E-Book, Englisch, Band Volume 72, 312 Seiten, Web PDF
E-Book, Englisch, Band Volume 72, 312 Seiten, Web PDF
Reihe: Advances in Protein Chemistry
ISBN: 978-0-08-046356-8
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark
Autoren/Hrsg.
Weitere Infos & Material
1;Cover page;1
2;Contents;6
3;New Directions in the Study of Peptide H-Bonds and.Peptide Solvation;10
4;Chapter 1: Potential Functions for Hydrogen Bonds in Protein Structure Prediction and Design;14
4.1;I. Introduction;15
4.2;II. Physical Mechanism of Hydrogen Bond Formation;17
4.3;III. Main Approaches to Modeling Hydrogen Bonds in Biomolecular Simulations;19
4.3.1;A. Potentials Derived from Hydrogen Bonding Geometries Observed in Crystal Structures;19
4.3.2;B. Molecular Mechanics: Comparison with the Structure-Derived, Orientation-Dependent Potential;22
4.3.3;C. Quantum Mechanics: Comparison with Molecular Mechanics and the Structure-Derived Potential;25
4.4;IV. Applications of Hydrogen Bonding Potentials;33
4.4.1;A. Protein Structure Prediction and Refinement;33
4.4.2;B. Prediction of Protein-Protein Interfaces;37
4.4.3;C. Protein Design;40
4.5;V. Conclusions and Perspectives;43
4.6;References;45
5;Chapter 2: Backbone-Backbone H-Bonds Make Context-Dependent Contributions to Protein Folding Kinetics and Thermodynamics: Lessons from Amide-to-Ester Mutations;52
5.1;I. Introduction;53
5.2;II. Nomenclature and Synthesis of Amide-to-Ester Mutants;55
5.3;III. Esters as Amide Replacements;57
5.3.1;A. Geometry and Conformation;57
5.3.2;B. Structural Effects of Amide-to-Ester Mutations;59
5.4;IV. Interpretation of Energetic Data from Amide-to-Ester Mutants;61
5.4.1;A. H-Bond Energies and the Thermodynamic Analysis of Amide-to-Ester Mutants;61
5.4.2;B. Kinetic Analysis of Amide-to-Ester Mutants;68
5.5;V. Amide-to-Ester Mutations in Studies of Protein Function;69
5.6;VI. Amide-to-Ester Mutations in Studies of Protein Folding Thermodynamics;71
5.7;VII. Analysis of DeltaDeltaGb and DeltaDeltaGf Values from Amide-to-Ester Mutants;74
5.7.1;A. General Observations;74
5.7.2;B. Quantitative Analysis of DeltaDeltaGf/b Values;77
5.8;VIII. Amide-to-Ester Mutations in Studies of Protein Folding Kinetics;81
5.9;IX. Conclusions and Future Directions;82
5.10;References;83
6;Chapter 3: Modeling Polarization in Proteins and Protein-ligand Complexes: Methods and Preliminary Results;92
6.1;I. Introduction;93
6.2;II. Incorporation of Polarization in Molecular Mechanics Models;94
6.2.1;A. Overview;94
6.2.2;B. Development of the OPLS/PFF Force Field;96
6.2.3;C. Simulation Methodology;98
6.2.4;D. Evaluation of the Polarizable Force Field in the Gas Phase and Condensed Phase;98
6.3;III. Aqueous Solvation Models for Polarizable Simulations;100
6.3.1;A. Overview;100
6.3.2;B. Polarizable Explicit Water Models;101
6.4;IV. Modeling Polarizability with Mixed Quantum Mechanics/Molecular Mechanics Methods;102
6.4.1;A. Overview;102
6.4.2;B. Protein-Ligand Docking Using a Mixed Mixed Quantum Mechanics/Molecular Mechanics Methodology to Compute Ligand Charges;103
6.5;V. Protein Simulations in Explicit Solvent Using a Polarizable Force Field;107
6.5.1;A. Overview;107
6.5.2;B. Simulations of BPTI with Polarizable and Fixed Charge Protein and Water Models;109
6.6;VI. Conclusion;111
6.7;References;112
7;Chapter 4: Hydrogen Bonds In Molecular Mechanics Force Fields;118
7.1;I. Introduction;118
7.2;II. Geometric Deformation;119
7.3;III. Nonbonded Interactions;124
7.4;IV. Conclusion;129
7.5;References;130
8;Chapter 5: Resonance Character of Hydrogen-bonding Interactions in Water and Other H-bonded Species;134
8.1;I. Introduction;135
8.2;II. Natural Bond Orbital Donor-Acceptor Description of H-Bonding;138
8.3;III. Quantum Cluster Equilibrium Theory of H-Bonded Fluids;144
8.4;IV. Recent Experimental Advances in Determining Water Coordination Structure;151
8.5;V. General Enthalpic and Entropic Principles of H-Bonding;154
8.5.1;A. Torsional, Angular, and Dissociative Entropic Contributions;154
