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A force field for virtual atom molecular mechanics of proteins

机译：蛋白质虚拟原子分子力学的力场

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摘要

Activities of many biological macromolecules involve large confor-mational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of Cα atoms in protein molecules. This force field is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting force field is applied to energy minimization and normal mode analysis of several proteins. We find robust convergence in minimizations to low energies and energy gradients with low degrees of structural distortion, and atomic fluctuations calculated from the normal mode analyses correlate well with the experimental B-factors obtained from high-resolution crystal structures. These findings suggest that the virtual atom force field is a suitable tool for various molecular mechanics applications on large macromolecular systems undergoing large conformational changes.
机译：许多生物大分子的活动涉及大的构象转变，晶体学可以为这些构象转变指定其他最终状态的原子细节，但是转变的过程通常超出了基于全原子势函数的计算范围。我们基于蛋白质分子中Cα原子的虚拟相互作用，开发了用于分子力学计算的粗粒度力场。该力场基于从晶体学数据中提取的能量项的统计分布进行参数化，并制定为捕获依赖于二级结构和残基特定接触信息的特征。由此产生的力场被应用于能量最小化和几种蛋白质的正常模式分析。我们发现在最小化到低能量和具有低结构变形度的能量梯度方面具有强大的收敛性，并且从正常模式分析计算得出的原子涨落与从高分辨率晶体结构获得的实验性B因子密切相关。这些发现表明虚拟原子力场是在经历大的构象变化的大分子系统上用于各种分子力学应用的合适工具。

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