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While much attention has been given tot he development of realistic macromolecular models, this book focuses on latest advances in modeling the equally important solvent environment in an accurate and efficient manner. A comprehensive view of the current methods for modeling solvent environments is presented in contributions from the leading researchers in the field. Throughout, the emphasis is placed on the application of such models in simulation studies of biological processes, although the coverage is sufficiently broad to extend to other systems as well.
The book presents a comprehensive account of the many recently developed new methods and contrasts their different strengths. As such, this monograph treats a full range of topics, from statistical mechanics-based approaches to popular mean field formalisms, coarse-grained solvent models, more established explicit, fully atomic solvent models, and recent advances in applying ab initio methods for modeling solvent properties.
List of contents
BIOMOLECULAR SOLVATION IN THEORY AND EXPERIMENTIntroductionTheoretical Views of SolvationComputer Simulation Methods in the Study of SolvationExperimental Methods in the Study of SolvationHydration of ProteinsHydration of Nucleic AcidsNon-Aqueous SolvationSummaryMODEL-FREE "SOLVENT MODELING" IN CHEMISTRY AND BIOCHEMISTRY BASED ON THE STATISTICAL MECHANICS OF LIQUIDSIntroductionOutline of the RISM and 3D-RISM TheoriesPartial Molar Volume of ProteinsDetecting Water Molecules Trapped Inside ProteinSelective Ion Binding by ProteinWater Molecules Identified as a Substrate for Enzymatic hydrolysis of CelluloseCO Escape Pathway in MyoglobinPerspectiveDEVELOPING FORCE FIELDS FROM THE MICROSCOPIC STRUCTURE OF SOLUTIONS: THE KIRKWOOD-BUFF APPROACHIntroductionBiomolecular Force FieldsExamples of Problems with Current Force FieldsKirkwood-Buff TheoryApplications of Kirkwood-Buff TheoryThe General KBFF ApproachTechnical Aspects of the KBFF ApproachResults for Urea and Water Binary SolutionsPreferential Interactions of UreaConclusions and Future DirectionsOSMOLYTE INFLUENCE ON PROTEIN STABILITY: PERSPECTIVES OF THEORY AND EXPERIMENTIntroductionDenaturing OsmolytesProtecting OsmolytesMixed OsmolytesConclusionsMODELING AQUEOUS SOLVENT EFFECTS THROUGH LOCAL PROPERTIES OF WATERThe Role of Water and Cosolutes on Macromolecular ThermodynamicsForces Induced by Water in Aqueous SolutionsContinuum Representation of WaterModeling Water Effects on Proteins and Nucleic AcidsCONTINUUM ELECTROSTATICS SOLVENT MODELING WITH THE GENERALIZED BORN MODELIntroduction: The Implicit Solvent FrameworkThe Generalized Born ModelApplications of the GB ModelSome Practical ConsiderationsLimitations of the GB ModelConclusions and OutlookIMPLICIT SOLVENT FORCE-FIELD OPTIMIZATIONIntroductionTheoretical Foundations of Implicit SolventOptimization of Implicit Solvent Force FieldsConcluding Remarks and OutlookMODELING PROTEIN SOLUBILITY IN IMPLICIT SOLVENTIntroductionThe ModelsApplicationsSummary and OutlookFAST ANALYTICAL CONTINUUM TREATMENTS OF SOLVATIONIntroductionThe SASA Implicit Solvent Model: A Fast Surface Area ModelThe FACTS Implicit Solvent Model. A Fast Generalized Born ApproachConclusionsON THE DEVELOPMENT OF STATE-SPECIFIC COARSE-GRAINED POTENTIALS OF WATERIntroductionMethods of Computing Coarse-Grained Potentials of Liquid WaterStructural Properties and the "Representability" Problem of Coarse-Grained Liquid Water ModelsConclusionsMOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES IN A POLARIZABLE COARSE-GRAINED SOLVENTIntroductionTheoryApplications: Solvation of All-Atom Models of BiomoleculesConclusions and ProspectsMODELING ELECTROSTATIC POLARIZATION IN BIOLOGICAL SOLVENTSIntroductionCurrent Approaches for Modeling Electrostatic Polarization in Classical Force FieldsParameterization of Charge Equilibration ModelsApplications of Charge Equilibration Models for Biological SolventsToward Modeling of Membrane Ion Channel Systems: Molecular Dynamics Simulations of DMPC-Water and DPPC-Water Bilayer SystemsConclusions and Future Directions
About the author
Michael Feig is Professor of Biochemistry & Molecular Biology and Chemistry at Michigan State University. His academic training began with a degree in physics from the Technical University of Berlin and continued with studies of computational chemistry at the University of Houston and at The Scripps Research Institute in San Diego, California. Prof. Feig has authored over 50 publications, most related to the solvation of biomolecules. He has recently been awarded an Alfred P. Sloan fellowship and won awards from the American Chemical Society and Sigma Xi.
Summary
A comprehensive view of the current methods for modeling solvent environments with contributions from the leading researchers in the field. Throughout, the emphasis is placed on the application of such models in simulation studies of biological processes, although the coverage is sufficiently broad to extend to other systems as well. As such, this monograph treats a full range of topics, from statistical mechanics-based approaches to popular mean field formalisms, coarse-grained solvent models, more established explicit, fully atomic solvent models, and recent advances in applying ab initio methods for modeling solvent properties.
