Non-covalent interactions in proteins:
Gespeichert in:
| 1. Verfasser: | |
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| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
New Jersey ; London ; Singapore
World Scientific
[2021]
|
| Ausgabe: | Second edition |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xix, 424 Seiten Illustrationen, Diagramme |
| ISBN: | 9789811228087 |
Internformat
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Datensatz im Suchindex
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| adam_text | Contents Dedication Preface to the Second Edition Preface to the First Edition About the Author vii ix xi xiii 1. Introduction 1.1 Some Historical Notes 1.2 Overview of Protein Structural Elements and Basic Definitions 1.2.1 The amino acids 1.2.2 The polypeptide chain 1.3 Non-Covalent Interactions and Structure-Function Relationshipsin Proteins 1.3.1 Some comments on Anfinsen s dogma 1.3.2 Experimental measurements of non-covalent interactions in proteins References 1 4 13 14 19 22 23 24 25 2. Van der Waals Interactions 2.1 Observation of van der Waals Interactions 2.2 Nature of van der Waals Interactions 2.2.1 Dispersion forces 2.2.2 Dipole-dipole interactions 2.2.3 Dipole-induced dipole interactions 2.2.4 Repulsive interactions 2.3 Potential Functions for Application in Proteins 2.4 Approximation for Polyatomic Systems References 27 28 30 31 44 49 51 54 57 59 3. Hydrogen Bonds 3.1 Nature of Hydrogen Bonds 3.1.1 Proton donors, electronegativity 3.1.2 Proton acceptors 60 60 61 64 XV
Non-Covalent Interactions in Proteins XVI 3.2 Geometry and Strengthof Hydrogen Bond 3.2.1 Directionality 3.2.2 Hydrogen bond length 3.2.3 Hydrogen bond strength 3.2.4 Hydrogen bond potential functions 3.3 Hydrogen Bonds in Proteins 3.3.1 Secondary structure elements 3.3.2 Hydrogen bonds involving sidechains 3.3.3 Salt bridges 3.3.4 Hydrogen bond networks 3.4 Hydrogen Bonds and Protein Stability 3.4.1 Hydrogen bonds within the polypeptide chain, role in folding 3.4.2 Hydrogen bonds involving side chain, role in stability References 4. Hydrophobic Interactions 4.1 Nature of Hydrophobic Interactions 4.2 Water 4.2.1 Flickering clusters model of water 4.2.2 Hydrocarbons in water, iceberg model 4.3 Hydrophobic Effect 4.3.1 Oil drop in water 4.3.2 Experimental assessment of hydrophobicinteraction 4.4 Hydrophobic Interactions in Proteins 4.4.1 Additivity of hydrophobic interactions 4.4.2 Solvent accessibility 4.4.3 Evaluation of hydrophobic interactions 4.4.4 Size of the hydrophobic core 4.4.5 Hydrophobic packing and packing defects References 5. Electrostatic Interactions 5.1 Debye-Hückel Theory 5.1.1 Poisson-Boltzmann equation 5.1.2 Parameter of Debye 5.1.3 The electrostatic potential of an ion in solution 5.1.4 Extension for proteins 5.2 Ion-solvent Interactions 5.2.1 Bom model 5.2.2 Application of the Bom model for proteins: Why do charges tend to be on the protein surface? 5.2.3 Generalised Bom theoryfor proteins 65 66 73 77 81 83 83 86 88 90 94 95 97 100 102 102 103 104 107 109 109 110 114 115 117 123 128 133 139 141 142 142 147 150 152 152 153 157 159
