Fast and Accurate Numerical Methods of Electrostatic Interactions in Biomolecules

生物分子静电相互作用快速准确的数值方法

• 批准号: 7662531
• 负责人: WEI CAI
• 金额: $ 36万
• 依托单位: UNIVERSITY OF NORTH CAROLINA CHARLOTTE
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-06 至 2011-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7662531
• 关键词: Behavior; Biological; Biopolymers; Cell physiology; Cells; Charge; Complex; Crowding; DNA; Electrostatics; Environment; Equilibrium; Ion Transport; Ions; Life; Methods; Modeling; Molecular; Play; Property; Proteins; RNA; Role; Signal Transduction; Solvents; Surface; Synapses; System; Water; aqueous; biological systems; macromolecule; molecular dynamics; molecular recognition; molecular scale; neglect; simulation; solute; transmission process

DESCRIPTION (provided by applicant): Electrostatic interactions play an essential role in molecular and cellular processes that include signal transmission at synaptic junctions, ion-transport, molecular recognition, and stability and function of DNA, RNA and proteins. Of paramount biological importance is the collective behavior of ions, molecules, and macromolecules having inhomogeneous charge distributions in the aqueous crowded environment of a living cell. Central to this environment is water, which is a complex solvent with non-bulk properties near ions, molecules and water-biopolymer interfaces. The main challenge for modeling electrostatics, as the core calculation of Molecular Dynamics and Monte Carlo simulations, is to balance the accuracy of interactions among charges and the efficiency required for realistic biological systems. For all-atom simulations the Ewald method is currently the most accurate method for large enough system where periodic boundary effects are negligible. Unfortunately, the simulation of a macromolecule requires a large simulation volume, making the Ewald method and similar methods too expensive while a smaller system size compromises accuracy. Meanwhile, modeling the solvent using continuum electrostatics is much faster, but accuracy is compromised by neglecting molecular scale inhomogeneity, such as atomic details near the surface of the solute.

描述（由申请人提供）：静电相互作用在分子和细胞过程中发挥重要作用，包括突触连接处的信号传递、离子转运、分子识别以及DNA、RNA和蛋白质的稳定性和功能。具有最重要的生物学意义的是在活细胞的水相拥挤环境中具有不均匀电荷分布的离子、分子和大分子的集体行为。这种环境的核心是水，它是一种复杂的溶剂，在离子、分子和水-生物聚合物界面附近具有非本体性质。作为分子动力学和蒙特卡罗模拟的核心计算，静电建模的主要挑战是平衡电荷之间相互作用的准确性和现实生物系统所需的效率。对于全原子模拟，Ewald方法是目前最精确的方法，适用于周期性边界效应可以忽略的足够大的系统。不幸的是，大分子的模拟需要大的模拟体积，使得Ewald方法和类似的方法太昂贵，而较小的系统尺寸会损害精度。同时，使用连续静电学对溶剂进行建模要快得多，但由于忽略了分子尺度的不均匀性，例如溶质表面附近的原子细节，精度受到影响。