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Method and a system for predicting protein functional site, a method for improving protein function, and a function-modified protein

外国特許コード F110003599
整理番号 E04401US3
掲載日 2011年6月30日
出願国 アメリカ合衆国
出願番号 80644807
公報番号 20080262201
公報番号 7820423
出願日 平成19年5月31日(2007.5.31)
公報発行日 平成20年10月23日(2008.10.23)
公報発行日 平成22年10月26日(2010.10.26)
国際出願番号 JP1998000430
国際公開番号 WO1998033900
国際出願日 平成10年2月2日(1998.2.2)
国際公開日 平成10年8月6日(1998.8.6)
優先権データ
  • 特願1997-019248 (1997.1.31) JP
  • 特願1997-019249 (1997.1.31) JP
  • 特願1997-332100 (1997.12.2) JP
  • 特願1998-018699 (1998.1.30) JP
  • 10/345,205 (2003.1.16) US
  • 09/697,138 (2000.10.27) US
  • 09/355,486 (1999.9.20) US
  • 1998JP000430 (1998.2.2) WO
発明の名称 (英語) Method and a system for predicting protein functional site, a method for improving protein function, and a function-modified protein
発明の概要(英語) The present application provides a method for predicting the functional site of a protein using data of the entire proteins of an organism of which genome data or cDNA data is known.
More specifically, the present application provides a method for predicting a protein functional site, comprising the steps of calculating the frequency of occurrence of an oligopeptide in the entire proteins, calculating the value of each amino-acid residue contributing to the frequency of occurrence as the representative value of the function, and predicting the protein functional site by using the representative value of function as an indicator.
The present also provides a system for predicting a functional site for automatically performing said methods.
Additionally, the present application provides a method for preparing a function-modified protein comprising subjecting the amino-acid residues composing the functional site identified by the method described above to artificial mutation, and a novel thermophilic DNA polymerase prepared by the method.
従来技術、競合技術の概要(英語) BACKGROUND ART
Following the progress of genome analysis and cDNA analysis of various organisms including pathogenic microorganisms, the number of novel genes whose functions are unknown is rapidly increasing, together with the number of proteins encoded by the genes.
So far, the analysis of the nucleotide sequence of the whole genome of a microorganism, for example Mycoplasma genitalium (Fraser et al., Science 270, 397-403, 1995), Haemophilus influenzae (Fleischman et al., Science 269, 496-512, 1995), and Methanococcus jannaschii (Bult et al., Science 273, 1058-1073, 1996), has been completed, so that numerous novel proteins predicted from the genome sequence have been discovered.
For humans and mice, the cDNA analysis is under way in combination with the genome analysis, which brings about the discovery of a great number of novel proteins.
In such circumstance, the prediction of the function of a functionally unknown protein or a functional site thereof has been a significant issue.
If not only a novel protein but also a novel function or a novel functional site of a protein with a known function is discovered, whether or not these proteins are worth industrial or clinical application is possibly determined.
Furthermore, such prediction of function possibly enables to prepare a modified protein with a further improved function.
Whether or not a protein encoded by a gene elucidated by genome analysis or cDNA analysis is novel or has a known function has been determined conventionally by searching the homology through protein databases such as Swiss-Prot.
So as to predict a functional site, additionally, functionally identical proteins derived from various organisms are extracted from a protein database and are then subjected to alignment, to identify a region conserved in common to them and predict the conserved region as a functional site.
However, disadvantageously, such alignment method cannot be used if a protein obtained by genome analysis or cDNA analysis is an absolutely novel protein.
Even if the protein has homology with known proteins in a protein database, the conserved region occupies most of the amino acid sequence of the protein in case that the protein is homologous to proteins derived from closely related organisms, so that it is impossible to predict the functional site.
As to modification of protein, generally, the function of a protein is potentially deteriorated irrespective of the fact that the function is known or unknown once the conserved region is modified, even if the functional site is predicted by alignment.
Accordingly, the amino-acid residues outside the conserved region should be modified to improve the function.
In other words, it is required to find a novel functional site in such protein to be modified.
Using the conventional alignment method, disadvantageously, a novel functional site cannot be discovered or which amino-acid residue should be modified cannot be predicted.
Taking account of such circumstance, the present invention has been carried out.
It is an object of the present invention to provide a novel method for predicting a functional site of a functionally unknown protein obtained by genome analysis or cDNA analysis.
In accordance with the present invention, furthermore, it is an object to provide a system for predicting the function.
In accordance with the present invention, still furthermore, it is an object to provide a method for predicting a novel functional site of a protein with an unknown function or with a known function and subjecting the functional site to mutation to prepare a modified protein.
Still furthermore, it is an object of the present invention to provide a protein with a function modified by the method described above.

特許請求の範囲(英語) [claim1]
1. A thermophilic DNA polymerase consisting of the amino acid sequence of SEQ ID NO: 6.
  • 発明者/出願人(英語)
  • DOI HIROFUMI
  • HIRAKI HIDEAKI
  • KANAI AKIO
  • JAPAN SCIENCE AND TECHNOLOGY AGENCY
国際特許分類(IPC)
米国特許分類/主・副
  • 435/194
  • 435/483
参考情報 (研究プロジェクト等) ERATO DOI Bioasymmetry AREA
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