Modular protein domains:
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| Format: | Buch |
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| Sprache: | English |
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Wiley-VCH
2005
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| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXII, 501 S. Ill., graph. Darst. |
| ISBN: | 352730813X |
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| 245 | 1 | 0 | |a Modular protein domains |c ed. by Giovanni Cesareni ... |
| 264 | 1 | |a Weinheim |b Wiley-VCH |c 2005 | |
| 300 | |a XXII, 501 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
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| 650 | 4 | |a Protein Structure, Tertiary | |
| 650 | 4 | |a Protein-protein interactions | |
| 650 | 4 | |a Proteins | |
| 650 | 4 | |a Proteomics | |
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| 700 | 1 | |a Cesareni, Giovanni |e Sonstige |0 (DE-588)129610607 |4 oth | |
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Datensatz im Suchindex
| _version_ | 1804133185060077568 |
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| adam_text | Contents
Preface V
List of Contributors XVII
Prologue: An Overview of Protein Modular Domains as Adaptors 1
Sir Tom L Blundell
1 The SH2 Domain: a Prototype for Protein Interaction Modules 5
Tony Pawson, Gerald D. Cish, and Piers Nash
1.1 The Multidomain Nature of Signaling Proteins and Identification
of the SH2 Domain 5
1.2 SH2 Domains as a Prototype for Interaction Domains 9
1.3 Structure and Binding Properties of SH2 Domains 9
1.4 Different Modes of SH2 Domain Phosphopeptide Recognition 12
1.5 Signaling Pathways and Networks 14
1.6 Plasticity of SH2 Domains 17
1.7 SH2 Domain Dimerization 19
1.8 Tandem SH2 Domains 20
1.9 Composite and Complex Interaction Domains 21
1.10 Allosteric Regulation 21
1.11 SH2 Domains and Disease 24
1.12 Summary 26
References 27
2 SH3 Domains 37
Bruce J. Mayer and Kalle Saksela
2.1 BriefOverview 37
2.2 Historical Perspective 39
2.2.1 Genetics to the Rescue 40
2.2.2 Structure and Specificity 41
2.3 Predicting Binding Partners 44
2.3.1 Core Peptide Docking vs. Extended Interactions 46
Modular Protein Domains. Edited by G. Cesareni, M. Gimona, M. Sudol, M. Yaffe
Copyright © 2005 WILEY VCH Verlag GmbH Co. KGaA, Weinheim
ISBN: 3 527 30813 X
2.3.2 Atypical SH3 Docking Motifs 49
2.4 Experimental Exploitation of SH3 Specificity 52
2.5 Conclusion 54
References 55
3 The WW Domain 59
Marias Sudol
3.1 Introduction and Brief History of Module Discovery 59
3.2 Structure of the WW Domain Ligand Complex 60
3.3 WW Domains and Human Diseases 62
3.3.1 From Liddle s Syndrome to Liddle s Disease 62
3.3.2 Amyloid Precursor Protein: APP and FE65 63
3.3.3 Dystrophin WW Domain and Muscular Dystrophy 64
3.4 Emerging Directions and Recent Developments 65
3.4.1 AxCell s Map 65
3.4.2 ErbB4 Receptor Protein Tyrosine Kinase and its WW Domain
containing Adaptor, YAP 65
3.4.3 Membrane Proteins with PPxYs Implicated in Cancer 67
3.5 Concluding Remarks 67
References 69
4 EVH1/WH1 Domains 73
Linda J. Ball, Urs Wiedemann, Jiirgen Zimmermann, and
Thomas Jarchau
4.1 Introduction 73
4.2 Occurrence and Distribution of EVH1 Domains 74
4.2.1 Proteins Containing EVH1 Domains 77
4.2.2 Modular Architecture of EVH1 containing Proteins:
