Modeling Solvent Environments. Applications to Simulations of Biomolecules

  • ID: 2183277
  • Book
  • 334 Pages
  • John Wiley and Sons Ltd
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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.

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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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