003-05-07
DAIICHI SEIYAKU CO LTD +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, since this method can obtain the information of the protein that constitutes the complex (Complex), but not the information of the interaction between proteins, it is necessary to confirm the interaction between which protein and which protein.

Method used

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  • Method of anticipating interaction between proteins
  • Method of anticipating interaction between proteins
  • Method of anticipating interaction between proteins

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0122] Fig. 1 is as the embodiment of step (1), is the first 20 residues [Fig. Oligopeptides [Fig. 1(b)]. Fig. 1(c) is an oligopeptide whose amino acid sequence is 6 long by decomposing the first 20 residues from the amino terminal of veirotoxin 2 (VTII). (Example 2)

Embodiment 2

[0123] In the step (4) of the method for predicting the interaction between proteins, the value calculated from the amino acid frequency and oligopeptide frequency obtained from the protein or polypeptide database is used as the predictive index of the interaction between proteins or polypeptides. The specificity of oligopeptides, calculated from the amino acid frequencies in proteins encoded by the E. coli genome shown in FIG. 4, is presented here as an example. The composition ratio Ai of each amino acid ai obtained from the frequencies of 20 amino acids in the total protein encoded by Escherichia coli [Fig. 4(a)] is shown in Fig. 4(b).

[0124] When the oligopeptide for specificity is a1a2a3a4a5, the specificity of the oligopeptide is calculated as A1×A2×A3×A4×A5. For example, when the oligopeptide is KCILF, the calculation is 4.406610×1.170608×6.004305×10.639652×3.898962×10 -10 . In addition, the specificity of oligopeptide LLLLL was calculated to be 136344.34×10 -10 , ...

Embodiment 3

[0127] In the step (4) of the above-mentioned protein-protein interaction prediction method, the result of the local arrangement is used as an index for predicting the interaction between proteins or polypeptides, but here as an example, the method using Gotoh (Gotoh, O., Pattern matching of biological sequences with limited storage, Comput.Appl.Biosci.3, 17-20, 1987) for fractional case of partial sequence alignment. In the following example, when the score reaches 25.0 or more, the amino acid partial sequences between the protein or polypeptide (A) and the protein or polypeptide (B) are aligned (identical).

[0128] The m amino acid partial sequences between the protein or polypeptide (A) and the protein or polypeptide (B) are arranged, the score is Si (1≤i≤m), and the length of the amino acid sequence of B is LB. The index for predicting the interaction between A and B calculated from the results of this local arrangement is defined as sum(Si) / LB. The higher the index, the...

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Abstract

The present invention relates a method for predicting a protein or polypeptide (B) that interacts with a specific protein or polypeptide (A), wherein the method is characterized by comprising: 1) decomposing the amino acid sequence of protein or polypeptide (A) into a series of oligopeptides having a pre-determined length as sequence information; 2) searching, within a database of protein or polypeptide amino acid sequences, for a protein or polypeptide (C) comprising an amino acid sequence for each member of the series or for a protein or polypeptide (D) comprising an amino acid sequence homologous to an amino acid sequence for each member of the series; 3) carrying out local amino acid sequence alignment between said protein or polypeptide (A) and the detected protein or polypeptide (C) or detected protein or polypeptide (D); and 4) predicting whether the detected protein or polypeptide (C) and / or protein or polypeptide (D) is a protein or polypeptide (B) that interacts with the protein or polypeptide (A) based on the results of the local amino acid sequence alignment and a value calculated from a frequency of amino acids and / or a frequency of said oligopeptides in said amino acid sequence database; and to a recording medium for carrying out the above method, a device comprising the recording medium, and proteins obtained thereby.

Description

technical field [0001] The present invention relates to the prediction of the interaction between proteins, the prediction method and device, and the protein obtained by the method and the device. technical background [0002] Many proteins perform their functions while interacting with other proteins or with the same protein. Elucidating the interaction between proteins is very important in the development of pharmaceuticals and the improvement of varieties in agriculture. In particular, with the progress of analysis of genomes and cDNAs of various organisms including pathogenic microorganisms, the number of newly discovered genes with unknown functions and their encoded proteins has increased rapidly. If the interaction between proteins can be clarified, it may be possible to predict the function of those proteins whose function is unknown. [0003] For the purpose of elucidating the interaction between proteins, for a certain protein, the method adopted in order to find...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C07K1/107C40B30/04G01N33/68G06F19/00G06F19/16
CPCC07K1/107C40B30/04G01N33/6803G01N33/6845
Inventor 土居洋文铃木敦
Owner DAIICHI SEIYAKU CO LTD
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