Peptide solvation and H-bonds:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, AP
2006
|
| Series: | Advances in protein chemistry
72 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XII, 300 S. Ill., graph. Darst. |
| ISBN: | 0120342723 9780120342723 |
Staff View
MARC
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| 245 | 1 | 0 | |a Peptide solvation and H-bonds |c ed. by Robert L. Baldwin ... |
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, AP |c 2006 | |
| 300 | |a XII, 300 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
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| 490 | 1 | |a Advances in protein chemistry |v 72 | |
| 650 | 4 | |a Hydrogen bonding | |
| 650 | 4 | |a Peptides | |
| 650 | 4 | |a Solvation | |
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Record in the Search Index
| _version_ | 1804135290134069248 |
|---|---|
| adam_text | CONTENTS
NEW DIRECTIONS IN THE STUDY OF PEPTIDE H BONDS
AND PEPTIDE SOLVATION ix
Potential Functions for Hydrogen Bonds in Protein Structure
Prediction and Design
Alexandre V. Morozov and Tanja Kortemme
I. Introduction 2
II. Physical Mechanism of Hydrogen Bond Formation 4
III. Main Approaches to Modeling Hydrogen Bonds in
Biomolecular Simulations 6
IV. Applications of Hydrogen Bonding Potentials 20
V. Conclusions and Perspectives 30
References 32
. Backbone Backbone H Bonds Make Context Dependent
Contributions to Protein Folding Kinetics and Thermodynamics:
Lessons from Amide to Ester Mutations
Evan T. Powers, Songpon Deechongkit, and Jeffery W. Kelly
I. Introduction 40
II. Nomenclature and Synthesis of Amide to Ester Mutants 42
III. Esters as Amide Replacements 44
IV. Interpretation of Energetic Data from
Amide to Ester Mutants 48
V. Amide to Ester Mutations in Studies of Protein Function .... 56
VI. Amide to Ester Mutations in Studies of Protein
Folding Thermodynamics 58
VII. Analysis of AAGb and AAGf Values from
Amide to Ester Mutants 61
VIII. Amide to Ester Mutations in Studies of Protein
Folding Kinetics 68
IX. Conclusions and Future Directions 69
References 70
V
Vi CONTENTS
Modeling Polarization in Proteins and Protein Ligand Complexes:
Methods and Preliminary Results
Richard A. Friesner
I. Introduction 80
II. Incorporation of Polarization in Molecular
Mechanics Models 81
III. Aqueous Solvation Models for Polarizable Simulations 87
IV. Modeling Polarizability with Mixed Quantum
Mechanics/Molecular Mechanics Methods 89
V. Protein Simulations in Explicit Solvent Using a
Polarizable Force Field 94
VI. Conclusion 98
References 99
Hydrogen Bonds in Molecular Mechanics Force Fields
Jan Hermans
I. Introduction 105
II. Geometric Deformation 106
III. Nonbonded Interactions Ill
IV. Conclusion 116
References 117
Resonance Character of Hydrogen Bonding Interactions in
Water and Other H Bonded Species
F. Weinhold
I. Introduction 122
II. Natural Bond Orbital Donor Acceptor Description
of H Bonding 125
III. Quantum Cluster Equilibrium Theory of
H Bonded Fluids 131
IV. Recent Experimental Advances in Determining Water
Coordination Structure 138
V. General Enthalpic and Entropic Principles of H Bonding. . . . 141
CONTENTS Vii
VI. Hydrophobic Solvation: A Cluster Equilibrium View 145
VII. Summary and Conclusions: The Importance of
Resonance in H Bonding and Its Possible Representation
by Molecular Dynamics Simulations 149
References 150
How Hydrogen Bonds Shape Membrane Protein Structure
Stephen H. White
I. Introduction 157
II. Structure of Fluid Lipid Bilayers 159
III. Energetics of Peptides in Bilayers 160
IV. Helix Helix Interactions in Bilayers 165
V. Perspectives 167
References 167
Peptide and Protein Folding and Conformational Equilibria:
Theoretical Treatment of Electrostatics and
Hydrogen Bonding with Implicit Solvent Models
Wonpil Im, Jianhan Chen, and Charles L. Brooks, III
I. Introduction 174
