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首页> 外文期刊>Journal of chemical theory and computation: JCTC >Universal Implementation of a Residue-Specific Force Field Based on CMAP Potentials and Free Energy Decomposition
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Universal Implementation of a Residue-Specific Force Field Based on CMAP Potentials and Free Energy Decomposition

机译：基于CMAP电位和自由能分解的残留特定力场的通用实施

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摘要

The coupling between neighboring backbone phi and Psi dihedral angles (torsions) has been well appreciated in protein force field development, as in correction map (CMAP) potentials. However, although preferences of backbone torsions are significantly affected by side-chain conformation, there has been no easy way to optimize this coupling. Herein, we prove that the three-dimensional (3D) free energy hypersurface of joint (phi, Psi, chi(1)) torsions can be decomposed into three separated 2D surfaces. Thus, each of the 2D torsional surfaces can be efficiently and automatically optimized using a CMAP potential. This strategy is then used to reparameterize an AMBER force field such that the resulting chi(1)-dependent backbone conformational preference can agree excellently with the reference protein coil library statistics. In various validation simulations (including the folding of seven peptides/proteins, backbone dynamics of three folded proteins, and two intrinsically disordered peptides), the new RSFF2C (residue-specific force field with CMAP potentials) force field gives similar or better performance compared with RSFF2. This strategy can be used to implement our RSFF force fields into a variety of molecular dynamics packages easily.
机译：与蛋白质力场显影中的相邻骨干PHI和PSI二面角（扭转）之间的耦合很好地理解，如校正图（CMAP）电位。然而，尽管骨干扭转的偏好受到侧链构象的显着影响，但是没有简单的方法来优化该耦合。在此，我们证明了关节（PHI，PSI，CHI（1））扭转的三维（3D）自由能度曲面可以分解成三个分离的2D表面。因此，可以使用CMAP电位有效和自动优化2D扭转表面。然后使用该策略进行琥珀色力域，使得所得的Chi（1）依赖性骨干构象偏好可以与参考蛋白线圈库统计相同。在各种验证模拟中（包括七种肽/蛋白质的折叠，三折叠蛋白的骨干动力学和两个本质上无序的肽），与...相比，新的RSFF2C（带有CMAP电位的残留型力场）赋予相似或更好的性能RSFF2。该策略可用于容易地将我们的RSFF力字段实施到各种分子动力学包中。

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    Kang Wei; Jiang Fan; Wu Yun-Dong;

  • 作者单位

    Peking Univ Lab Computat Chem &

    Drug Design State Key Lab Chem Oncogen Shenzhen Grad Sch Shenzhen 518055 Peoples R China;

    Peking Univ Lab Computat Chem &

    Drug Design State Key Lab Chem Oncogen Shenzhen Grad Sch Shenzhen 518055 Peoples R China;

    Peking Univ Lab Computat Chem &

    Drug Design State Key Lab Chem Oncogen Shenzhen Grad Sch Shenzhen 518055 Peoples R China;

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  • 正文语种 eng
  • 中图分类 化学键的量子力学理论;化学;
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