Department of Physics, University of California, Davis, California 95616, USA.
J Chem Phys. 2011 Jan 21;134(3):035103. doi: 10.1063/1.3532931.
We have combined graphics processing unit-accelerated all-atom molecular dynamics with parallel tempering to explore the folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this methodology to the synthetic β-hairpin, trpzip2, and one of its sequence variants, W2W9. Each simulation consisted of over 8 μs of aggregated virtual time. Several measures of folding behavior showed good convergence, allowing comparison with experimental equilibrium properties. Our simulations suggest that the intramolecular interactions of tryptophan side chains are responsible for much of the stability of the native fold. We conclude that the ff99 force field combined with ff96 φ and ψ dihedral energies and an implicit solvent can reproduce plausible folding behavior in both trpzip2 and W2W9.
我们结合图形处理单元加速的全原子分子动力学和并行温度处理，探索了在微秒时间尺度下隐溶剂中小肽的折叠性质。我们将这种方法应用于合成的β-发夹结构 trpzip2 及其序列变体 W2W9 上。每个模拟都包含超过 8 μs 的聚合虚拟时间。几种折叠行为的度量指标显示出良好的收敛性，允许与实验平衡性质进行比较。我们的模拟表明，色氨酸侧链的分子内相互作用是天然折叠稳定性的主要原因。我们的结论是，ff99 力场结合 ff96 φ 和 ψ 二面角能和隐溶剂可以在 trpzip2 和 W2W9 中再现合理的折叠行为。