Contents 5.3 Calculation of Electrostatic Interactions in Proteins 5.3.1 The protein molecule as a dielectric material 5.3.2 Dielectric model for calculation of electrostatic interactions in proteins 5.3.3 Numerical solution of the Poisson-Boltzmann equation, finite difference method 5.3.4 Boundary conditions 5.3.5 Electrostatic potential calculated by means of the finite difference method References xvii 165 165 171 174 183 186 190 6. Ionisation Equilibria in Protein 6.1 Why Does One Need to Know Ionisation Equilibria? 6.2 Basic Definitions 6.2.1 Protonation/deprotonation equilibria 6.2.2 Henderson-Hasselbalch equation 6.2.3 Degree of deprotonation and degree of protonation 6.2.4 Ionisation equilibrium constants of model compounds 6.3 Factors Determining Ionisation Equilibria in Proteins 6.3.1 Desolvation 6.3.1.1 Bom energy 6.3.1.2 Calculation of the Bom energy 6.3.2 Interactions with the protein permanent charges 6.3.3 Definition of intrinsic pK 6.3.4 Charge-charge interactions 6.4 Combinatorial Problem 6.4.1 Solution based on the Boltzmann weighted sum 6.4.2 Solution based on the Monte Carlo simulation 6.5 Cooperative Ionisation References 192 194 196 196 197 199 202 205 207 207 210 213 214 215 217 219 223 226 232 7. Conformational Flexibility 7.1 Location Variation of Polar Hydrogen Atoms 7.1.1 Titratable and pH-sensitive sites 7.1.2 Microscopic pK 7.1.3 Population of the microscopic states 7.2 Examples for pH-Dependent Hydrogen Bonding 7.2.1 Ionisation properties of Asp76 in ribonucléase T і 7.2.2 Hydrogen bond rearrangement related to protein fonction 7.3
Conformational Flexibility Involving Non-Hydrogen Atoms 7.3.1 Conformations generated by means of molecular dynamics simulation 7.3.2 Average pR values 233 233 234 235 240 246 246 251 257 258 267
Non-Covalent Interactions in Proteins xviii 7.3.3 Desolvation and charge-dipole energy compensation 7.3.4 Dynamics of salt bridges References 275 280 283 8. Protein States 8.1 Folded and Unfolded States 8.2 Misfolded Proteins 8.3 Metamorphic Proteins 8.4 Intrinsically Disordered Proteins References 284 284 287 291 296 305 9. Modelling of Electrostatic Interactions in Unfoided Proteins 9.1 Spherical Model of Unfolded Proteins 9.2 Size of the Dielectric Sphere 9.2.1 Radius of gyration vs hydrodynamic radius 9.2.2 Modelling of electrostatic interactions 9.3 Average Distance Between Charges 9.4 Ionisation Equilibria in Unfolded Proteins References 307 307 309 3 09 ЗП 320 322 326 10. 328 328 329 335 342 343 346 351 352 358 Protein Stability 10.1 Definitions 10.2 Kinetic Stability 10.3 pH Dependence of Protein Stability 10.4 Temperature Dependence of Protein Stability 10.4.1 Differential scanning microcalorimetry 10.4.2 Thermodynamic analysis 10.4.3 Cold dénaturation 10.5 Thermal Stability of Proteins References Appendix A Basic Concepts in Thermodynamics and Statistical Physics A. 1 Subject and Main Definitions of Thermodynamics A.1.1 Macroscopic system A. 1.2 Equilibrium, thermodynamic state of a system A. 1.3 Process A.1.4 Function of state A. 1.5 Intensive and extensive parameters A. 1.6 First law of thermodynamics, energy A.1.7 Heat and work A. 1.8 Internal energy A. 1.9 Enthalpy 359 359 360 360 361 361 363 363 364 365 367
Contents A.1.10 АЛЛІ Second law of thermodynamics, entropy Connection between the first and second laws of thermodynamics АЛЛ2 Free energy АЛ Л 3 Processes at constant pressure and temperature АЛЛ4 Heat capacity АЛЛ5 Direction of processes АЛЛ6 Temperature A.2 Subject and Main Definitions of Statistical Thermodynamics А.2Л Postulates of statistical thermodynamics A.2.2 Ensemble average A.2.3 Partition function Appendix В Electric Dipoles ВЛ Definition B.2 Electrostatic Field of a Dipole 368 375 375 377 377 380 381 382 383 385 392 396 396 402 Appendix C СЛ C.2 C.3 C.4 Index Nabla-operator, Solutions of the Poisson-Boltzmann Equations Laplace Operator Spherical Symmetrical Form of the Laplace and Poisson-Boltzmann Equations Solution of Laplace and Poisson-BoltzmannEquation in the Debye-Hiickel Theory С.ЗЛ Boundary conditions C.3.2 Solution Gauss Theorem xix 405 405 406 410 410 412 415 417
