Structure and function of intrinsically disordered proteins:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Boca Raton [u.a.]
CRC Press
2010
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Includes bibliographical references and index |
| Beschreibung: | XXVII, 331 S. Ill., graph. Darst. |
| ISBN: | 9781420078923 1420078925 |
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| 245 | 1 | 0 | |a Structure and function of intrinsically disordered proteins |c Peter Tompa |
| 264 | 1 | |a Boca Raton [u.a.] |b CRC Press |c 2010 | |
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| adam_text | Titel: Structure and function of intrinscially [intrinsically] disordered proteins
Autor: Tompa, Peter
Jahr: 2010
Contents
Foreword, Professor Sir Alan Fersht xv
Preface xvii
About the Author xix
Acknowledgments xxi
Abbreviations and Acronyms xxiii
1 Principles of Protein Structure and Function 1
1.1 Physical Forces That Shape Protein Structure 1
1.2 Primary Structure: Amino Acid Sequence 3
1.3 Protein-Coding Genes 4
1.4 Post-Translational Modifications of Amino Acids 5
1.5 Hierarchical Description of Structure 6
1.5.1 Secondary Structure 6
1.5.2 Tertiary Structure 9
1.5.3 Quaternary Structure 11
1.6 Folding of a Protein 12
1.6.1 Thermodynamic Aspects of Protein Folding 12
1.6.2 Kinetic Aspects of Protein Folding 13
1.6.3 Mechanism of Protein Folding 14
1.6.4 Folding and Chaperones 14
1.7 Unfolding of a Protein: Lessons from Polymer Theory 15
1.8 The Limits of Global Descriptions of the Unfolded State 17
1.9 Databases of Proteins and Protein Structures 17
1.10 DisProt: The Database of Disordered Proteins 18
1.11 The Classical Structure-Function Paradigm 18
2 A Brief History of Protein Disorder 21
2.1 Can We Define Disorder? 21
2.2 The History of Disorder 22
2.2.1 The Legacy of the Lock-and-Key Hypothesis 22
2.2.2 Structural Adaptability of Binding Sites 23
2.2.3 Polymer Theory and Protein Folding 23
2.2.4 Caseins Are Different 24
2.2.5 If a Protein Does Not Crystallize 24
2.2.6 The Advent of NMR 25
2.3 So We Have Disordered Proteins 27
vii
viii Contents
3 Indirect Techniques for Recognizing and Characterizing Protein
Disorder 31
3.1 Resistance to Heat 31
3.2 Resistance to Chemical Denaturation 33
3.3 Unusual SDS-PAGE Mobility 33
3.4 Enhanced Proteolytic Sensitivity 34
3.5 Limited Proteolysis and Local Structure 35
3.6 Differential Scanning Calorimetry 35
3.6.1 Transition to a More Ordered State 37
3.6.2 Residual Structure in Calpastatin 37
3.7 Isothermal Titration Calorimetry 37
3.7.1 The Energetics of Binding of a PPII Helix to Its
Cognate SH3 Domain 38
3.7.2 Binding of the KID Domain of p27K P1 to Cyclin A-Cdk2 38
3.8 Chemical Cross-Linking 40
3.9 H/D Exchange 41
4 Hydrodynamic Techniques 43
4.1 Gel Filtration (Size-Exclusion) Chromatography 43
4.2 Dynamic Light Scattering 45
4.3 Analytical Ultracentrifugation 46
4.4 Small-Angle X-Ray Scattering 47
4.4.1 Measles Virus Nucleoprotein 50
4.4.2 Bacterial Cellulase 51
4.4.3 p53 52
4.5 Pulsed-Field Gradient NMR 53
5 Spectroscopic Techniques for Characterizing Disorder 55
5.1 X-Ray Crystallography 55
5.2 Fluorescence Spectroscopy 57
5.2.1 UV Fluorescence 58
5.2.2 Fluorescence Quenching 58
5.2.3 ANS Binding 60
5.2.4 Fluorescence Resonance Energy Transfer 60
5.2.5 Fluorescence Correlation Spectroscopy 61
5.2.5.1 Dimensions of an IDP and the Effect of
Crowding 61
5.2.5.2 Internal Protein Dynamics 62
5.3 Fourier-Transform Infrared Resonance Spectroscopy 62
5.4 Circular Dichroism 63
5.5 Raman Optical Activity Spectroscopy 65
5.6 Electron Paramagnetic Resonance Spectroscopy 66
5.7 Electron Microscopy 69
5.8 Atomic Force Microscopy 71
5.8.1 Matrix Metalloproteinase 9 72
5.8.2 oc-Synuclein 72
___ Contents ix
6 Nuclear Magnetic Resonance 73
6.1 Basic Principles 73
6.2 Global Characterization by NMR 74
6.2.1 1-D HNMR 74
6.2.2 Wide-Line NMR 75
6.2.3 Pulsed-Field Gradient NMR 76
6.2.4 HSQC 76
6.3 Sequence-Specific Structural Information 78
6.3.1 Chemical Shifts 79