Domain Location, Domain Combinations, and Copy Number 80
4.2.3 Classification of EVH1 Domains 82
4.3 Structures of EVH1 Domains and Their Complexes 83
4.3.1 High resolution Structures of EVH1 and Related Domains 83
4.3.2 Structures of EVH1 Complexes and Determinants of Ligand
Specificity 86
4.3.3 Comparisons with RanBDs, PTB Domains, and PH Domains 90
4.4 Biological Function and Signaling Pathways Involving EVH1
Domains 91
4.4.1 Ena/VASP Interactions 91
4.4.2 Homer/Vesl Interactions 92
4.4.3 WASP/N WASP Interactions 92
4.4.4 Spred Interactions 93
4.5 Emerging Research Directions and Recent Developments 94
4.5.1 Use of Sequence and Structural Data in Prediction of Binding
Partners 94
4.5.2 Use of Structural Data from Complexes to Guide the Rational Design
of New Ligands 94
4.6 Concluding Remarks 95
References 96
5 The CYF Domain 203
Christian Freund
5.1 Introduction 103
5.2 Structure of the CD2BP2 GYF Domain and Its Interaction
with the CD2 Signaling Peptide SHRPPPPGHRV 205
5.3 Molecular and Signaling Function of GYF Domains 107
5.3.1 Sequence Specificity of the CD2BP2 GYF Domain 107
5.3.2 Spliceosomal Proteins Contain Binding Motifs for CD2BP2 GYF 108
5.3.3 Phage Display of CD2BP2 GYF 108
5.3.4 Sequence Repetition in GYF Domain mediated Interactions 109
5.3.5 Functional Relevance of the CD2BP2 GYF Domain Interaction with
CD2 110
5.3.5.1 Competitive Binding of CD2BP2 GYF and Fyn SH3 to the CD2 Tail
in Vitro 110
5.3.5.2 In Vivo Compartmentalization of CD2 Binding Proteins 111
5.3.6 Other GYF Domain Containing Proteins 112
5.4 Emerging Research Directions and Recent Developments 113
5.5 Concluding Remarks 114
References 115
6 PTB Domains 117
Ben Margolis and Linton M. Traub
6.1 Introduction 127
6.2 Function of PTB Domain Proteins 118
6.2.1 Role of PTB Domain Proteins in Tyrosine Kinase Signaling 119
6.2.1.1 She 129
6.2.1.2 Proteins with PTB I Domains 229
6.2.1.3 Additional PTB Domain Proteins Involved in Tyrosine Kinase
Signaling 121
6.2.2 PTB Domain Proteins That Function Independent of
Phosphotyrosine 222
6.2.2.1 PTB Domain Proteins That Bind APP 222
6.2.2.2 PTB Domain Proteins That Bind Integrins 124
6.2.2.3 PTB Domain Proteins That Control Endocytosis 225
6.3 PTB Domain Structure 127
6.3.1 Broad Binding Specificity 229
6.3.2 Diverse Modes of Engagement 130
6.3.3 Phospholipid Binding 232
6.4 Conclusions 232
References 133
7 The FHA Domain 143
Daniel Durocher
7.1 Introduction 143
7.2 FHA Domain Structure 147
7.2.1 Topology 147
7.2.2 FHA Phosphopeptide Interaction 149
7.2.3 A Second Binding Interface? 150
7.2.4 The FHA Domain is Part of a Domain Superfamily 151
7.3 Molecular and Signaling Function 152
7.3.1 FHA Domain Can Regulate Protein Localization 152
7.3.2 FHA Domain Binding to Enzyme Substrates 152
7.3.3 FHA Domain Binding to Regulators 153
7.3.4 Reversible Protein Protein Interactions 153
7.3.5 FHA Domain as a Transcriptional Activator Domain 154
7.4 Emerging Research Direction 155
7.4.1 Bacterial FHA Domains 155
7.4.2 A Potential Role for FHA Domains During Innate Immunity? 156
7.4.3 FHA Domain and Phosphothreonine Proline Motifs 156
7.4.4 FHA Domain Chimeras as Phosphorylation Biosensors 157
7.5 Concluding Remarks 158
References 159
8 Phosphoserine/Threonine Binding Domains 163
Andrew E. H. Elia and Michael B. Yaffe
8.1 Introduction 163
8.2 The 14 3 3 Proteins 164
8.2.1 History and Functions 164