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| adam_txt |
Contents Dedication Preface to the Second Edition Preface to the First Edition About the Author vii ix xi xiii 1. Introduction 1.1 Some Historical Notes 1.2 Overview of Protein Structural Elements and Basic Definitions 1.2.1 The amino acids 1.2.2 The polypeptide chain 1.3 Non-Covalent Interactions and Structure-Function Relationshipsin Proteins 1.3.1 Some comments on Anfinsen's dogma 1.3.2 Experimental measurements of non-covalent interactions in proteins References 1 4 13 14 19 22 23 24 25 2. Van der Waals Interactions 2.1 Observation of van der Waals Interactions 2.2 Nature of van der Waals Interactions 2.2.1 Dispersion forces 2.2.2 Dipole-dipole interactions 2.2.3 Dipole-induced dipole interactions 2.2.4 Repulsive interactions 2.3 Potential Functions for Application in Proteins 2.4 Approximation for Polyatomic Systems References 27 28 30 31 44 49 51 54 57 59 3. Hydrogen Bonds 3.1 Nature of Hydrogen Bonds 3.1.1 Proton donors, electronegativity 3.1.2 Proton acceptors 60 60 61 64 XV
Non-Covalent Interactions in Proteins XVI 3.2 Geometry and Strengthof Hydrogen Bond 3.2.1 Directionality 3.2.2 Hydrogen bond length 3.2.3 Hydrogen bond strength 3.2.4 Hydrogen bond potential functions 3.3 Hydrogen Bonds in Proteins 3.3.1 Secondary structure elements 3.3.2 Hydrogen bonds involving sidechains 3.3.3 Salt bridges 3.3.4 Hydrogen bond networks 3.4 Hydrogen Bonds and Protein Stability 3.4.1 Hydrogen bonds within the polypeptide chain, role in folding 3.4.2 Hydrogen bonds involving side chain, role in stability References 4. Hydrophobic Interactions 4.1 Nature of Hydrophobic Interactions 4.2 Water 4.2.1 Flickering clusters model of water 4.2.2 Hydrocarbons in water, iceberg model 4.3 Hydrophobic Effect 4.3.1 Oil drop in water 4.3.2 Experimental assessment of hydrophobicinteraction 4.4 Hydrophobic Interactions in Proteins 4.4.1 Additivity of hydrophobic interactions 4.4.2 Solvent accessibility 4.4.3 Evaluation of hydrophobic interactions 4.4.4 Size of the hydrophobic core 4.4.5 Hydrophobic packing and packing defects References 5. Electrostatic Interactions 5.1 Debye-Hückel Theory 5.1.1 Poisson-Boltzmann equation 5.1.2 Parameter of Debye 5.1.3 The electrostatic potential of an ion in solution 5.1.4 Extension for proteins 5.2 Ion-solvent Interactions 5.2.1 Bom model 5.2.2 Application of the Bom model for proteins: Why do charges tend to be on the protein surface? 5.2.3 Generalised Bom theoryfor proteins 65 66 73 77 81 83 83 86 88 90 94 95 97 100 102 102 103 104 107 109 109 110 114 115 117 123 128 133 139 141 142 142 147 150 152 152 153 157 159
Contents 5.3 Calculation of Electrostatic Interactions in Proteins 5.3.1 The protein molecule as a dielectric material 5.3.2 Dielectric model for calculation of electrostatic interactions in proteins 5.3.3 Numerical solution of the Poisson-Boltzmann equation, finite difference method 5.3.4 Boundary conditions 5.3.5 Electrostatic potential calculated by means of the finite difference method References xvii 165 165 171 174 183 186 190 6. Ionisation Equilibria in Protein 6.1 Why Does One Need to Know Ionisation Equilibria? 