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Extracting Characteristic Properties of Fitness Landscape from In Vitro Molecular Evolution: A Case Study on Infectivity of fd Phage to E.coli.
https://sucra.repo.nii.ac.jp/records/13345
https://sucra.repo.nii.ac.jp/records/13345c74eccae-bebd-418b-a1eb-1e4b04633520
名前 / ファイル | ライセンス | アクション |
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A1002789.pdf (252.4 kB)
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Item type | 学術雑誌論文 / Journal Article(1) | |||||
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公開日 | 2008-10-21 | |||||
タイトル | ||||||
タイトル | Extracting Characteristic Properties of Fitness Landscape from In Vitro Molecular Evolution: A Case Study on Infectivity of fd Phage to E.coli. | |||||
言語 | ||||||
言語 | eng | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | fitness landscape | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | sequence space | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | adaptive walk | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | NK model | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | in vitro evolution | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
資源タイプ | journal article | |||||
著者 |
相田, 拓洋
× 相田, 拓洋× Hayashi, Yuuki× Toyota, Hitoshi× 伏見, 譲× Urabe, Itaru× Yomo, Tetsuya |
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著者 ローマ字 | ||||||
Aita, Takuyo | ||||||
著者 ローマ字 | ||||||
Hayashi, Yuuki | ||||||
著者 ローマ字 | ||||||
Toyota, Hitoshi | ||||||
著者 ローマ字 | ||||||
Husimi, Yuzuru | ||||||
著者 ローマ字 | ||||||
Urabe, Itaru | ||||||
著者 ローマ字 | ||||||
Yomo, Tetsuya | ||||||
著者 所属 | ||||||
産業技術総合研究所生命情報科学研究センター(現 : 埼玉大学大学院理工学研究科) | ||||||
著者 所属 | ||||||
著者 所属 | ||||||
著者 所属 | ||||||
埼玉大学工学部機能材料工学科 | ||||||
著者 所属(別言語) | ||||||
Rational Evolutionary Design of Advanced Biomolecules(REDS) Group/JST, Saitama Small Enterprise Promotion Corporation SKIP City(Present : Graduate School of Science and Engineering, Saitama University) | ||||||
著者 所属(別言語) | ||||||
Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University | ||||||
著者 所属(別言語) | ||||||
Department of Biotechnology, Graduate School of Engineering, Osaka University | ||||||
著者 所属(別言語) | ||||||
Department of Functional Materials Science, Saitama University | ||||||
著者 所属(別言語) | ||||||
Department of Biotechnology, Graduate School of Engineering, Osaka University | ||||||
著者 所属(別言語) | ||||||
Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University | ||||||
書誌情報 |
JOURNAL OF THEORETICAL BIOLOGY 巻 246, 号 3, p. 538-550, 発行日 2007 |
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年月次 | ||||||
2007-6 | ||||||
出版者名 | ||||||
出版者 | ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 00225193 | |||||
DOI | ||||||
関連タイプ | isVersionOf | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1016/j.jtbi.2006.12.037 | |||||
関連サイト | ||||||
内容記述タイプ | Other | |||||
内容記述 | http://www.sciencedirect.com/science/journal/00225193 | http://www.sciencedirect.com/science/journal/00225193 | |||||
抄録 | ||||||
内容記述タイプ | Abstract | |||||
内容記述 | We have developed a methodology for extracting characteristic properties of a fitness landscape of interest by analyzing fitness data on an in vitro molecular evolution. The in vitro evolution is required to be conducted as the following '' adaptive walk '': a single parent sequence generates N mutant sequences as its offsprings, and the fittest individual among the N offsprings will become a new parent in the next generation. N is the library size of mutants to be screened in a single generation. Our theory of the adaptive walk on the '' NK landscape '' suggests the following: the adaptive walker starting from a random sequence climbs the landscape easily in an early stage, and then reaches a stationary phase in which the mutation-selection-random drift balance sets in. The stationary fitness value is nearly proportional to root In N. Our analysis is performed from the following points: (1) stationary fitness values, (2) time series of fitness in the transitional state, (3) mutant's fitness distribution, and (4) the strength of selection pressure. Applying our methodology, we analyzed experimental data on the in vitro evolution of a random polypeptide (139 amino acids) toward acquiring infectivity (= ability to infect) of fd phage. As a result, we estimated that k is about 27 in this system, indicating that an arbitrary residue in a sequence is affected from other 23% residues. In this article, we demonstrated that the experimental data is consistent with our theoretical equations quantitatively, and that our methodology for extracting characteristic properties of a fitness landscape may be effective. (C) 2007 Elsevier Ltd. All rights reserved. | |||||
版 | ||||||
[著者版] | ||||||
著者版フラグ | ||||||
出版タイプ | AM | |||||
出版タイプResource | http://purl.org/coar/version/c_ab4af688f83e57aa | |||||
資源タイプ | ||||||
内容記述タイプ | Other | |||||
内容記述 | text | |||||
フォーマット | ||||||
内容記述タイプ | Other | |||||
内容記述 | application/pdf | |||||
作成日 | ||||||
日付 | 2008-10-20 | |||||
日付タイプ | Created | |||||
アイテムID | ||||||
A1002789 |