8.2.2 Structure and Binding 165
8.3 WW Domains 167
8.4 FHA Domains 168
8.5 WD40 Repeats of F box Proteins 170
8.6 Polo box Domains 172
8.7 Conclusions and Future Directions 174
References 175
9 The Eukaryotic Protein Kinase Domain 181
Arvin C. Dar, Leanne E. Wybenga Croot, and Frank Sicheri
9.1 Introduction 181
9.2 Architecture of the Kinase Domain 181
9.2.1 ATP Binding Pocket 183
9.2.2 Peptide Binding and Catalytic Residues 184
9.3 Catalytic Switching Mechanisms 185
9.3.1 Kinase Regulation by the A Loop 185
9.3.2 Regulation of Catalysis by Elements External to the Kinase Domain 187
9.3.2.1 Pseudosubstrate Regulation 188
9.3.2.2 Receptor Tyrosine Kinase Regulation by the Juxtamembrane Region 190
9.3.2.3 Intramolecular Regulation Involving Autonomously Folded Domains 191
9.4 Protein Kinase Substrate Recognition 193
9.4.1 Canonical Peptide Substrate Recognition 193
9.4.2 Phospho priming Dependent Substrate Recognition 195
9.4.3 Regulation of AGC Kinases by the Hydrophobic Motif 196
9.4.4 CDK Cyclin Interactions with Substrates Mediated through the
CY Motif 198
9.4.5 MAPK Docking Site Interactions:
Common Recognition Mechanisms for Substrates, Activators, and
Scaffolds 198
9.4.6 Substrate Recognition through a Phosphorylated Epitope in TGF|3 199
9.4.7 Substrate Recognition by the eIF2ct Protein Kinases:
Recognition of a Complex Epitope Presented by Globular Fold 200
9.5 Conclusions 201
References 201
10 Structure, Specificity, and Mechanism of Protein Lysine Methylation
by SET Domain Enzymes 211
James H. Hurley and Raymond C. Trievel
10.1 Discovery and Biology of SET Domains 211
10.2 Structure of the SET Domain 212
10.2.1 The SET Domain Fold 213
10.2.2 The Active Site 214
10.2.3 Interactions with Other Domains 215
10.3 Substrate Specificity and Catalytic Mechanism 217
10.3.1 Substrate Specificity 217
10.3.2 Catalytic Mechanism 219
10.3.3 Methylation Multiplicity 221
10.4 Emerging Directions and Conclusions 221
References 222
11 The Structure and Function of the Bromodomain 227
Kelley S. Yan and Ming Ming Zhou
11.1 Introduction 227
11.2 The Bromodomain Structure 229
11.3 The Bromodomain as an Acetyl lysine Binding Domain 230
11.3.1 Acetyl lysine Binding 230
11.3.2 Molecular Determinants of Ligand Specificity 232
11.4 Emerging Developments 234
11.5 Concluding Remarks 235
References 236
12 Chromo and Chromo Shadow Domains 241
Joel C. Eissenberg and Sepideh Khorasanizadeh
12.1 Introduction and Brief History of the Module s Discovery 241
12.2 Structures of the Chromo and Chromo Shadow Domains 242
12.3 Function of the Chromo Domain 246
12.4 Genetic, Cytological, and Molecular Properties of the Chromo
Domain 248
12.5 Emerging Research Directions and Recent Developments 250
References 251
13 PDZ Domains: Intracellular Mediators of Carboxy terminal Protein
Recognition and Scaffolding 257
Laurence A. Lasky, Nicholas J. Skelton, and Sachdev S. Sidhu
13.1 Introduction 257
13.2 Structural Analysis of PDZ Domains 259
13.3 Analysis of PDZ Domain Ligand Interactions with Mutagenesis
and Synthetic Peptides 261
13.4 Molecular and Signaling Functions of PDZ Domains 263
13.4.1 INAD as a Molecular Scaffold 263
13.4.2 LIN 7 Receptor Tyrosine Kinase Interactions and Subcellular
Localization 265
13.4.3 PDZ Domain Proteins and Epithelial Polarity Induction and
Maintenance 267
13.4.4 A Few Miscellaneous Examples: The Synapse, Disheveled,
