Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins.
Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins.
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DOI：
10.1021/acs.jpclett.5b00654
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发表时间：
2015-06-04
期刊：
影响因子：
--
通讯作者：
Elcock AH
中科院分区：
文献类型：
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作者：
Li S;Elcock AH
最近关于成百上千个双残基多肽的3JHNHα标量偶联常数的报道为测试蛋白质的模拟力场提供了一个重要的机会。在这里，我们比较了琥珀ff99Sb力场的三个导数复制这些数据的能力。我们报道了256个两个残基的多肽的分子动力学(MD)模拟，并表明最近发展的残基特定力场(RSFF2)与实验3JHNHα耦合常数的一致性有了显著的改善。我们进一步表明，RSFF2在重现五种模型蛋白质的3JHNHα偶联常数方面似乎也有轻微的改善。也许令人惊讶的是，对两个残基多肽的3JHNHα偶联常数的邻近残基效应(NRES)的分析表明，力场复制实验NRES的能力几乎没有差异。我们推测，这可能表明力场对相邻侧链之间或与末端封顶基团之间的非成键相互作用的描述存在局限性。
A recent report of 3JHNHα scalar coupling constants for hundreds of two-residue peptides has provided an important opportunity to test simulation force fields for proteins. Here we compare the abilities of three derivatives of the Amber ff99SB force field to reproduce these data. We report molecular dynamics (MD) simulations of 256 two-residue peptides and show that the recently developed residue-specific force field (RSFF2) produces a dramatic improvement in the agreement with experimental 3JHNHα coupling constants. We further show that RSFF2 also appears to produce a modest improvement in reproducing the 3JHNHα coupling constants of five model proteins. Perhaps surprisingly, an analysis of neighboring residue effects (NREs) on the 3JHNHα coupling constants of the two-residue peptides indicates little difference between the force fields’ abilities to reproduce experimental NREs. We speculate that this might indicate limitations in the force fields’ descriptions of nonbonded interactions between adjacent sidechains or with terminal capping groups.