6.3.2 Dynamic Information from Relaxation Data 79
6.3.3 Distance Information from NOE 81
6.3.4 Coupling Constants 82
6.4 Special Applications 83
6.4.1 Combinations with MD 83
6.4.2 Amide Proton Exchange Rate 83
6.4.3 In-Cell NMR 84
7 Proteomic Approaches for the Identification of IDPs 85
7.1 Expectations and Limitations of Proteomic Studies 85
7.2 2DE-MS Identification of Proteins in Extracts Enriched
for Disorder 86
7.3 Native/Urea 2DE Provides Direct Information on Disorder 88
8 IDPs under Conditions Approaching In Vivo 91
8.1 Macromolecular Crowding in the Cell 91
8.2 In Vitro Approaches to Mimicking Crowding Conditions 92
8.3 The State of IDPs In Vivo 95
8.3.1 Proteasomal Degradation 95
8.3.2 In-Cell NMR 97
8.4 Physiological Half-Life of IDPs: No Signs of Rapid Degradation 99
8.5 Indirect Considerations Underscoring Disorder of IDPs In Vivo 100
9 Prediction of Disorder 103
9.1 General Points 103
9.2 Propensity-Based Predictors 103
9.2.1 Prediction of Low-Complexity Regions 106
9.2.2 Charge-Hydropathy Plot 106
9.2.3 Prediction of Globularity and Disorder 107
9.2.4 Composition and Hydrophobic Cluster Analysis 108
9.3 Machine-Learning Algorithms 109
9.3.1 Neural Networks 109
9.3.2 Support-Vector Machines 110
9.4 Prediction Based on Interresidue Contacts 111
9.4.1 Contact Numbers of Amino Acids 111
9.4.2 Estimating Pair-Wise Interresidue Interaction Energies 112
9.4.3 Predictor of Contact Potentials 112
x Contents
9.5 Prediction of Short and Long Regions of Disorder Separately 112
9.6 Combination of Predictors: Meta-Servers 114
9.7 Prediction of Functional Motifs In IDPs 115
9.8 Comparison of the Accuracy of Predictors:
The CASP Experiment 116
9.9 A Better Target Prioritization in Structural Genomics 119
10 Structure of IDPs 121
10.1 Primary Structure of Disordered Proteins 121
10.1.1 Amino Acid Composition 121
10.1.2 Sequence Features Characterizing Disorder 123
10.1.3 Flavors of Disorder? 124
10.2 Secondary Structure of Disordered Proteins 125
10.2.1 Secondary Structure in Solution State: Signs of
Transient Order 125
10.2.2 A Lot of PPII Helix Conformation 126
10.2.3 Secondary Structure in Solution State:
Sequence-Specific Information 127
10.2.3.1 p27«P1 127
10.2.3.2 CREBKID 130
10.2.3.3 Tau Protein 131
10.2.3.4 Fibronectin-Binding Protein A 131
10.2.3.5 a-Synuclein 132
10.2.3.6 p53 132
10.2.3.7 Calpastatin 132
10.2.4 Secondary Structure in the Bound State 133
10.3 Ambiguity in Structure 134
10.3.1 Chameleon Sequences 134
10.3.2 Dual-Personality Sequences 135
10.3.3 The Twilight Zone between Order and Disorder 135
10.4 Tertiary Structure: Global Features of IDP Structures 136
10.4.1 Hydrodynamic Description 136
10.4.2 Spectroscopic Approaches 137
10.4.3 Global Structure: Is It Related to the Structure in the
Bound State? 139
10.5 Dynamics of IDP Structure: The Time-Course of Fluctuations
within the Ensemble 140
10.5.1 The Importance of Dynamics in Structural
Descriptions 140
10.5.1.1 Local/Segmental Motions 140
10.5.1.2 Restricted Segmental Motions 141
10.5.1.3 Reduced Local Motion Signals Transient
Structural Elements 141
10.5.2 A Reduction in Motility Signals Disorder-to-Order
Transition 142
10.6 A Readout of Structure: The Hydrate Layer of IDPs 142
Contents xi
11 Biological Processes Enriched in Disorder 143
11.1 Biological Functions Enriched in Disorder 143
11.2 Disorder in Transcription/Transcription Regulation 145
11.2.1 Transcription Factors 145
11.2.2 Transcription Co-Activators 146
11.2.3 Disorder in the Core Apparatus 148
11.3 Disorder in Signaling Proteins 149
11.3.1 Receptors and Membrane Proteins 149
11.3.2 Scaffold Proteins and Hub Proteins 151
11.3.3 Regulation of the Cell Cycle 152
11.4 Nucleic Acid-Containing Organells 152
11.4.1 Ribosome 152
11.4.2 Disorder in Chromatin Organization 153
11.4.2.1 Histones 153
11.4.2.2 Other Chromatin Organizing Proteins 154
11.5 Disorder in RNA-Binding Proteins: Transcription and RNA Folding 155
11.6 Cytoskeletal Proteins 157
