Collaborative research: Geometric flow approach to implicit solvation modeling

合作研究：隐式溶剂化建模的几何流方法

• 批准号: 8309088
• 负责人: Guowei Wei
• 金额: $ 30.79万
• 依托单位: MICHIGAN STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2015-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8309088
• 关键词: Address; Affinity; Algorithms; Area; Automobile Driving; Behavior; Binding; Biological; Biological Models; Biological Process; Biology; Biomedical Research; Charge; Chemical Models; Chemicals; Chemistry; Commit; Communities; Computer software; Computer-Aided Design; Coupled; Drug Design; Education; Educational Curriculum; Educational process of instructing; Educational workshop; Electrostatics; Ensure; Environment; Equation; Equilibrium; Evaluation; Fostering; Free Energy; Freedom; Ions; Kinetics; Lead; Link; Liquid substance; Literature; Mathematical Biology; Mechanics; Methodology; Methods; Microscopic; Modeling; Molecular; Molecular Models; Molecular Structure; Mutation; Physics; Process; Property; Research; Research Personnel; Sampling; Solvents; Structure; Students; Surface; Surface Properties; Surface Tension; System; Thermodynamics; Titrations; Training Support; Validation; Variant; aqueous; base; design; experience; image processing; innovation; interest; intermolecular interaction; molecular modeling; multi-scale modeling; physical property; pressure; programs; simulation; software development; solute

Solvation is a fundamental process of interactions between solute molecules and solvent or ions in the aqueous environment. Accurate models of solvation are essential prerequisites for the quantitative description and analysis of important biological processes involving the folding, encounter, recognition, and binding of biomolecular assemblies. Solvation models can be roughly divided into two classes: explicit ones that treat the solvent in molecular or atomic detail and implicit solvent models that treat the solvent as a dielectric continuum. Because of their efficiency, implicit solvent models have become very popular for a variety of biological applications, including rational drug design, estimations of folding energies, binding affinities, pKa values, and the analysis of structure, mutation, and many other thermodynamic and kinetic quantities. However, ad hoc assumptions about solvent-solute interfaces are currently used in most implicit solvent models, impeding their reliability, accuracy and efficiency. The proposed project addresses this problem by developing a differential geometry-based multiscale framework. Upon energy minimization, our framework generates the interface between the continuum solvent and the discrete atomistic solute. In particular, variation of the full free energy functional gives rise to selfconsistently coupled geometric and Poisson-Boltzmann equations. The resulting equations will be solved with advanced algorithms. Extensive validations and applications are designed to ensure that the proposed multiscale paradigm yields accurate solvation properties. The importance of implicit solvent models is supported by the thousands of applications in the literature. The proposed research addresses serious limitations in existing models arising from ad hoc assumptions of the solvent-solute interface by the introduction of a new mathematical framework to construct physical interfaces. In total, this proposal offers an innovative approach to an important area in biomolecular modeling .

溶剂化是水溶液中溶质分子与溶剂或离子相互作用的基本过程。精确的溶剂化模型是定量描述和分析重要生物过程的必要前提，这些过程涉及分子的折叠、相遇、识别和结合。 生物分子组装体溶剂化模型可以大致分为两类：显式的，处理溶剂的分子或原子的细节和隐式溶剂模型，处理溶剂作为一个介电连续。 由于其效率，隐式溶剂模型已成为非常受欢迎的各种生物学应用，包括合理的药物设计，折叠能，结合亲和力，pKa值的估计，以及结构，突变和许多其他热力学和动力学量的分析。然而，特设 目前，大多数隐式溶剂模型都采用关于溶剂-溶质界面的假设，这影响了它们的可靠性、准确性和效率。 拟议的项目通过开发基于微分几何的多尺度框架来解决这个问题。能量最小化后，我们的框架产生的连续溶剂和离散原子溶质之间的接口。特别是，全自由能泛函的变化引起自洽耦合几何和泊松-玻尔兹曼方程。由此产生的方程将用先进的算法求解。广泛的验证和应用程序的设计，以确保所提出的多尺度范式产生准确的溶剂化属性。 隐含溶剂模型的重要性得到了文献中数千种应用的支持。 拟议的研究解决了严重的局限性，在现有的模型所产生的特设假设的溶剂-溶质界面引入一个新的数学框架来构建物理接口。总的来说，该提案为生物分子建模的一个重要领域提供了一种创新方法。