CARD MAGUKs, and Beta Adrenergic Receptors 269
13.5 Concluding Remarks 272
References 273
14 EH Domains and Their Ligands 279
Brian K. Kay, Michael D. Scholle, and FredJ. Stevens
14.1 Introduction 279
14.2 EH Domain containing Proteins 279
14.3 Peptide Ligands 282
14.4 Cellular Ligands 284
14.5 Structures of the Domain and Its Ligands 285
14.6 Evolutionary Origins of the EH Domain 286
14.7 Functions of the EH Domain 288
References 289
15 Ubiquitin Binding Modules:
The Ubiquitin Network Beyond the Proteasome 291
Stefano Confalonieri and Pier Paolo Di Fiore
15.1 Introduction: The Ubiquitin System in Proteolysis and Beyond 291
15.2 CUE and UBA Domains 293
15.3 The Ubiquitin interacting Motif 299
15.4 The UEV Domain 302
15.5 The PAZ and NZF Domains 305
15.6 Ubiquitin based Networks 308
15.7 Conclusions 312
References 313
16 TheCalponin Homology (CH) Domain 321
Mario Gimona and Steven J. Winder
16.1 Introduction and Brief History 321
16.2 Structure of the Domain The CH Domain Fold 323
16.2.1 Structures of Single CH Domains 325
16.2.2 Structures of Tandem CH Domains 325
16.3 Molecular and Signaling Function 326
16.3.1 Actin binding Domains 326
16.3.2 Single EB type CH Domains Function as Microtubule Anchors 327
16.3.3 Kinases, Phospholipids, and Other Cytoskeletal Components 328
16.3.4 CH Domain containing Proteins and Human Diseases 330
16.3.4.1 The Dystrophin ABD and Muscular Dystrophy 330
16.3.4.2 The Filamin ABD and Otopalatodigital Syndromes 330
16.3.4.3 The a Actinin ABD and Glomerulosclerosis 330
16.3.4.4 The (i Spectrin ABD and Spherocytosis 331
16.4 Emerging Research Directions and Recent Developments 331
16.5 Concluding Remarks 332
References 332
17 PH Domains 337
Mark A. Lemmon and David Keleti
17.1 Introduction 337
17.2 PH Domain Structure and Phosphoinositide Binding 338
17.2.1 Overall Structure The PH Domain Fold 338
17.2.2 Structural Basis for Phosphoinositide Binding 340
17.2.2.1 High affinity PtdIns(4,5)P2 Binding 340
17.2.2.2 Low affinity PtdIns(4,5)P2 Binding 340
17.2.2.3 Specific Recognition of Phosphoinositide 3 Kinase Products 341
17.2.2.4 PH Domains with Other Phosphoinositide binding Specificities 345
17.2.2.5 Sequence Predictors of Phosphoinositide Binding 345
17.3 Molecular and Signaling Function of PH Domains 346
17.3.1 PH Domains as Phosphoinositide dependent Membrane targeting
Domains 346
17.3.1.1 PtdIns(4,5)P2 specific PH Domains 347
17.3.1.2 PI 3 kinase Product binding PH Domains 348
17.3.1.3 Membrane Targeting by PH Domains with Little Phosphoinositide
binding Specificity 349
17.3.2 Function of Low affinity PH Domains That Are Not Independently
Membrane Targeted 350
17.3.2.1 The Dynamin PH Domain 351
17.3.2.2 PH Domains of Dbl family Proteins 351
17.3.3 Protein Targets of PH Domains 353
17.3.3.1 Small GTPases as PH Domain Targets 353
17.3.3.2 Other Protein Targets of PH Domain Targets 354
17 .4 Emerging Research Directions and Recent Developments 356
References 357
18 ENTH and VHS Domains 365
Vimal Parkash, Olli Lohi, Ismo Virtanen, and Veli Pekka Lehto
18.1 Introduction 365
18.2 History of ENTH 366
18.3 Structure of ENTH Domains 369
18.4 Signaling and Molecular Functions of ENTH 371
18.5 History of VHS 374
18.6 Structure of VHS Domains 375
18.7 Function of GGA VHS Domains 377
18.8 Function of Non GGA VHS Domains 379