11.6.1 Microfilaments 157
11.6.2 Intermediate Filaments 158
11.6.3 Microtubules 159
11.7 Disorder in Stress Proteins 159
11.8 Disorder and Metal Binding 160
11.9 Disorder and Enzyme Activity 161
11.10 Is There a Link between the Pattern of Disorder and Function? 162
12 Molecular Functions of Disordered Proteins 163
12.1 Entropic Chain Functions 163
12.1.1 Linkers and Spacers 163
12.1.2 Entropic Clocks 165
12.1.3 Entropic Springs 166
12.1.4 Entropic Bristles/Brushes 166
12.2 Display Site Functions 168
12.2.1 Phosphorylation Sites 168
12.2.2 Sites of Proteolytic Processing 170
12.2.3 Ubiquitination Sites 171
12.2.4 Acetylation Sites 172
12.3 Chaperone Functions 172
12.3.1 Disorder in Protein Chaperones 174
12.3.2 Disorder in RNA Chaperones 174
12.4 Effector Functions 176
12.4.1 Inhibitors 177
12.4.2 Activators 177
12.5 Scavenger Functions 178
12.5.1 Salivary Proline-Rich Glycoproteins 178
12.5.2 Caseins 178
12.5.3 Calsequestrin 179
xii Contents
12.6 Assembler Functions 179
12.6.1 Targeting Activity 179
12.6.2 Assembling Complexes 180
12.6.2.1 HMGA, a Fully Disordered Hub Protein 183
12.6.2.2 MDM2, a Partially Disordered Hub Protein 183
12.6.2.3 Calmodulin, an Ordered Hub Protein 184
12.6.2.4 Disorder and Complex Size 185
12.6.2.5 Scaffold Proteins 185
12.7 Prion Functions 187
12.7.1 Sup35 187
12.7.2 Cytoplasmic Polyadenylation Element Binding Protein 188
13 Evolution and Prevalence of Disorder 189
13.1 Phylogenetic Distribution of Disorder 189
13.1.1 Predicted Disorder in Genomes and Proteomes 189
13.1.2 The Origin of Disordered Proteins in Eukaryotes 191
13.1.3 The Generation of Disordered Domains by
Gene Duplication and Module Exchange 192
13.2 Fast Evolution of IDPs by Point Mutations 193
13.2.1 Neutrality in the Evolution of IDPs 194
13.2.2 Disordered Regions May Also Be Conserved 195
13.3 Fast Evolution of IDPs by Repeat Expansion 195
13.3.1 Micro-and Minisatellites in Protein Evolution 196
13.3.1.1 Mechanisms of Repeat Expansion 197
13.3.1.2 Tandem Repeats in the CTD of RNA
Polymerase II 198
13.3.1.3 Tandem Repeats in the PEVK
Region of Titin 198
13.3.1.4 Tandem Repeats in Prion Protein 199
13.3.2 A Functional Model of Repeat Expansion in IDPs 199
13.4 Fast Evolution and Functionality of Disordered Proteins 200
13.4.1 Retention of Entropic-Chain Functions and
Recognition Functions 200
13.4.2 Recognition Another Way: The Lessons from Fuzziness 202
13.4.3 Co-Evolution of IDPs and Their Partners 202
13.5 Structural Variability and Evolvability of New Functions 203
14 Extension of the Structure-Function Paradigm 205
14.1 Functions That Stem Directly from the Disordered State 205
14.2 Recognition Functions: Recognition by Short Motifs 206
14.2.1 Preformed Structural Elements 206
14.2.2 Linear Motifs 208
14.2.3 Molecular Recognition Elements/Features 210
14.2.4 Recognition by Domain-Sized Motifs and
Mutual Folding 210
Contents xiii
14.2.5 Recognition Interfaces 212
14.2.6 Unification of Concepts? 214
14.3 Disorder-to-Order Transition in Recognition: Mechanistic and
Thermodynamic Aspects 214
14.3.1 Site-Directed Mutagenesis Studies of Induced Folding 215
14.3.2 Molecular Dynamics Simulations of Induced Folding 216
14.3.3 NMR Studies of the Mechanism of Induced Folding 217
14.3.4 The Analogy of Folding and Induced Folding 218
14.4 Recognition Functions: Uncoupling Specificity from Binding
Strength 219
14.4.1 Disorder May Contribute to Recognition of
Specific Sites 219
14.4.2 Disorder May Make Interactions Weaker 220
14.4.3 Strong Multivalent Binding and Weak
Aspecific Binding 220
14.5 Implications of Disorder for the Kinetics of Interactions 221
14.5.1 Primary Contact Sites 222
14.5.2 Fly-Casting in Recognition 222
14.6 Adaptability and Moonlighting 223
14.7 Nested Interfaces 225
14.8 Disorder in the Bound State: Fuzziness 226
14.8.1 Structural Polymorphism in the Bound State 226
14.8.2 Clamp-Type of Fuzziness 227
14.8.3 Flanking-Type of Fuzziness 228
14.8.4 Random-Type of Fuzziness 228