II. Generalized Born (GB) Models 176
III. Peptide Folding and Conformational Equilibria 184
IV. Concluding Discussion 190
References 192
Thermodynamics of a Helix Formation
George I. Makhatadze
I. First 50 Years of Study of the Thermodynamics of the
Helix Coil Transition 199
II. The Quest for Enthalpy of the Helix Coil Transition 205
III. Temperature Dependence of Enthalpy of the
Helix Coil Transition 213
Viii CONTENTS
IV. Thermodynamic Helix Propensity Scale: Importance of
Peptide Backbone Hydration 215
V. Other Instances When Peptide Backbone Hydration is
Important for Stability 216
VI. Future Directions 218
References 220
The Importance of Cooperative Interactions and a Solid State
Paradigm to Proteins: What Peptide Chemists Can Learn from
Molecular Crystals
J. J. Dannenberg
I. Introduction 228
II. Similarities and Differences Between Proteins/Peptides
and Molecular Crystals 229
III. The Importance of H Bond Cooperativity in
Molecular Crystals 231
IV. Structural Consequences of H Bond Cooperativity in
Molecular Crystals 234
V. How Does the Use of the Crystal Paradigm Affect
Protein/Peptide Study? 240
VI. Are H Bonds Electrostatic? 242
VII. How Strong are Peptide H Bonds? 243
VIII. Comparison with Experimental Data from Studies
in Solution 255
IX. The Importance of a Suitable Reference State(s) 257
X. How Protein Chemists Can Deal with Problems Posed by
Dual Paradigms 260
XI. Water, the Hydrophobic Effect and Entropy 263
XII. Concluding Remarks 267
References 267
AUTHOR INDEX 275
SUBJECT INDEX 291
|
| adam_txt |
CONTENTS
NEW DIRECTIONS IN THE STUDY OF PEPTIDE H BONDS
AND PEPTIDE SOLVATION ix
Potential Functions for Hydrogen Bonds in Protein Structure
Prediction and Design
Alexandre V. Morozov and Tanja Kortemme
I. Introduction 2
II. Physical Mechanism of Hydrogen Bond Formation 4
III. Main Approaches to Modeling Hydrogen Bonds in
Biomolecular Simulations 6
IV. Applications of Hydrogen Bonding Potentials 20
V. Conclusions and Perspectives 30
References 32
. Backbone Backbone H Bonds Make Context Dependent
Contributions to Protein Folding Kinetics and Thermodynamics:
Lessons from Amide to Ester Mutations
Evan T. Powers, Songpon Deechongkit, and Jeffery W. Kelly
I. Introduction 40
II. Nomenclature and Synthesis of Amide to Ester Mutants 42
III. Esters as Amide Replacements 44
IV. Interpretation of Energetic Data from
Amide to Ester Mutants 48
V. Amide to Ester Mutations in Studies of Protein Function . 56
VI. Amide to Ester Mutations in Studies of Protein
Folding Thermodynamics 58
VII. Analysis of AAGb and AAGf Values from
Amide to Ester Mutants 61
VIII. Amide to Ester Mutations in Studies of Protein
Folding Kinetics 68
IX. Conclusions and Future Directions 69
References 70
V
Vi CONTENTS
Modeling Polarization in Proteins and Protein Ligand Complexes:
Methods and Preliminary Results
Richard A. Friesner
I. Introduction 80
II. Incorporation of Polarization in Molecular
Mechanics Models 81
III. Aqueous Solvation Models for Polarizable Simulations 87
IV. Modeling Polarizability with Mixed Quantum
Mechanics/Molecular Mechanics Methods 89
V. Protein Simulations in Explicit Solvent Using a
Polarizable Force Field 94
VI. Conclusion 98
References 99
Hydrogen Bonds in Molecular Mechanics Force Fields
Jan Hermans
I. Introduction 105
II. Geometric Deformation 106
III. Nonbonded Interactions Ill
IV. Conclusion 116
References 117
Resonance Character of Hydrogen Bonding Interactions in
Water and Other H Bonded Species
F. Weinhold
I. Introduction 122
II. Natural Bond Orbital Donor Acceptor Description
of H Bonding 125
III. Quantum Cluster Equilibrium Theory of
H Bonded Fluids 131
IV. Recent Experimental Advances in Determining Water
Coordination Structure 138
V. General Enthalpic and Entropic Principles of H Bonding. . . . 141
CONTENTS Vii
VI. Hydrophobic Solvation: A Cluster Equilibrium View 145
