LEADER 05206nam 2200601Ia 450 001 9910830153503321 005 20230725044907.0 010 $a1-282-47232-1 010 $a9786612472329 010 $a3-527-62925-4 010 $a3-527-62926-2 035 $a(CKB)2550000000000263 035 $a(EBL)481261 035 $a(OCoLC)521036186 035 $a(SSID)ssj0000354498 035 $a(PQKBManifestationID)11275365 035 $a(PQKBTitleCode)TC0000354498 035 $a(PQKBWorkID)10314478 035 $a(PQKB)10326037 035 $a(MiAaPQ)EBC481261 035 $a(EXLCZ)992550000000000263 100 $a20000327d2010 uy 0 101 0 $aeng 135 $aur|n|---||||| 181 $ctxt 182 $cc 183 $acr 200 00$aModeling solvent environments$b[electronic resource] $eapplications to simulations of biomolecules /$fedited by Michael Feig 210 $aWeinheim $cWiley-VCH Verlag GmbH$dc2010 215 $a1 online resource (336 p.) 300 $aDescription based upon print version of record. 311 $a3-527-32421-6 320 $aIncludes bibliographical references and index. 327 $aModeling Solvent Environments: Applications to Simulations of Biomolecules; Contents; Preface; List of Contributors; 1: Biomolecular Solvation in Theory and Experiment; 1.1 Introduction; 1.2 Theoretical Views of Solvation; 1.2.1 Equilibrium Thermodynamics of Solvation; 1.2.2 Radial Distribution Functions; 1.2.3 Integral Equation Formalisms; 1.2.4 Kirkwood-Buff Theory; 1.2.5 Kinetic Effects of Solvation; 1.3 Computer Simulation Methods in the Study of Solvation; 1.3.1 Molecular Dynamics and Monte Carlo Simulations; 1.3.2 Water Models; 1.3.3 Solvent Structure and Dynamics from Simulations 327 $a1.3.4 Free Energy Simulations1.4 Experimental Methods in the Study of Solvation; 1.4.1 X-Ray/Neutron Diffraction and Scattering; 1.4.2 Nuclear Magnetic Relaxation; 1.4.3 Optical Spectroscopy; 1.4.4 Dielectric Dispersion; 1.5 Hydration of Proteins; 1.5.1 Protein Folding and Peptide Conformations in Aqueous Solvent; 1.5.2 Molecular Properties of Water Near Protein Surfaces; 1.5.3 Water Molecules at Protein-Ligand and Protein-Protein Interfaces; 1.6 Hydration of Nucleic acids; 1.7 Non-Aqueous Solvation; 1.7.1 Alcohols; 1.7.2 Urea; 1.7.3 Glycerol; 1.8 Summary; References 327 $a2: Model-Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids2.1 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; 2.7.1 Effect of Protein Structure on the Distribution of Xe; 2.7.2 Partial Molar Volume Change Through the CO Escape Pathway of Myoglobin; 2.8 Perspective; References 327 $a3: Developing Force Fields From the Microscopic Structure of Solutions: The Kirkwood-Buff Approach3.1 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; 4.1 Introduction 327 $a4.2 Denaturing Osmolytes4.2.1 Does Urea Weaken Water Structure?; 4.2.2 Effect of Urea on Hydrophobic Interactions; 4.2.3 Direct Interaction of Urea with Proteins; 4.3 Protecting Osmolytes; 4.3.1 Do Protecting Osmolytes Increase Water Structure?; 4.3.2 Effect of Protecting Osmolytes on Hydrophobic Interactions; 4.4 Mixed Osmolytes; 4.5 Conclusions; Acknowledgments; References; 5: Modeling Aqueous Solvent Effects through Local Properties of Water; 5.1 The Role of Water and Cosolutes on Macromolecular Thermodynamics; 5.2 Forces Induced by Water in Aqueous Solutions 327 $a5.2.1 Interactions in Water-Accessible Regions of Proteins 330 $aA 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 me 606 $aSolvents 606 $aBiomolecules 615 0$aSolvents. 615 0$aBiomolecules. 676 $a541.3482011 701 $aFeig$b Michael$01698187 801 0$bMiAaPQ 801 1$bMiAaPQ 801 2$bMiAaPQ 906 $aBOOK 912 $a9910830153503321 996 $aModeling solvent environments$94079482 997 $aUNINA