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Modeling Solvent Environments: Applications to Simulations of Biomolecules

Michael Feig (Editor)
ISBN: 978-3-527-32421-7
334 pages
March 2010
Modeling Solvent Environments: Applications to Simulations of Biomolecules (3527324216) cover image
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.
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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
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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.
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