Manchester Institute of Biotechnology (MIB), University of Manchester, 131 Princess Street, Manchester, M1 7DN, Great Britain.
School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain.
J Mol Model. 2019 Jul 10;25(8):216. doi: 10.1007/s00894-019-4095-3.
We present a rare comparison of structures of the same protein but generated by different potentials. We used four popular water potentials (SPC, TIP3P, TIP4P, TIP5P) in conjunction with the equally popular ff99SB. However, the ff12SB protein potential was used with TI3P only. Simulations (60 ns) were run on the catabolite activator protein (CAP), which is a textbook case of allosteric interaction. Overall, all potentials generated largely similar structures but failed to reproduce a crucial structural feature determined by NMR experiment. This example shows the need to develop next-generation potentials. Graphical abstract Catabolite activator protein.
我们呈现了同一蛋白质的不同势能产生的结构的罕见比较。我们使用了四种流行的水势能（SPC、TIP3P、TIP4P、TIP5P）与同样流行的 ff99SB 结合。然而，ff12SB 蛋白质势能仅与 TI3P 一起使用。模拟（60ns）在分解代谢物激活蛋白（CAP）上进行，CAP 是别构相互作用的典型案例。总体而言，所有势能产生的结构大致相似，但未能重现 NMR 实验确定的关键结构特征。这个例子表明需要开发下一代势能。
