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首页> 外文期刊>The Journal of Chemical Physics >Electrostatics of proteins in dielectric solvent continua.II.First applications in molecular dynamics simulations
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Electrostatics of proteins in dielectric solvent continua.II.First applications in molecular dynamics simulations

机译：介电溶剂中蛋白质的静电学连续性II。分子动力学模拟的首次应用

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In the preceding paper by Stork and Tavan,[J.Chem.Phys.126,165105 (2007)],the authors have reformulated an electrostatic theory which treats proteins surrounded by dielectric solvent continua and approximately solves the associated Poisson equation [B.Egwolf and P.Tavan,J.Chem.Phys.118,2039 (2003)].The resulting solution comprises analytical expressions for the electrostatic reaction field (RF) and potential,which are generated within the protein by the polarization of the surrounding continuum.Here the field and potential are represented in terms of Gaussian RF dipole densities localized at the protein atoms.Quite like in a polarizable force field,also the RF dipole at a given protein atom is induced by the partial charges and RF dipoles at the other atoms.Based on the reformulated theory,the authors have suggested expressions for the RF forces,which obey Newton's third law.Previous continuum approaches,which were also built on solutions of the Poisson equation,used to violate the reactio principle required by this law,and thus were inapplicable to molecular dynamics (MD) simulations.In this paper,the authors suggest a set of techniques by which one can surmount the few remaining hurdles still hampering the application of the theory to MD simulations of soluble proteins and peptides.These techniques comprise the treatment of the RF dipoles within an extended Lagrangian approach and the optimization of the atomic RF polarizabilities.Using the well-studied conformational dynamics of alanine dipeptide as the simplest example,the authors demonstrate the remarkable accuracy and efficiency of the resulting RF-MD approach.
机译：在Stork和Tavan的前一篇论文中，[J.Chem.Phys.126,165105（2007）]，作者重新制定了静电学原理，该理论处理被介电溶剂连续体包围的蛋白质，并近似求解相关的泊松方程[B.Egwolf和P.Tavan，J.Chem.Phys.118，2039（2003）]。所得溶液包含静电反应场（RF）和电势的解析表达式，其通过周围连续体的极化在蛋白质内产生。这里的场和电势用位于蛋白质原子上的高斯RF偶极子密度来表示。就像在极化力场中一样，给定蛋白质原子上的RF偶极子也是由其他原子上的部分电荷和RF偶极子诱发的基于重新形成的理论，作者提出了服从牛顿第三定律的射频力的表达式。以前的连续体方法也基于泊松方程的解，用于违反面积ctio原理是该定律所必需的，因此不适用于分子动力学（MD）模拟。本文中，作者提出了一组技术，通过这些技术，人们可以克服仍然存在的少量障碍，仍然阻碍了该理论在MD模拟中的应用。这些技术包括在扩展的拉格朗日方法中处理RF偶极子和优化原子RF极化率。以研究充分的丙氨酸二肽构象动力学为最简单的例子，作者证明了其卓越的准确性和产生的RF-MD方法的效率。

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