The successful simulation of proteins by molecular dynamics (MD) critically depends on the accuracy of the applied force field. Here, we modify the AMBER-family ff99SBnmr2 force field through improvements to the side-chain χ1 dihedral angle potentials in a residue-specific manner using conformational dihedral angle distributions from an experimental coil library as targets. Based on significant deviations observed for the parent force field with respect to the coil library, the χ1 dihedral angle potentials of seven amino acids were modified, namely, Val, Ser, His, Asn, Trp, Tyr, and Phe. The new force field, named ff99SBnmr2Chi1, was benchmarked against NMR-derived χ1 rotamer populations of denatured proteins, overall resulting in much better agreement and without any noticeable adverse consequences on the quality of the simulation of folded proteins. The new force field should allow more realistic modeling of protein side-chain properties by MD of both folded and unfolded protein systems, such as for the better in-silico characterization of protein-protein and protein-ligand interactions.

中文翻译：

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Coil-Library 衍生的氨基酸特异性侧链 χ1 琥珀型蛋白质力场的二面角电位。


分子动力学 （MD） 对蛋白质的成功模拟在很大程度上取决于施加力场的准确性。在这里，我们以来自实验线圈库的构象二面角分布为目标，以残基特异性方式改进侧链 χ1 二面角电位，从而修改 AMBER 家族 ff99SBnmr2 力场。基于观察到的母力场相对于线圈库的显着偏差，修改了 7 个氨基酸的 χ1 二面角电位，即 Val、Ser、His、Asn、Trp、Tyr 和 Phe。名为 ff99SBnmr2Chi1 的新力场与 NMR 衍生的变性蛋白质的 χ1 rotamer 群体进行了基准测试，总体上产生了更好的一致性，并且对折叠蛋白质的模拟质量没有任何明显的不利影响。新的力场应该允许通过折叠和未折叠蛋白质系统的 MD 对蛋白质侧链特性进行更真实的建模，例如更好地对蛋白质-蛋白质和蛋白质-配体相互作用进行计算机表征。