6.2 Basic Definitions 6.2.1 Protonation/deprotonation equilibria 6.2.2 Henderson-Hasselbalch equation 6.2.3 Degree of deprotonation and degree of protonation 6.2.4 Ionisation equilibrium constants of model compounds 6.3 Factors Determining Ionisation Equilibria in Proteins 6.3.1 Desolvation 6.3.1.1 Bom energy 6.3.1.2 Calculation of the Bom energy 6.3.2 Interactions with the protein permanent charges 6.3.3 Definition of intrinsic pK 6.3.4 Charge-charge interactions 6.4 Combinatorial Problem 6.4.1 Solution based on the Boltzmann weighted sum 6.4.2 Solution based on the Monte Carlo simulation 6.5 Cooperative Ionisation References 192 194 196 196 197 199 202 205 207 207 210 213 214 215 217 219 223 226 232 7. Conformational Flexibility 7.1 Location Variation of Polar Hydrogen Atoms 7.1.1 Titratable and pH-sensitive sites 7.1.2 Microscopic pK 7.1.3 Population of the microscopic states 7.2 Examples for pH-Dependent Hydrogen Bonding 7.2.1 Ionisation properties of Asp76 in ribonucléase T і 7.2.2 Hydrogen bond rearrangement related to protein fonction 7.3
Conformational Flexibility Involving Non-Hydrogen Atoms 7.3.1 Conformations generated by means of molecular dynamics simulation 7.3.2 Average pR values 233 233 234 235 240 246 246 251 257 258 267
Non-Covalent Interactions in Proteins xviii 7.3.3 Desolvation and charge-dipole energy compensation 7.3.4 Dynamics of salt bridges References 275 280 283 8. Protein States 8.1 Folded and Unfolded States 8.2 Misfolded Proteins 8.3 Metamorphic Proteins 8.4 Intrinsically Disordered Proteins References 284 284 287 291 296 305 9. Modelling of Electrostatic Interactions in Unfoided Proteins 9.1 Spherical Model of Unfolded Proteins 9.2 Size of the Dielectric Sphere 9.2.1 Radius of gyration vs hydrodynamic radius 9.2.2 Modelling of electrostatic interactions 9.3 Average Distance Between Charges 9.4 Ionisation Equilibria in Unfolded Proteins References 307 307 309 3 09 ЗП 320 322 326 10. 328 328 329 335 342 343 346 351 352 358 Protein Stability 10.1 Definitions 10.2 Kinetic Stability 10.3 pH Dependence of Protein Stability 10.4 Temperature Dependence of Protein Stability 10.4.1 Differential scanning microcalorimetry 10.4.2 Thermodynamic analysis 10.4.3 Cold dénaturation 10.5 Thermal Stability of Proteins References Appendix A Basic Concepts in Thermodynamics and Statistical Physics A. 1 Subject and Main Definitions of Thermodynamics A.1.1 Macroscopic system A. 1.2 Equilibrium, thermodynamic state of a system A. 1.3 Process A.1.4 Function of state A. 1.5 Intensive and extensive parameters A. 1.6 First law of thermodynamics, energy A.1.7 Heat and work A. 1.8 Internal energy A. 1.9 Enthalpy 359 359 360 360 361 361 363 363 364 365 367
Contents A.1.10 АЛЛІ Second law of thermodynamics, entropy Connection between the first and second laws of thermodynamics АЛЛ2 Free energy АЛ Л 3 Processes at constant pressure and temperature АЛЛ4 Heat capacity АЛЛ5 Direction of processes АЛЛ6 Temperature A.2 Subject and Main Definitions of Statistical Thermodynamics А.2Л Postulates of statistical thermodynamics A.2.2 Ensemble average A.2.3 Partition function Appendix В Electric Dipoles ВЛ Definition B.2 Electrostatic Field of a Dipole 368 375 375 377 377 380 381 382 383 385 392 396 396 402 Appendix C СЛ C.2 C.3 C.4 Index Nabla-operator, Solutions of the Poisson-Boltzmann Equations Laplace Operator Spherical Symmetrical Form of the Laplace and Poisson-Boltzmann Equations Solution of Laplace and Poisson-BoltzmannEquation in the Debye-Hiickel Theory С.ЗЛ Boundary conditions C.3.2 Solution Gauss Theorem xix 405 405 406 410 410 412 415 417 |
