School of Chemistry and Molecular Engineering and School of Physics and Materials Science, East China Normal University, Shanghai 200062, China.
J Chem Phys. 2017 Feb 14;146(6):065101. doi: 10.1063/1.4975303.
A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.
最近开发的双珠多极力场（TMFF）与可极化 CG 水分子模型（如 Martini 可极化水分子模型和改良大多极水分子模型）结合，用于蛋白质的粗粒化（CG）分子动力学（MD）模拟。与使用 Martini 不可极化水分子模型的模拟结果相比，本模拟中蛋白质结构和动力学的模拟结果得到了显著改善，表现在结构的均方根偏差（RMSD）和残基均方根波动（RMSF）与天然结构的偏差都更小。我们的结果表明，使用 CG 水分子模型进行 TMFF 模拟可以使蛋白质的二级结构更加稳定，而无需添加额外的相互作用势来约束二级结构。我们的结果还表明，通过将 MD 时间步长从 2 fs 增加到 6 fs，可以使 RMSD 和 RMSF 的结果仍然与全原子模拟的结果非常吻合。本研究清楚地表明，TMFF 与可极化 CG 水分子模型的结合，显著提高了 CG 模拟蛋白质的准确性和效率。
