Oda Akifumi, Fukuyoshi Shuichi
Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan,
Orig Life Evol Biosph. 2015 Jun;45(1-2):183-93. doi: 10.1007/s11084-015-9418-5. Epub 2015 Mar 21.
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.
GADV假说 是蛋白质世界假说的一种形式，该假说认为生命起源于蛋白质（Lacey等人，1999年；Ikehara，2002年；Andras，2006年）。在GADV假说中，生命被认为起源于仅由甘氨酸、丙氨酸、天冬氨酸和缬氨酸构成的原始蛋白质（[GADV]蛋白质）。在本研究中，使用复制交换分子动力学（REMD）模拟（Sugita和Okamoto，1999年）对随机生成的短[GADV]肽的三维（3D）构象进行了计算研究。由于本研究中使用的肽每条仅由20个残基组成，它们无法形成特定的3D结构。然而，通过分析REMD模拟生成的构象集合，阐明了肽的构象趋势。结果表明，在几种随机生成的[GADV]肽中可以形成二级结构。在其中一种疏水肽中发现了长螺旋结构，这支持了GADV假说的推测，即在原始汤中许多肽聚集形成具有酶活性的肽多聚体。此外，这些结果表明REMD模拟可用于短肽的结构研究。