8.5.2;B. Binary and Cooperative Enthalpic Contributions;156
8.6;VI. Hydrophobic Solvation: A Cluster Equilibrium View;158
8.7;VII. Summary and Conclusions: The Importance of Resonance in H-Bonding and Its Possible Representation by Molecular Dynamics Simulations;162
8.8;References;163
9;Chapter 6: How hydrogen bonds shape membrane protein structure;170
9.1;I. Introduction;170
9.2;II. Structure of Fluid Lipid Bilayers;172
9.3;III. Energetics of Peptides in Bilayers;173
9.3.1;A. Folding in the Membrane Interface;174
9.3.2;B. Transmembrane Helices;176
9.4;IV. Helix-Helix Interactions in Bilayers;178
9.5;V. Perspectives;180
9.6;References;180
10;Chapter 7: Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models;186
10.1;I. Introduction;187
10.2;II. Generalized Born (GB) Models;189
10.2.1;A. GB Electrostatics Theory;189
10.2.2;B. Advances and Achievements;192
10.2.3;C. Remaining Opportunities for Continued Improvement;195
10.3;III. Peptide Folding and Conformational Equilibria;197
10.3.1;A. Influence of Backbone H-Bond Strength on Conformational Equilibria;197
10.3.2;B. Influence of Backbone Dihedral Energetics on Conformational Equilibria;202
10.4;IV. Concluding Discussion;203
10.5;References;205
11;Chapter 8: Thermodynamics Of alpha-Helix Formation;212
11.1;I. First 50 Years of Study of the Thermodynamics of the Helix-Coil Transition;212
11.2;II. The Quest for Enthalpy of the Helix-Coil Transition;218
11.3;III. Temperature Dependence of Enthalpy of the Helix-Coil Transition;226
11.4;IV. Thermodynamic Helix Propensity Scale: Importance of Peptide Backbone Hydration;228
11.5;V. Other Instances When Peptide Backbone Hydration is Important for Stability;229
11.6;VI. Future Directions;231
11.7;References;233
12;Chapter 9: The Importance of Cooperative Interactions and a Solid-State Paradigm to Proteins: What Peptide Chemists Can Learn from Molecular Crystals;240
12.1;I. Introduction;241
12.2;II. Similarities and Differences Between Proteins/Peptides and Molecular Crystals;242
12.2.1;A. Similarities;242
12.2.2;B. Differences;243
12.3;III. The Importance of H-Bond Cooperativity in Molecular Crystals;244
12.3.1;A. Enthalpy Is Relatively More Important in the Solid Than in the Liquid;244
12.3.2;B. H-Bonds Are More Stable in the Solid Than in the Liquid State;245
12.4;IV. Structural Consequences of H-Bond Cooperativity in Molecular Crystals;247
12.4.1;A. Acetic Acid;248
12.4.2;B. 1,3-Cyclohexanedione;248
12.4.3;C. Urea;250
12.4.4;D. Formamide;251
12.4.5;E. CH...O H-Bonding Interactions and Parabenzoquinone;251
12.5;V. How Does the Use of the Crystal Paradigm Affect Protein/Peptide Study?;253
12.5.1;A. Low-Barrier H-Bonds;253
12.6;VI. Are H-Bonds Electrostatic?;255
12.6.1;A. Water-Water H-Bonding Cannot be Described Adequately Purely by Electrostatic Interactions;255
12.6.2;B. Comparison of H-Bonds with the Behavior of Molecules in an Electric Field;256
12.7;VII. How Strong are Peptide H-Bonds?;256
12.7.1;A. Amide Dimers;257
12.7.2;B. Formamide Chains;257
12.7.3;C. alpha-Helices;260
12.7.4;D. Protonated alpha-Helices;263
12.7.5;E. beta-Sheets;263
12.7.6;F. Collagen-like Triple Helices;265
12.8;VIII. Comparison with Experimental Data from Studies in Solution;268
12.8.1;A. alpha-Helices;268
12.9;IX. The Importance of a Suitable Reference State(s);270
12.9.1;A. Differences between Reference States for Experimental and Theoretical Studies;270
12.9.2;B. Multiple Reference States;270
12.9.3;C. Component Amino Acids;270
12.9.4;D. Extended beta-Strand;271
12.9.5;E. Choosing More Than One Reference State;272
12.10;X. How Protein Chemists Can Deal with Problems Posed by Dual Paradigms;273
12.10.1;A. Theoretical and Modeling Studies;273
12.10.2;B. Experimental Studies;274
12.11;XI. Water, the Hydrophobic Effect and Entropy;276
12.11.1;A. Water;276
12.11.2;B. The Hydrophobic Effect and Entropy;277
12.11.3;C. Another Origin of Entropy Control of Protein Folding;278
12.12;XII. Concluding Remarks;280
12.13;References;280
13;Author Index;288
14;Subject Index;304
