Key Lab of Biophysics in universities of Shandong (Dezhou University) Dezhou, China, 253023.
J Biomol Struct Dyn. 2010 Apr;27(5):651-61. doi: 10.1080/07391102.2010.10508579.
The dynamics and thermodynamics character of H1 peptide in aqueous solution has been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations using two different force fields (OPLS-AA and GROMOS 43A1). The two independent T-REMD simulations were completed starting from initial conformations alpha-helix and beta-sheet, respectively. Each replica was run for 300 ns. The performance of each force field was assessed from the parameters such as the distributions of backbone dihedral angles, the number of native hydrogen bond, root mean square deviations (RMSD) of C(alpha) atoms and all heavy atoms, formation of beta-turn, the stability of folded beta-hairpin structure and the favorite conformations of different force fields. The simulation using GROMOS 43A1 force field starting from alpha-helix structure sampled the conformation cluster which C(alpha) RMSD was 0.05 nm from beta-sheet structure and the cluster contains 39% of all conformations. The simulation using OPLS-AA force field produced more sampling in P(II)region than in GROMOS 43A1 force field. The both force field simulations produced some sampling in the alpha region, but the probabilities of the conformations including any helical content were only 1-2%. Under the both force fields, the beta-turn structures exhibited higher stability than alpha-helix structures and the folded beta-hairpin structures. In the GROMOS 43A1 force field, the free energy change from the unfolded state to the hairpin state was in good agreement with the results of several experiments about some beta-peptides (not the H1 peptide) and the other molecular dynamics simulations of H1 peptide. However, the folded beta-hairpin structure was more destabilized in the OPLS-AA force field than in the GROMOS 43A1 force field and experiments.
已经通过使用两种不同力场（OPLS-AA 和 GROMOS 43A1）的温度复制交换分子动力学（T-REMD）模拟研究了 H1 肽在水溶液中的动力学和热力学特性。这两个独立的 T-REMD 模拟分别从起始构象α-螺旋和β-折叠开始进行。每个副本运行 300ns。通过评估力场的参数（如主链二面角分布、天然氢键数量、Cα原子和所有重原子的均方根偏差（RMSD）、β-转角的形成、折叠β-发夹结构的稳定性和不同力场的首选构象）来评估每个力场的性能。使用 GROMOS 43A1 力场从α-螺旋结构开始的模拟采样了构象簇，该构象簇的 Cα RMSD 与β-折叠结构相差 0.05nm，该簇包含所有构象的 39%。使用 OPLS-AA 力场的模拟在 P(II) 区域产生的采样比 GROMOS 43A1 力场多。两种力场模拟都在α区域产生了一些采样，但包含任何螺旋内容的构象的概率仅为 1-2%。在两种力场下，β-转角结构比α-螺旋结构和折叠β-发夹结构更稳定。在 GROMOS 43A1 力场中，从展开状态到发夹状态的自由能变化与一些β-肽（不是 H1 肽）的几个实验结果和 H1 肽的其他分子动力学模拟结果一致。然而，在 OPLS-AA 力场中，折叠的β-发夹结构比 GROMOS 43A1 力场和实验更不稳定。