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| illustrated | Illustrated |
| index_date | 2024-07-03T18:48:19Z |
| indexdate | 2024-07-10T09:18:08Z |
| institution | BVB |
| isbn | 9789811228087 |
| language | English |
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| physical | xix, 424 Seiten Illustrationen, Diagramme |
| publishDate | 2021 |
| publishDateSearch | 2021 |
| publishDateSort | 2021 |
| publisher | World Scientific |
| record_format | marc |
| spelling | Karshikoff, Andrey Verfasser aut Non-covalent interactions in proteins Andrey Karshikoff (Bulgarian Academy of Sciences, Bulgaria) Second edition New Jersey ; London ; Singapore World Scientific [2021] xix, 424 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Proteine - Elektrostatische Wechselwirkung Proteine - Schwache Wechselwirkung Proteine - Van-der-Waals-Kraft Proteins Analysis Proteins Structure Elektrostatische Wechselwirkung (DE-588)4329545-9 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf Van-der-Waals-Kraft (DE-588)4187406-7 gnd rswk-swf Schwache Wechselwirkung (DE-588)4129644-8 gnd rswk-swf Proteine (DE-588)4076388-2 s Schwache Wechselwirkung (DE-588)4129644-8 s DE-604 Van-der-Waals-Kraft (DE-588)4187406-7 s Elektrostatische Wechselwirkung (DE-588)4329545-9 s b DE-604 Erscheint auch als Online-Ausgabe 978-981-122-809-4 Erscheint auch als Online-Ausgabe 978-981-122-810-0 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=033028276&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Karshikoff, Andrey Non-covalent interactions in proteins Proteine - Elektrostatische Wechselwirkung Proteine - Schwache Wechselwirkung Proteine - Van-der-Waals-Kraft Proteins Analysis Proteins Structure Elektrostatische Wechselwirkung (DE-588)4329545-9 gnd Proteine (DE-588)4076388-2 gnd Van-der-Waals-Kraft (DE-588)4187406-7 gnd Schwache Wechselwirkung (DE-588)4129644-8 gnd |
| subject_GND | (DE-588)4329545-9 (DE-588)4076388-2 (DE-588)4187406-7 (DE-588)4129644-8 |
| title | Non-covalent interactions in proteins |
| title_auth | Non-covalent interactions in proteins |
| title_exact_search | Non-covalent interactions in proteins |
| title_exact_search_txtP | Non-covalent interactions in proteins |
| title_full | Non-covalent interactions in proteins Andrey Karshikoff (Bulgarian Academy of Sciences, Bulgaria) |
| title_fullStr | Non-covalent interactions in proteins Andrey Karshikoff (Bulgarian Academy of Sciences, Bulgaria) |
| title_full_unstemmed | Non-covalent interactions in proteins Andrey Karshikoff (Bulgarian Academy of Sciences, Bulgaria) |
| title_short | Non-covalent interactions in proteins |
| title_sort | non covalent interactions in proteins |
| topic | Proteine - Elektrostatische Wechselwirkung Proteine - Schwache Wechselwirkung Proteine - Van-der-Waals-Kraft Proteins Analysis Proteins Structure Elektrostatische Wechselwirkung (DE-588)4329545-9 gnd Proteine (DE-588)4076388-2 gnd Van-der-Waals-Kraft (DE-588)4187406-7 gnd Schwache Wechselwirkung (DE-588)4129644-8 gnd |
| topic_facet | Proteine - Elektrostatische Wechselwirkung Proteine - Schwache Wechselwirkung Proteine - Van-der-Waals-Kraft Proteins Analysis Proteins Structure Elektrostatische Wechselwirkung Proteine Van-der-Waals-Kraft Schwache Wechselwirkung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=033028276&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT karshikoffandrey noncovalentinteractionsinproteins |