Predicting three-dimensional conformations of peptides constructed of only glycine, alanine, aspartic acid, and valine

Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life
Akifumi Oda, Shuichi Fukuyoshi

Abstract

The GADV hypothesis is a form of the protein world hypothesis, which suggests that life originated from proteins (Lacey et al. 1999; Ikehara 2002; Andras 2006). In the GADV hypothesis, life is thought to have originated from primitive proteins constructed of only glycine, alanine, aspartic acid, and valine ([GADV]-proteins). In this study, the three-dimensional (3D) conformations of randomly generated short [GADV]-peptides were computationally investigated using replica-exchange molecular dynamics (REMD) simulations (Sugita and Okamoto 1999). Because the peptides used in this study consisted of only 20 residues each, they could not form certain 3D structures. However, the conformational tendencies of the peptides were elucidated by analyzing the conformational ensembles generated by REMD simulations. The results indicate that secondary structures can be formed in several randomly generated [GADV]-peptides. A long helical structure was found in one of the hydrophobic peptides, supporting the conjecture of the GADV hypothesis that many peptides aggregated to form peptide multimers with enzymatic activity in the primordial soup. In addition, these results indicate that REMD simulations can be used for the structural investigation ...Continue Reading

References

Jan 1, 1977·Annual Review of Biophysics and Bioengineering·F M Richards
Mar 1, 1985·Equine Veterinary Journal·S Dyson
Aug 14, 1971·Journal of Molecular Biology·E ZuckerkandlH Vogel
Jan 1, 1983·Journal of Molecular Evolution·G Schlesinger, S L Miller
Dec 22, 1995·Journal of Medicinal Chemistry· Ajay, M A Murcko
May 2, 1996·Nature·J P FerrisL E Orgel
Jan 1, 1996·Rapid Communications in Mass Spectrometry : RCM·K VékeyV H Wysocki
Jun 6, 2000·The Journal of Biological Chemistry·L JinF Zhang
Sep 7, 2001·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·K KobayashiT Oshima
Sep 7, 2001·Advances in Space Research : the Official Journal of the Committee on Space Research (COSPAR)·K KobayashiT Saito
Mar 19, 2002·Emerging Infectious Diseases·Susan S HuangArthur L Reingold
Apr 17, 2002·Journal of Molecular Evolution·Kenji IkeharaAkiko Hirose
Jan 22, 2005·Nature·I King JordanShamil Sunyaev
Apr 14, 2005·Chemical Record : an Official Publication of the Chemical Society of Japan ... [et Al.]·Kenji Ikehara
Oct 19, 2005·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·Takae ObaKenji Ikehara
May 15, 1957·Proceedings of the National Academy of Sciences of the United States of America·F H CrickL E Orgel
Aug 2, 2008·Biological & Pharmaceutical Bulletin·Noriyuki YamaotsuShuichi Hirono
Apr 29, 2009·Journal of Computational Chemistry·Akifumi OdaShuichi Hirono
May 27, 2009·International Journal of Molecular Sciences·Kenji Ikehara
Sep 19, 2009·Journal of Theoretical Biology·Peter van der GulikMarianne Rooman
Jan 1, 2007·Journal of Chemical Theory and Computation·John MonganAlexey Onufriev
Jan 25, 2011·Organic & Biomolecular Chemistry·Harri Lönnberg
Aug 30, 2011·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Akifumi OdaOhgi Takahashi
Dec 25, 2012·Journal of Chemical Theory and Computation·T SteinbrecherD A Case
Apr 9, 2013·Journal of Chemical Theory and Computation·Hai NguyenCarlos Simmerling

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Citations

Apr 5, 2016·Current Opinion in Chemical Biology·Woodward W FischerJoan Selverstone Valentine
Oct 13, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Koichi KatoAkifumi Oda
Aug 30, 2017·Proceedings of the National Academy of Sciences of the United States of America·Jay G ForsytheFacundo M Fernández
May 2, 2018·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·Marko Vitas, Andrej Dobovišek
Jul 1, 2020·Biochimica Et Biophysica Acta. Proteins and Proteomics·Tomoki NakayoshiAkifumi Oda

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