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首页> 美国卫生研究院文献>International Journal of Molecular Sciences >Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions
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Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

机译：TMD模拟与伞形采样相结合在分子构象转变的PMF计算中的应用研究

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摘要

Free energy calculations of the potential of mean force (PMF) based on the combination of targeted molecular dynamics (TMD) simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35). The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD) variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg) presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes.
机译：基于目标分子动力学（TMD）模拟和伞形采样与物理坐标的函数相结合的平均力势（PMF）的自由能计算已用于探索构象的详细途径和相应的自由能概图丁烷分子和35个残基的villin头域（HP35）的过渡过程。基于来自相同TMD模拟的不同伞状采样，获得了用于描述在二面角旋转坐标和均方根偏差（RMSD）变量下丁烷的二面角旋转的精确PMF曲线。伞形采样的初始结构可以方便地从TMD轨迹中选择。对于此计算方法在HP35蛋白质展开过程中的应用，PMF计算以及回转半径（Rg）的坐标表示随着能量波动，自由能逐渐增加约1 kcal / mol。 HP35蛋白展开过程的构象转变特征表明，球形结构首先延伸，中间的α-螺旋首先展开，然后其他α-螺旋展开。基于TMD模拟和伞状采样相结合的PMF计算方法为研究其他变构过程的详细构象过渡途径提供了一种有价值的策略。

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