Journal of Computer Aided Chemistry
Online ISSN : 1345-8647
ISSN-L : 1345-8647
Structural Prediction of [GADV]-Proteins Using Threading and Ab initio Modeling for Investigations of the Origin of Life
Akifumi OdaShuichi FukuyoshiRyoichi Nakagaki
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2013 Volume 14 Pages 23-35

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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.

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© 2013 The Chemical Society of Japan
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