Predicting Three-Dimensional Conformations of Peptides Constructed of Only Glycine, Alanine, Aspartic Acid, and Valine

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 of short peptides.

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Acknowledgments

Parts of the computations were performed by the Research Center for Computational Science, Okazaki. This work was supported by a grant-in-aid for scientific research [26460034] from the Japan Society for the Promotion of Science.

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Correspondence to Akifumi Oda.

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Oda, A., Fukuyoshi, S. Predicting Three-Dimensional Conformations of Peptides Constructed of Only Glycine, Alanine, Aspartic Acid, and Valine. Orig Life Evol Biosph 45, 183–193 (2015). https://doi.org/10.1007/s11084-015-9418-5

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Keywords

  • GADV hypothesis
  • Protein structure prediction
  • Secondary structure formation
  • Replica-exchange molecular dynamics simulation