Modeling solvent environments : applications to simulations of biomolecules
Modeling solvent environments : applications to simulations of biomolecules
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溶剂环境建模：在生物分子模拟中的应用
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发表时间：
2010
期刊：
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通讯作者：
M. Feig
中科院分区：
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作者：
M. Feig
生物分子溶剂化的理论与实验简介溶剂化的理论观点溶剂化研究中的计算机模拟方法溶剂化研究中的实验方法蛋白质的水化核酸的水化非水溶剂化综述基于生物统计力学的化学和生物化学中的无模型“溶剂建模”RISM和3D-RISM理论蛋白质的偏摩尔体积检测蛋白质内部捕获的水分子通过蛋白质的选择性离子结合水分子被鉴定为纤维素酶水解的底物肌红蛋白中的CO逃逸途径透视图从溶液的微观结构看溶解力场：Kirkwood-Buff方法介绍生物分子力场当前力场问题的实例Kirkwood-Buff理论Kirkwood-Buff理论的应用KBFF方法的一般技术方面尿素和水二元溶液的结果尿素的优先相互作用结论和未来方向渗透酸对蛋白质稳定性的影响：理论和实验的观点引言变性渗透剂保护渗透剂混合渗透剂结论通过水的性质模拟水溶剂效应水和共溶质对水溶液中水诱导的大分子热力学力的作用水模拟水对蛋白质和核酸的影响连续统表示连续统静电溶剂模拟与广义Born模型引言：隐式溶剂框架广义玻恩模型GB模型的应用GB模型的一些实际考虑GB模型的局限性结论和展望隐式溶剂力-场优化介绍隐式溶剂优化的理论基础隐式溶剂力场的总结和展望隐式溶剂中蛋白质溶解度模型介绍模型应用总结和展望快速分析连续体介绍SASA隐式溶剂模型：一个快速的表面积模型的事实隐式溶剂模型。快速广义Born方法关于水的状态特异性粗粒势发展的结论介绍计算液态水的粗粒势的方法结构性质和粗粒液态水模型的“可表示性”问题结论可极化粗粒溶剂中生物分子的分子动力学模拟介绍理论应用：所有的溶剂化-生物分子的原子模型结论与展望生物溶剂中静电极化的模拟引言经典力场中静电极化的模拟方法电荷平衡模型的参数化生物溶剂电荷平衡模型的应用膜离子通道系统的模拟：DMPC-水和DPPC-水双层系统的分子动力学模拟结论和未来方向
BIOMOLECULAR SOLVATION IN THEORY AND EXPERIMENT Introduction Theoretical Views of Solvation Computer Simulation Methods in the Study of Solvation Experimental Methods in the Study of Solvation Hydration of Proteins Hydration of Nucleic Acids Non-Aqueous Solvation Summary MODEL-FREE "SOLVENT MODELING" IN CHEMISTRY AND BIOCHEMISTRY BASED ON THE STATISTICAL MECHANICS OF LIQUIDS Introduction Outline of the RISM and 3D-RISM Theories Partial Molar Volume of Proteins Detecting Water Molecules Trapped Inside Protein Selective Ion Binding by Protein Water Molecules Identified as a Substrate for Enzymatic hydrolysis of Cellulose CO Escape Pathway in Myoglobin Perspective DEVELOPING FORCE FIELDS FROM THE MICROSCOPIC STRUCTURE OF SOLUTIONS: THE KIRKWOOD-BUFF APPROACH Introduction Biomolecular Force Fields Examples of Problems with Current Force Fields Kirkwood-Buff Theory Applications of Kirkwood-Buff Theory The General KBFF Approach Technical Aspects of the KBFF Approach Results for Urea and Water Binary Solutions Preferential Interactions of Urea Conclusions and Future Directions OSMOLYTE INFLUENCE ON PROTEIN STABILITY: PERSPECTIVES OF THEORY AND EXPERIMENT Introduction Denaturing Osmolytes Protecting Osmolytes Mixed Osmolytes Conclusions MODELING AQUEOUS SOLVENT EFFECTS THROUGH LOCAL PROPERTIES OF WATER The Role of Water and Cosolutes on Macromolecular Thermodynamics Forces Induced by Water in Aqueous Solutions Continuum Representation of Water Modeling Water Effects on Proteins and Nucleic Acids CONTINUUM ELECTROSTATICS SOLVENT MODELING WITH THE GENERALIZED BORN MODEL Introduction: The Implicit Solvent Framework The Generalized Born Model Applications of the GB Model Some Practical Considerations Limitations of the GB Model Conclusions and Outlook IMPLICIT SOLVENT FORCE-FIELD OPTIMIZATION Introduction Theoretical Foundations of Implicit Solvent Optimization of Implicit Solvent Force Fields Concluding Remarks and Outlook MODELING PROTEIN SOLUBILITY IN IMPLICIT SOLVENT Introduction The Models Applications Summary and Outlook FAST ANALYTICAL CONTINUUM TREATMENTS OF SOLVATION Introduction The SASA Implicit Solvent Model: A Fast Surface Area Model The FACTS Implicit Solvent Model. A Fast Generalized Born Approach Conclusions ON THE DEVELOPMENT OF STATE-SPECIFIC COARSE-GRAINED POTENTIALS OF WATER Introduction Methods of Computing Coarse-Grained Potentials of Liquid Water Structural Properties and the "Representability" Problem of Coarse-Grained Liquid Water Models Conclusions MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES IN A POLARIZABLE COARSE-GRAINED SOLVENT Introduction Theory Applications: Solvation of All-Atom Models of Biomolecules Conclusions and Prospects MODELING ELECTROSTATIC POLARIZATION IN BIOLOGICAL SOLVENTS Introduction Current Approaches for Modeling Electrostatic Polarization in Classical Force Fields Parameterization of Charge Equilibration Models Applications of Charge Equilibration Models for Biological Solvents Toward Modeling of Membrane Ion Channel Systems: Molecular Dynamics Simulations of DMPC-Water and DPPC-Water Bilayer Systems Conclusions and Future Directions