肽折叠模拟中的二级结构倾向：分子力学相互作用方案的系统比较
Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes.
作者信息
Matthes Dirk, de Groot Bert L
机构信息
Department of Theoretical and Computational Biophysics, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
出版信息
Biophys J. 2009 Jul 22;97(2):599-608. doi: 10.1016/j.bpj.2009.04.061.
Abstract
We present a systematic study directed toward the secondary structure propensity and sampling behavior in peptide folding simulations with eight different molecular dynamics force-field variants in explicit solvent. We report on the combinational result of force field, water model, and electrostatic interaction schemes and compare to available experimental characterization of five studied model peptides in terms of reproduced structure and dynamics. The total simulation time exceeded 18 mus and included simulations that started from both folded and extended conformations. Despite remaining sampling issues, a number of distinct trends in the folding behavior of the peptides emerged. Pronounced differences in the propensity of finding prominent secondary structure motifs in the different applied force fields suggest that problems point in particular to the balance of the relative stabilities of helical and extended conformations.
摘要
我们展示了一项系统研究，该研究针对在明确溶剂中使用八种不同分子动力学力场变体的肽折叠模拟中的二级结构倾向和采样行为。我们报告了力场、水模型和静电相互作用方案的组合结果，并根据重现的结构和动力学，将其与五种研究的模型肽的现有实验表征进行比较。总模拟时间超过18微秒，包括从折叠和伸展构象开始的模拟。尽管存在采样问题，但肽折叠行为中出现了一些明显的趋势。在不同应用力场中发现突出二级结构基序的倾向存在显著差异，这表明问题尤其指向螺旋构象和伸展构象相对稳定性的平衡。
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