18.9 Involvement of ENTH and VHS Domains in Human Disease 380
18.10 Emerging Research Directions 380
18.11 Concluding Remarks 382
References 382
19 PX Domains 389
Matthew L Cheever and Michael Overduin
19.1 Introduction and History of the PX Domain Discovery 389
19.2 Structure of the PX Domain 392
19.2.1 Mechanism of PtdIns(3)P Coordination 394
19.3 Biological Function of the PX Domain 397
19.3.1 PI Binding Specificity 397
19.3.2 Synergistic Phospholipid Interactions 398
19.3.3 Membrane Insertion 398
19.3.4 Regulatory Protein Interactions 399
19.3.5 Signaling Pathways of the PX Proteins 400
19.4 Emerging Research Directions and Recent Developments 403
References 404
20 Peptide and Protein Repertoires for Global Analysis of Modules 409
Krzysztof Bialek, Andrzej Swistowski, and Ronald Frank
20.1 Introduction 409
20.2 Repertoires from Cell Extracts 410
20.3 Repertoires of Proteins Based on Expression Cloning of DNA
Libraries 410
20.3.1 Ligand Repertoires Used with the Yeast Two Hybrid System 411
20.3.2 Module Repertoires Used with the Yeast Two Hybrid System 412
20.3.3 Phage Expression Libraries of Ligands 413
20.3.4 Phage Expression Libraries of Modules 413
20.3.5 Phage Display of Protein Ligands 415
20.3.6 Phage Display of Protein Domains 415
20.3.7 Protein Arrays as Ligand Repertoires 416
20.3.8 Protein Arrays as Domain Repertoires 416
20.3.9 Mutagenized Domain Libraries 417
20.3.9.1 Site directed Mutagenesis 417
20.3.9.2 Random Mutagenesis 418
20.4 Repertoires of Peptide Ligands Based on Expression Cloning of
Oligonucleotide Libraries 419
20.4.1 Random Peptide Libraries 420
20.4.2 Dedicated Peptide Libraries 422
20.5 Synthetic Peptide Repertoires 424
20.5.1 Soluble Peptide Libraries as Ligand Repertoires 426
20.5.2 Bead bound Peptide Libraries as Ligand Repertoires 426
20.5.3 Peptide Arrays as Ligand Repertoires 427
20.5.3.1 Sublibrary Pools for Iterative A Priori Deconvolution 427
20.5.3.2 Protein Scanning Repertoires (Peptide Walking) 428
20.5.3.3 Replacement Repertoires 428
20.5.3.4 Genome/Proteome Scanning 428
20.5.4 Peptide Arrays as Domain Repertoires 429
References 430
21 Computational Analysis of Modular Protein Architectures 439
Rune Linding, Ivica Letunic, TobyJ. Gibson, and Peer Bork
21.1 Introduction 439
21.2 Protein Architecture: Sequence, Structure, and Function 439
21.2.1 The Modular Model of Protein Function 439
21.2.2 Partitioning of Protein Space 441
21.3 Analyzing Globular Domains 442
21.3.1 Globularity of Domains 443
21.3.2 Resources for Analysis of Globular Domains 444
21.3.3 SMART: Simple Modular Architecture Research Tool 444
21.3.3.1 The SMART Alignment Set 445
21.3.3.2 SMART Relational Database System 447
21.3.3.3 Web Interface 447
21.3.3.4 Application of S MART 450
21.3.4 Other Features and Resources 451
21.3.4.1 Globular Repeats 451
21.3.4.2 Domain Interaction Prediction 451
21.3.4.3 No Domains? 453
21.4 Analyzing Nonglobular Protein Segments 452
21.4.1 Unstructured Regions: Protein Disorder 453
21.4.1.1 What Role Does Protein Disorder Play in Biology? 454
21.4.1.2 What is Protein Disorder? 455
21.4.1.3 Methods for Finding Protein Disorder 457
21.4.1.4 GlobPlotting 457
21.4.1.5 Prediction of Multiple Types of Disorder with DisEMBL 459
21.4.1.6 Design of Protein Expression Vectors 462
21.4.2 Function Prediction for Nonglobular Protein Segments 462
21.4.2.1 Available Resources 463
