Structural Prediction of [GADV]-Proteins Using Threading and Ab initio Modeling for Investigations of the Origin of Life

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  • Oda Akifumi
    Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University Institute for Protein Research, Osaka University
  • Fukuyoshi Shuichi
    Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University
  • Nakagaki Ryoichi
    Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University

Bibliographic Information

Other Title
  • 生命の起源におけるタンパク質ワールド仮説に登場する [GADV]-タンパク質のスレッディングおよびab initioモデリングによる立体構造推定

Abstract

In the GADV hypothesis, it is assumed that the primordial life originate from the proteins constructed from glycine, alanine, aspartic acid, and valine ([GADV]-proteins). Three-dimensional structures of [GADV]-proteins have not been observed experimentally, in fact, even computational predictions have not been carried out. In this study, computational modeling methods for three-dimensional structures of proteins were adopted for [GADV]-proteins, and the availabilities of the methods were compared. The prediction methods are frequently based on the structure conservation throughout evolution, and the model constructions depend on the knowledge of protein structures in existence. The predicted structures of [GADV]-proteins were mainly composed of β structures because of high β strand capability for valine residue. Because many of predicted structures were immediately broken by molecular dynamics (MD) simulations, instabilities of these structures were indicated. On the other hand, not only β structures but also helices were observed for the resulted structures by MD simulations. The results suggest that MD simulations using only Newton’s equation were useful for the structural predictions of [GADV]-proteins.

Journal

  • Journal of Computer Aided Chemistry

    Journal of Computer Aided Chemistry 14 (0), 23-35, 2013

    Division of Chemical Information and Computer Sciences The Chemical Society of Japan

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