The replica-exchange Monte Carlo method based on the single amino acid potential (SAAP) force field, i.e., REMC/SAAP3D, was recently developed by our group for the molecular simulation of short peptides. In this study, the method has been improved by applying a distance-dependent dielectric (DDD) constant and extended to the peptides containing d-amino acid (AA) residues. For chignolin (10 AAs), a sigmoidal DDD model reasonably allocated the native-like β-hairpin structure with all-atom root mean square deviation (RMSD) = 2.0 Å as a global energy minimum. The optimal DDD condition was subsequently applied for Trp-cage (20 AAs) and its G10q mutant. The native-like α-rich folded structures with main-chain RMSD = 3.7 and 3.8 Å were obtained as global energy minima for Trp-cage and G10q, respectively. The results suggested that the REMC/SAAP3D method with the sigmoidal DDD model is useful for structural prediction for the short peptides comprised of up to 20 AAs. In addition, the relative contributions of SAAP to the total energy (%SAAP) were evaluated by energetic component analysis. The ratios of %SAAP were about 40 and 20% for chignolin and Trp-cage (or G10q), respectively. It was proposed that SAAP is more important for the secondary structure formation than for the assembly to a higher-order folded structure, in which the attractive van der Waals interaction may play a more important role.

我们小组最近基于单氨基酸势（SAAP）力场即REMC / SAAP3D进行了副本交换蒙特卡罗方法，用于短肽的分子模拟。在这项研究中，通过应用距离相关介电常数（DDD）常数对方法进行了改进，并将其扩展至包含d的肽段。-氨基酸（AA）残基。对于chignolin（10 AAs），S型DDD模型合理地分配了类似天然的β-发夹结构，其全原子均方根偏差（RMSD）= 2.0Å作为全局能量最小值。最佳DDD条件随后应用于Trp笼（20 AAs）及其G10q突变体。对于Trp笼和G10q，分别获得了主链RMSD = 3.7和3.8Å的类似天然的富含α的折叠结构。结果表明，具有S型DDD模型的REMC / SAAP3D方法可用于预测由多达20个AA组成的短肽的结构。此外，通过能量成分分析评估了SAAP对总能量的相对贡献（％SAAP）。几丁质和Trp笼（或G10q）的％SAAP比率分别约为40％和20％。