Fogolari Federico, Brigo Alessandro, Molinari Henriette
Dipartimento Scientifico e Tecnologico, Università di Verona, 37134 Verona, Italy.
Biophys J. 2003 Jul;85(1):159-66. doi: 10.1016/S0006-3495(03)74462-2.
Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poisson-Boltzmann equation has been very seldom used to obtain solvation forces for molecular dynamics simulation. We propose here a fast and reliable methodology to implement continuum forces in standard molecular mechanics and dynamics algorithms. Results for a totally unrestrained 1 ns molecular dynamics simulation of a small protein are quantitatively similar to results obtained by explicit solvent molecular dynamics simulations.
连续介质溶剂模型在过去几年中被用于理解诸如蛋白质折叠或生物分子缔合等过程。在过去十年里，人们进行了多次尝试，将原子细节分子动力学模拟与溶剂连续介质模型相结合。在连续介质模型中，泊松-玻尔兹曼溶剂可及表面积模型是最古老且最基础的模型之一。尽管它在生物分子静电势模拟中被广泛使用，但泊松-玻尔兹曼方程很少被用于获得分子动力学模拟的溶剂化力。我们在此提出一种快速且可靠的方法，用于在标准分子力学和动力学算法中实现连续介质力。对一种小蛋白质进行的完全无约束的1纳秒分子动力学模拟结果，在定量上与通过显式溶剂分子动力学模拟获得的结果相似。
