Frederix Pim W J M, Ulijn Rein V, Hunt Neil T, Tuttle Tell
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom ; SUPA, Department of Physics, University of Strathclyde , 107 Rottenrow East, Glasgow, G4 0NG, United Kingdom.
J Phys Chem Lett. 2011 Oct 6;2(19):2380-2384. doi: 10.1021/jz2010573. Epub 2011 Sep 2.
Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system.
已知有几种短肽序列可自组装成具有有趣特性的超分子纳米结构。在本研究中，采用粗粒度分子动力学方法快速筛选所有400种二肽组合，并预测它们作为自组装潜在前体的聚集能力。所提出的模拟方案和评分方法能够快速确定给定的肽序列在水性条件下是否可能聚集（这是自组装能力的一个指标）。在初始筛选中显示出强烈聚集倾向的系统被选来进行更长时间的模拟，结果与文献中报道的二肽已知自组装或聚集情况吻合良好。我们对二苯基丙氨酸系统进行的扩展模拟表明，粗粒度模型能够再现纳米级系统的显著特征，并为该系统的自组装过程提供深入见解。
