ArticleOrigins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life2015
Predicting three-dimensional conformations of peptides constructed of only glycine, alanine, aspartic acid, and valine.
Article in Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Effect of the Addition of the Fifth Amino Acid to [GADV]-Protein on the Three-Dimensional Structure.Life (Basel, Switzerland) · 2023Article
- A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism.Frontiers in microbiology · 2023Article
- Article
- Three dimensional structures of putative, primitive proteins to investigate the origin of homochirality.Scientific reports · 2019Article
- In the Beginning was a Mutualism - On the Origin of Translation.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2018Article
- Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.Molecules (Basel, Switzerland) · 2017Article
- Surveying the sequence diversity of model prebiotic peptides by mass spectrometry.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
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2 authors.
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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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