National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA.
J Chem Phys. 2013 May 7;138(17):174110. doi: 10.1063/1.4803099.
Effective coarse-grained representations of protein-protein interaction potentials are vital in the modeling of large scale systems. We develop a method to fit an arbitrary number of effective charges to approximate the electrostatic potential of a protein at a given pH in an ionic solution. We find that the effective charges can reproduce an input potential calculated from a high resolution Poisson-Boltzmann calculation. Since the effective charges used in this model are not constrained to the locations of the original charged groups, the extra degrees of freedom allows us to reproduce the field anisotropy with fewer charges. The fitting procedure uses a number of approximations in the charge magnitudes, initial conditions, and multipoles to speed convergence. The most significant gains are found by fitting the multipole moments of the effective charge potential to the moments of the original field. We show that the Yukawa potential is not only sufficient as a pairwise summation in reproducing the potential, but comes naturally from the linearized expansion of the Poisson-Boltzmann equation. We compute interaction energies and find excellent agreement to the original potential. From the effective charge model we compute the electrostatic contribution to the second virial coefficient.
有效粗粒化的蛋白质-蛋白质相互作用势在大规模系统建模中至关重要。我们开发了一种方法，可以拟合任意数量的有效电荷，以近似在离子溶液中给定 pH 值下蛋白质的静电势。我们发现，有效电荷可以重现从高分辨率泊松-玻尔兹曼计算得出的输入电势。由于该模型中使用的有效电荷不受原始带电基团位置的限制，因此额外的自由度允许我们用更少的电荷再现场各向异性。拟合过程在电荷大小、初始条件和多极矩方面使用了许多近似值来加速收敛。通过将有效电荷势的多极矩拟合到原始场的矩，可以获得最大的收益。我们表明，在重现电势时，Yukawa 势不仅可以作为对易组合进行很好的近似，而且可以从泊松-玻尔兹曼方程的线性展开自然得出。我们计算了相互作用能，并发现与原始电势非常吻合。从有效电荷模型中，我们计算了静电对第二维里系数的贡献。
