Free Energies in Biomolecular Systems: Development and Application of Computational Approaches

生物分子系统中的自由能：计算方法的开发和应用

• 批准号: 0110847
• 负责人: Benoit Roux
• 金额: $ 33万
• 依托单位: Joan and Sanford I. Weill Medical College of Cornell University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-09-01 至 2004-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0110847&HistoricalAwards=false
• 关键词: Free; Energies; Biomolecular; Systems; Development

By and large, biological processes involving ligand binding specificity, protein-protein association, protein-membrane association, protonation and unprotonation of ionizable groups, and macromolecular conformational changes, are given thermodynamically by a reversible work function, the free energy, or more generally by its configuration-dependent equivalent. A quantitative determination of free energies is, therefore, a problem of central importance in theoretical biophysics. Computational approaches at different levels of complexity and sophistication can be used to try and address this problem. Those range from (relatively expensive) molecular dynamics free energy simulations (MD/FES) based on all-atom models in which the solvent is treated explicitly to (relative inexpensive) Poisson-Boltzmann (PB) continuum electrostatic models in which the influence of the solvent is incorporated implicitly. The goal of this research is to refine and extend current computational approaches used in the modeling of biomolecular systems. More particularly, protocols that will provide increased accuracy and reliability in estimating free energies while remaining computationally tractable will be developed and tested. Progress in these computational methodologies is expected to have a great impact on the rational design of drugs and biomolecules.

总的来说，包括配体结合特异性、蛋白质-蛋白质结合、蛋白质-膜结合、可电离基团的质子化和非质子化以及大分子构象变化在内的生物过程，都是由可逆功函数、自由能或更一般地由构型依赖的等价物给出的热力学过程。因此，自由能的定量测定是理论生物物理学中一个极为重要的问题。可以使用不同复杂程度和复杂程度的计算方法来尝试解决这个问题。这些范围从（相对昂贵的）基于明确处理溶剂的全原子模型的分子动力学自由能模拟（MD/FES）到（相对便宜的）隐含纳入溶剂影响的泊松-玻尔兹曼（PB）连续静电模型。本研究的目标是改进和扩展目前用于生物分子系统建模的计算方法。更具体地说，将开发和测试在估计自由能方面提供更高的准确性和可靠性，同时保持计算易于处理的协议。这些计算方法的进展有望对药物和生物分子的合理设计产生重大影响。