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无规卷曲蛋白的分子动力学模拟:关于 TIP4P-D 水模型的准确性和蛋白质无序模型的代表性。

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: On the Accuracy of the TIP4P-D Water Model and the Representativeness of Protein Disorder Models.

机构信息

Division of Theoretical Chemistry, Lund University , Post Office Box 124, S-221 00 Lund, Sweden.

出版信息

J Chem Theory Comput. 2016 Jul 12;12(7):3407-15. doi: 10.1021/acs.jctc.6b00429. Epub 2016 Jun 10.

Abstract

Here, we first present a follow-up to a previous work by our group on the problematic of molecular dynamics simulations of intrinsically disordered proteins (IDPs) [ Henriques et al. J. Chem. Theory Comput. 2015 , 11 , 3420 - 3431 ], using the recently developed TIP4P-D water model. When used in conjunction with the standard AMBER ff99SB-ILDN force field and applied to the simulation of Histatin 5, our IDP model, we obtain results which are in excellent agreement with the best performing IDP-suitable force field from the earlier study and with experiment. We then assess the representativeness of the IDP models used in these and similar studies, finding that most are too short in comparison to the average IDP and contain a bias toward hydrophilic amino acid residues. Moreover, several key order- and disorder-promoting residues are also found to be misrepresented. It seems appropriate for future studies to address these issues.

摘要

在这里,我们首先介绍了我们小组之前关于使用最近开发的 TIP4P-D 水模型对无序蛋白质(IDP)分子动力学模拟的问题的后续研究[Henriques 等人,J. Chem. Theory Comput. 2015, 11, 3420-3431]。当与标准 AMBER ff99SB-ILDN 力场结合并应用于 Histatin 5 的模拟时,我们的 IDP 模型得到的结果与早期研究中表现最佳的 IDP 适用力场以及实验结果非常吻合。然后,我们评估了这些和类似研究中使用的 IDP 模型的代表性,发现与平均 IDP 相比,大多数模型都太短,并且偏向亲水氨基酸残基。此外,还发现几个关键的促进有序和无序的残基也被错误表示。未来的研究似乎需要解决这些问题。

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