Modeling Solvent Environments Applications To Simulations Of Biomolecules

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.

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.

Preface.
List of Contributors.
1 Biomolecular Solvation in Theory and Experiment (Michael Feig).
1.1 Introduction.
1.2 Theoretical Views of Solvation.
1.3 Computer Simulation Methods in the Study of Solvation.
1.4 Experimental Methods in the Study of Solvation.
1.5 Hydration of Proteins.
1.6 Hydration of Nucleic acids.
1.7 Non-Aqueous Solvation.
1.8 Summary.
References.
2 Model-Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids (Norio Yoshida, Yasuomi Kiyota, Yasuhiro Ikuta, Takashi Imai, and Fumio Hirata).
2.1 Introduction.
2.2 Outline of the RISM and 3D-RISM theories.
2.3 Partial Molar Volume of Proteins.
2.4 Detecting Water Molecules Trapped Inside Protein.
2.5 Selective Ion Binding by Protein.
2.6 Water Molecules Identified as a Substrate for Enzymatic Hydrolysis of Cellulose.
2.7 CO Escape Pathway in Myoglobin.
2.8 Perspective.
References.
3 Developing Force Fields From the Microscopic Structure of Solutions: The Kirkwood–Buff Approach (Samantha Weerasinghe, Moon Bae Gee, Myungshim Kang, Nikolaos Bentenitis, and Paul E. Smith).
3.1 Introduction.
3.2 Biomolecular Force Fields.
3.3 Examples of Problems with Current Force Fields.
3.4 Kirkwood–Buff Theory.
3.5 Applications of Kirkwood–Buff Theory.
3.6 The General KBFF Approach.
3.7 Technical Aspects of the KBFF Approach.
3.8 Results for Urea and Water Binary Solutions.
3.9 Preferential Interactions of Urea.
3.10 Conclusions and Future Directions.
Acknowledgments.
References.
4 Osmolyte Influence on Protein Stability: Perspectives of Theory and Experiment (Char Hu, Jörg Rösgen, and B. Montgomery Pettitt).
4.1 Introduction.
4.2 Denaturing Osmolytes.
4.3 Protecting Osmolytes.
4.4 Mixed Osmolytes.
4.5 Conclusions.
Acknowledgments.
References.
5 Modeling Aqueous Solvent Effects through Local Properties of Water (Sergio A. Hassan and Ernest L. Mehler).
5.1 The Role of Water and Cosolutes on Macromolecular Thermodynamics.
5.2 Forces Induced by Water in Aqueous Solutions.
5.3 Continuum Representation of Water.
5.4 Modeling Water Effects on Proteins and Nucleic Acids.
Acknowledgments.
References.
6 Continuum Electrostatics Solvent Modeling with the Generalized Born Model (Alexey Onufriev).
6.1 Introduction: the Implicit Solvent Framework.
6.2 The Generalized Born Model.
6.3 Applications of the GB Model.
6.4 Some Practical Considerations.
6.5 Limitations of the GB Model.
6.6 Conclusions and Outlook.
Acknowledgments.
References.
7 Implicit Solvent Force-Field Optimization (Jianhan Chen, WonpilIm, and Charles L. Brooks III).
7.1 Introduction.
7.2 Theoretical Foundations of Implicit Solvent.
7.3 Optimization of Implicit Solvent Force Fields.
7.4 Concluding Remarks and Outlook.
Acknowledgments.
References.
8 Modeling Protein Solubility in Implicit Solvent (Harianto Tjong and Huan-Xiang Zhou).
8.1 Introduction.
8.2 The Models.
8.3 Applications.
8.4 Summary and Outlook.
References.
9 Fast Analytical Continuum Treatments of Solvation (François Marchand and Amedeo Caflisch).
9.1 Introduction.
9.2 The SASA Implicit Solvent Model: A Fast Surface Area Model.
9.3 The FACTS Implicit Solvent Model: A Fast Generalized Born Approach.
9.4 Conclusions.
Acknowledgments.
References.
10 On the Development of State-Specific Coarse-Grained Potentials of Water (Hyung Min Cho and Jhih-Wei Chu).
10.1 Introduction.
10.2 Methods of Computing Coarse-Grained Potentials of Liquid Water.
10.3 Structural Properties and the "Representability" Problem of Coarse-Grained Liquid Water Models.
10.4 Conclusions.
Acknowledgment.
References.
11 Molecular Dynamics Simulations of Biomolecules in a Polarizable Coarse-Grained Solvent (Tap Ha-Duong, Nathalie Basdevant, and Daniel Borgis).
11.1 Introduction.
11.2 Theory.
11.3 Applications: Solvation of All-Atom Models of Biomolecules.
11.4 Conclusion and Prospects.
References.
12 Modeling Electrostatic Polarization in Biological Solvents (Sandeep Patel).
12.1 Introduction.
12.2 Current Approaches for Modeling Electrostatic Polarization in Classical Force Fields.
12.3 Parameterization of Charge Equilibration Models.
12.4 Applications of Charge Equilibration Models for Biological Solvents.
12.5 Toward Modeling of Membrane Ion Channel Systems: Molecular Dynamics Simulations of DMPC–Water and DPPC–Water Bilayer Systems.
12.6 Conclusions and Future Directions.
Acknowledgments.
References.
Subject Index.