Todorova Nevena, Legge F Sue, Treutlein Herbert, Yarovsky Irene
Applied Physics, School of Applied Sciences, RMIT University, Melbourne, Victoria, Australia.
J Phys Chem B. 2008 Sep 4;112(35):11137-46. doi: 10.1021/jp076825d. Epub 2008 Aug 12.
The use of atomistic simulation methodologies based on empirical forcefields has enhanced our understanding of many physical processes governing protein structure and dynamics. However, the forcefields used in classical modeling studies are often designed for a particular class of proteins and rely on continuous improvement and validation by comparison of simulations with experimental data. We present a comprehensive comparison of five popular forcefields for simulating insulin. The effect of each forcefield on the conformational evolution and structural properties of the peptide is analyzed in detail and compared with available experimental results. In this study we observed that different forcefields favor different structural trends. However, the all-atom forcefield CHARMM27 and the united-atom forcefield GROMOS 43A1 delivered the best representation of the experimentally observed dynamic behavior of chain B of insulin.
基于经验力场的原子模拟方法的使用，增强了我们对许多支配蛋白质结构和动力学的物理过程的理解。然而，经典建模研究中使用的力场通常是为特定类别的蛋白质设计的，并且依赖于通过将模拟与实验数据进行比较来不断改进和验证。我们对用于模拟胰岛素的五种流行力场进行了全面比较。详细分析了每个力场对肽的构象演变和结构性质的影响，并与现有实验结果进行了比较。在本研究中，我们观察到不同的力场有利于不同的结构趋势。然而，全原子力场CHARMM27和联合原子力场GROMOS 43A1对胰岛素B链实验观察到的动态行为给出了最佳表征。