14.9 Processivity of Binding 229
14.10 Sequence Independence In Recognition 230
14.11 Ultrasensitivity of Recognition 230
14.11.1 Recognition of Sid by Cdc4 231
14.11.2 Regulation of CFTR by Its Disordered R Domain 231
14.11.3 Electrostatics in Ultrasensitivity 232
14.12 Signal Propagation in the Structural Ensemble of IDPs 232
14.12.1 The Signaling Conduit P27K|p] 232
14.12.2 Tailored Auto-Activation of WASP 233
14.12.3 Allostery Mediated by Order-Disorder Transitions 234
14.13 Disorder and Alternative Splicing 234
14.14 Molecular Mimicry by a Disordered Region 235
14.15 Entropy Transfer in Chaperone Action 235
15 Structural Disorder and Disease 237
15.1 Structural Disorder and Cancer 237
15.1.1 Disorder in Cancer-Associated Proteins 237
15.1.2 P53 238
15.1.3 Cip/Kip Cdk Inhibitors 240
15.1.4 Breast-Cancer! 242
xiv Contents
15.1.5 Securin (PTTG) 243
15.1.6 Disorder in Proteins Generated by Chromosomal
Translocations 244
15.2 Structural Disorder in Proteins Involved in Cardiovascular
Diseases, Diabetes, and Autoimmune Diseases 245
15.3 Structural Disorder and Neurodegenerative Diseases 246
15.3.1 Alzheimer s Disease 248
15.3.1.1 A(3Peptide 248
15.3.1.2 Tau Protein 248
15.3.2 Parkinson s Disease 249
15.3.2.1 oc-Synuclein (NACP) 250
15.3.3 Glutamine-Repeat Diseases 251
15.3.3.1 Huntington s Disease 252
15.3.3.2 Huntingtin 253
15.3.4 Prion Diseases 253
15.3.4.1 Prion Protein 254
15.4 Systemic Amyloidoses 255
15.5 Common Themes in Amyloid Formation 255
15.5.1 Kinetics of Amyloid Formation • 256
15.5.2 Disorder in Amyloidogenic Proteins 256
15.5.3 The Structure of the Amyloid 257
15.5.4 Molecular Mechanism of Transition to the
Amyloid State 258
15.6 Does Structural Disorder Pose a Danger? 259
15.7 Disorder in Pathogenic Organisms 260
15.8 Rational Drug Design Based on Protein Disorder 262
References 265
Index 313
|
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| id | DE-604.BV025602697 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:37:18Z |
| institution | BVB |
| isbn | 9781420078923 1420078925 |
| language | English |
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| physical | XXVII, 331 S. Ill., graph. Darst. |
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| publisher | CRC Press |
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| spelling | Tompa, Peter Verfasser aut Structure and function of intrinsically disordered proteins Peter Tompa Boca Raton [u.a.] CRC Press 2010 XXVII, 331 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Unfolded Proteins (DE-588)4730138-7 gnd rswk-swf Proteinfaltung (DE-588)4324567-5 gnd rswk-swf Unfolded Proteins (DE-588)4730138-7 s Proteinfaltung (DE-588)4324567-5 s DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020197971&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Tompa, Peter Structure and function of intrinsically disordered proteins Unfolded Proteins (DE-588)4730138-7 gnd Proteinfaltung (DE-588)4324567-5 gnd |
| subject_GND | (DE-588)4730138-7 (DE-588)4324567-5 |
| title | Structure and function of intrinsically disordered proteins |
| title_auth | Structure and function of intrinsically disordered proteins |
| title_exact_search | Structure and function of intrinsically disordered proteins |
| title_full | Structure and function of intrinsically disordered proteins Peter Tompa |
| title_fullStr | Structure and function of intrinsically disordered proteins Peter Tompa |
| title_full_unstemmed | Structure and function of intrinsically disordered proteins Peter Tompa |
| title_short | Structure and function of intrinsically disordered proteins |
| title_sort | structure and function of intrinsically disordered proteins |
| topic | Unfolded Proteins (DE-588)4730138-7 gnd Proteinfaltung (DE-588)4324567-5 gnd |
| topic_facet | Unfolded Proteins Proteinfaltung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020197971&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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