21.4.3 The Eukaryotic Linear Motif Resource: ELM 463
21.4.3.1 ELM Annotation Site seeing 465
21.4.3.2 ELM Resource Architecture 465
21.4.3.3 Knowledge based Decision Support (KBDS): ELM Filtering 466
21.4.3.4 Using ELM 469
21.5 URLs 469
21.6 Concluding Remarks 471
References 472
22 Nomenclature for Protein Modules and Their Cognate Motifs 477
Pal Puntervoll and Rein Aastand
22.1 Introduction 477
22.2 Protein Modules 477
22.3 Functional Sites and Their Recognition Modules 479
22.4 Representation of Motifs and Functional Sites 480
22.5 Application of the Seefeld Convention to a Complex Example 483
22.6 New Directions 484
References 485
Epilogue:
New Levels of Complexity in the Functional Roles of Modular Protein
Interaction Domains: Switches and Sockets in the Circuit Diagrams
of Cellular Systems Biology 487
Harel Weinstein
Subject Index 493
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| discipline | Chemie / Pharmazie Biologie Chemie |
| format | Book |
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| id | DE-604.BV019724969 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T20:04:41Z |
| institution | BVB |
| isbn | 352730813X |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-013052025 |
| oclc_num | 57283483 |
| open_access_boolean | |
| owner | DE-703 DE-M49 DE-BY-TUM DE-29 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-20 DE-526 DE-11 |
| owner_facet | DE-703 DE-M49 DE-BY-TUM DE-29 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-20 DE-526 DE-11 |
| physical | XXII, 501 S. Ill., graph. Darst. |
| publishDate | 2005 |
| publishDateSearch | 2005 |
| publishDateSort | 2005 |
| publisher | Wiley-VCH |
| record_format | marc |
| spelling | Modular protein domains ed. by Giovanni Cesareni ... Weinheim Wiley-VCH 2005 XXII, 501 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Protein Structure, Tertiary Protein-protein interactions Proteins Proteomics Proteine (DE-588)4076388-2 gnd rswk-swf Domäne Biochemie (DE-588)4582302-9 gnd rswk-swf Proteine (DE-588)4076388-2 s Domäne Biochemie (DE-588)4582302-9 s DE-604 Cesareni, Giovanni Sonstige (DE-588)129610607 oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013052025&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Modular protein domains Protein Structure, Tertiary Protein-protein interactions Proteins Proteomics Proteine (DE-588)4076388-2 gnd Domäne Biochemie (DE-588)4582302-9 gnd |
| subject_GND | (DE-588)4076388-2 (DE-588)4582302-9 |
| title | Modular protein domains |
| title_auth | Modular protein domains |
| title_exact_search | Modular protein domains |
| title_full | Modular protein domains ed. by Giovanni Cesareni ... |
| title_fullStr | Modular protein domains ed. by Giovanni Cesareni ... |
| title_full_unstemmed | Modular protein domains ed. by Giovanni Cesareni ... |
| title_short | Modular protein domains |
| title_sort | modular protein domains |
| topic | Protein Structure, Tertiary Protein-protein interactions Proteins Proteomics Proteine (DE-588)4076388-2 gnd Domäne Biochemie (DE-588)4582302-9 gnd |
| topic_facet | Protein Structure, Tertiary Protein-protein interactions Proteins Proteomics Proteine Domäne Biochemie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013052025&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT cesarenigiovanni modularproteindomains |