VII. Summary and Conclusions: The Importance of
Resonance in H Bonding and Its Possible Representation
by Molecular Dynamics Simulations 149
References 150
How Hydrogen Bonds Shape Membrane Protein Structure
Stephen H. White
I. Introduction 157
II. Structure of Fluid Lipid Bilayers 159
III. Energetics of Peptides in Bilayers 160
IV. Helix Helix Interactions in Bilayers 165
V. Perspectives 167
References 167
Peptide and Protein Folding and Conformational Equilibria:
Theoretical Treatment of Electrostatics and
Hydrogen Bonding with Implicit Solvent Models
Wonpil Im, Jianhan Chen, and Charles L. Brooks, III
I. Introduction 174
II. Generalized Born (GB) Models 176
III. Peptide Folding and Conformational Equilibria 184
IV. Concluding Discussion 190
References 192
Thermodynamics of a Helix Formation
George I. Makhatadze
I. First 50 Years of Study of the Thermodynamics of the
Helix Coil Transition 199
II. The Quest for Enthalpy of the Helix Coil Transition 205
III. Temperature Dependence of Enthalpy of the
Helix Coil Transition 213
Viii CONTENTS
IV. Thermodynamic Helix Propensity Scale: Importance of
Peptide Backbone Hydration 215
V. Other Instances When Peptide Backbone Hydration is
Important for Stability 216
VI. Future Directions 218
References 220
The Importance of Cooperative Interactions and a Solid State
Paradigm to Proteins: What Peptide Chemists Can Learn from
Molecular Crystals
J. J. Dannenberg
I. Introduction 228
II. Similarities and Differences Between Proteins/Peptides
and Molecular Crystals 229
III. The Importance of H Bond Cooperativity in
Molecular Crystals 231
IV. Structural Consequences of H Bond Cooperativity in
Molecular Crystals 234
V. How Does the Use of the Crystal Paradigm Affect
Protein/Peptide Study? 240
VI. Are H Bonds Electrostatic? 242
VII. How Strong are Peptide H Bonds? 243
VIII. Comparison with Experimental Data from Studies
in Solution 255
IX. The Importance of a Suitable Reference State(s) 257
X. How Protein Chemists Can Deal with Problems Posed by
Dual Paradigms 260
XI. Water, the Hydrophobic Effect and Entropy 263
XII. Concluding Remarks 267
References 267
AUTHOR INDEX 275
SUBJECT INDEX 291 |
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| publishDate | 2006 |
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| publisher | Elsevier, AP |
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| series | Advances in protein chemistry |
| series2 | Advances in protein chemistry |
| spelling | Peptide solvation and H-bonds ed. by Robert L. Baldwin ... Amsterdam [u.a.] Elsevier, AP 2006 XII, 300 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Advances in protein chemistry 72 Hydrogen bonding Peptides Solvation Baldwin, Robert L. 1927- Sonstige (DE-588)131549456 oth Advances in protein chemistry 72 (DE-604)BV002527411 72 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014755792&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Peptide solvation and H-bonds Advances in protein chemistry Hydrogen bonding Peptides Solvation |
| title | Peptide solvation and H-bonds |
| title_auth | Peptide solvation and H-bonds |
| title_exact_search | Peptide solvation and H-bonds |
| title_exact_search_txtP | Peptide solvation and H-bonds |
| title_full | Peptide solvation and H-bonds ed. by Robert L. Baldwin ... |
| title_fullStr | Peptide solvation and H-bonds ed. by Robert L. Baldwin ... |
| title_full_unstemmed | Peptide solvation and H-bonds ed. by Robert L. Baldwin ... |
| title_short | Peptide solvation and H-bonds |
| title_sort | peptide solvation and h bonds |
| topic | Hydrogen bonding Peptides Solvation |
| topic_facet | Hydrogen bonding Peptides Solvation |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014755792&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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