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Du Xinzheng, Xinfan Hua, Zhiyong Zhang. Choice of Force Fields and Water Models for Sampling Solution Conformations of Bacteriophage T4 Lysozyme[J]. Chinese Journal of Chemical Physics .
Citation: Du Xinzheng, Xinfan Hua, Zhiyong Zhang. Choice of Force Fields and Water Models for Sampling Solution Conformations of Bacteriophage T4 Lysozyme[J]. Chinese Journal of Chemical Physics .

Choice of Force Fields and Water Models for Sampling Solution Conformations of Bacteriophage T4 Lysozyme

  • Received Date: 2020-10-16
  • Accepted Date: 2020-11-17
  • Rev Recd Date: 2020-11-08
  • Available Online: 2020-12-01
  • A protein may exist as an ensemble of different conformations in solution, which cannot be represented by a single static structure. Molecular dynamics (MD) simulation has become a useful tool for sampling protein conformations in solution, but force fields and water models are important issues. This work presents a case study of the bacteriophage T4 lysozyme (T4L). We have found that MD simulations using a classic AMBER99SB force field and TIP4P water model cannot well describe hinge-bending domain motion of the wild-type T4L at the timescale of one micorsecond. Other combinations, such as a residue-specific force field called RSFF2+ and a dispersion-corrected water model TIP4P-D, are able to sample reasonable solution conformations of T4L, which are in good agreement with experimental data. This primary study may provide candidates of force fields and water models for further investigating conformational transition of T4L. 蛋白质在溶液中可能以不同构象的集合形式存在,不能用单一的静态结构来表示。分子动力学模拟已成为对蛋白质溶液构象进行采样的有用工具,但力场和水模型的准确性是一个关键问题。这项工作介绍了对噬菌体T4溶菌酶(T4L)的个例研究。我们发现,使用经典的力场和水模型,如AMBER99SB/TIP4P,1微秒时间尺度的分子动力学模拟不能很好地描述野生型T4L的结构域开合运动。但是其它力场和水模型组合,如残基特异性力场RSFF2+和离散校正的水模型TIP4P-D,能够对T4L溶液构象进行较为合理的采样,且与实验数据有良好的一致性。我们的初步研究可为进一步通过长时间分子动力学模拟及自由能计算研究T4L的构象转变机制提供力场和水模型的选择。
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    沈阳化工大学材料科学与工程学院 沈阳 110142

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Choice of Force Fields and Water Models for Sampling Solution Conformations of Bacteriophage T4 Lysozyme

Abstract: A protein may exist as an ensemble of different conformations in solution, which cannot be represented by a single static structure. Molecular dynamics (MD) simulation has become a useful tool for sampling protein conformations in solution, but force fields and water models are important issues. This work presents a case study of the bacteriophage T4 lysozyme (T4L). We have found that MD simulations using a classic AMBER99SB force field and TIP4P water model cannot well describe hinge-bending domain motion of the wild-type T4L at the timescale of one micorsecond. Other combinations, such as a residue-specific force field called RSFF2+ and a dispersion-corrected water model TIP4P-D, are able to sample reasonable solution conformations of T4L, which are in good agreement with experimental data. This primary study may provide candidates of force fields and water models for further investigating conformational transition of T4L. 蛋白质在溶液中可能以不同构象的集合形式存在,不能用单一的静态结构来表示。分子动力学模拟已成为对蛋白质溶液构象进行采样的有用工具,但力场和水模型的准确性是一个关键问题。这项工作介绍了对噬菌体T4溶菌酶(T4L)的个例研究。我们发现,使用经典的力场和水模型,如AMBER99SB/TIP4P,1微秒时间尺度的分子动力学模拟不能很好地描述野生型T4L的结构域开合运动。但是其它力场和水模型组合,如残基特异性力场RSFF2+和离散校正的水模型TIP4P-D,能够对T4L溶液构象进行较为合理的采样,且与实验数据有良好的一致性。我们的初步研究可为进一步通过长时间分子动力学模拟及自由能计算研究T4L的构象转变机制提供力场和水模型的选择。

Du Xinzheng, Xinfan Hua, Zhiyong Zhang. Choice of Force Fields and Water Models for Sampling Solution Conformations of Bacteriophage T4 Lysozyme[J]. Chinese Journal of Chemical Physics .
Citation: Du Xinzheng, Xinfan Hua, Zhiyong Zhang. Choice of Force Fields and Water Models for Sampling Solution Conformations of Bacteriophage T4 Lysozyme[J]. Chinese Journal of Chemical Physics .

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