E-raamat: Modular Protein Domains

Preface.
List of Contributors.
Prologue: An Overview of Protein Modular Domains as Adaptors (Sir Tom L. Blundell).
1 The SH2 Domain: a Prototype for Protein Interaction Modules (Tony Pawson, Gerald D. Gish, and Piers Nash).
1.1 The Multidomain Nature of Signaling Proteins and Identification of the SH2 Domain.
1.2 SH2 Domains as a Prototype for Interaction Domains.
1.3 Structure and Binding Properties of SH2 Domains.
1.4 Different Modes of SH2 Domain–Phosphopeptide Recognition.
1.5 Signaling Pathways and Networks.
1.6 Plasticity of SH2 Domains.
1.7 SH2 Domain Dimerization.
1.8 Tandem SH2 Domains.
1.9 Composite and Complex Interaction Domains.
1.10 Allosteric Regulation.
1.11 SH2 Domains and Disease.
1.12 Summary.
References.
2 SH3 Domains (Bruce J. Mayer and Kalle Saksela).
2.1 Brief Overview.
2.2 Historical Perspective.
2.3 Predicting Binding Partners.
2.4 Experimental Exploitation of SH3 Specificity.
2.5 Conclusion.
References.
3 The WW Domain (Marius Sudol).
3.1 Introduction and Brief History of Module Discovery.
3.2 Structure of the WW Domain–Ligand Complex.
3.3 WW Domains and Human Diseases.
3.4 Emerging Directions and Recent Developments.
3.5 Concluding Remarks.
References.
4 EVH1/WH1 Domains (Linda J. Ball, Urs Wiedemann, Jürgen Zimmermann, and Thomas Jarchau).
4.1 Introduction.
4.2 Occurrence and Distribution of EVH1 Domains.
4.3 Structures of EVH1 Domains and Their Complexes.
4.4 Biological Function and Signaling Pathways Involving EVH1 Domains.
4.5 Emerging Research Directions and Recent Developments.
4.6 Concluding Remarks.
References.
5 The GYF Domain (Christian Freund).
5.1 Introduction.
5.2 Structure of the CD2BP2-GYF Domain and Its Interaction with the CD2 Signaling Peptide SHRPPPPGHRV.
5.3 Molecular and Signaling Function of GYF Domains.
5.4 Emerging Research Directions and Recent Developments.
5.5 Concluding Remarks.
References.
6 PTB Domains (Ben Margolis and Linton M. Traub).
6.1 Introduction.
6.2 Function of PTB Domain Proteins.
6.3 PTB Domain Structure.
6.4 Conclusions.
References.
7 The FHA Domain (Daniel Durocher).
7.1 Introduction.
7.2 FHA Domain Structure.
7.3 Molecular and Signaling Function.
7.4 Emerging Research Direction.
7.5 Concluding Remarks.
References.
8 Phosphoserine/Threonine Binding Domains (Andrew E. H. Elia and Michael B. Yaffe).
8.1 Introduction.
8.2 The 14-3-3 Proteins.
8.3 WW Domains.
8.4 FHA Domains.
8.5 WD40 Repeats of F-box Proteins.
8.6 Polo-box Domains.
8.7 Conclusions and Future Directions.
References.
9 The Eukaryotic Protein Kinase Domain (Arvin C. Dar, Leanne E. Wybenga-Groot, and Frank Sicheri).
9.1 Introduction.
9.2 Architecture of the Kinase Domain.
9.3 Catalytic Switching Mechanisms.
9.4 Protein Kinase Substrate Recognition.
9.5 Conclusions.
References.
10 Structure, Specificity, and Mechanism of Protein Lysine Methylation by SET Domain Enzymes (James H. Hurley and Raymond C. Trievel).
10.1 Discovery and Biology of SET Domains.
10.2 Structure of the SET Domain.
10.3 Substrate Specificity and Catalytic Mechanism.
10.4 Emerging Directions and Conclusions.
References.
11 The Structure and Function of the Bromodomain (Kelley S. Yan and Ming-Ming Zhou).
11.1 Introduction.
11.2 The Bromodomain Structure.
11.3 The Bromodomain as an Acetyl-lysine Binding Domain.
11.4 Emerging Developments.
11.5 Concluding Remarks.
References.
12 Chromo and Chromo Shadow Domains (Joel C. Eissenberg and Sepideh Khorasanizadeh).
12.1 Introduction and Brief History of the Module’s Discovery.
12.2 Structures of the Chromo and Chromo Shadow Domains.
12.3 Function of the Chromo Domain.
12.4 Genetic, Cytological, and Molecular Properties of the Chromo Domain.
12.5 Emerging Research Directions and Recent Developments.
References.
13 PDZ Domains: Intracellular Mediators of Carboxy-terminal Protein Recognition and Scaffolding (Laurence A. Lasky, Nicholas J. Skelton, and Sachdev S. Sidhu).
13.1 Introduction.
13.2 Structural Analysis of PDZ Domains.
13.3 Analysis of PDZ Domain–Ligand Interactions with Mutagenesis and Synthetic Peptides.
13.4 Molecular and Signaling Functions of PDZ Domains.
13.5 Concluding Remarks.
References.
14 EH Domains and Their Ligands (Brian K. Kay, Michael D. Scholle, and Fred J. Stevens).
14.1 Introduction.
14.2 EH Domain-containing Proteins.
14.3 Peptide Ligands.
14.4 Cellular Ligands.
14.5 Structures of the Domain and Its Ligands.
14.6 Evolutionary Origins of the EH Domain.
14.7 Functions of the EH Domain.
References.
15 Ubiquitin Binding Modules: The Ubiquitin Network Beyond the Proteasome (Stefano Confalonieri and Pier Paolo Di Fiore).
15.1 Introduction: The Ubiquitin System in Proteolysis and Beyond.
15.2 CUE and UBA Domains.
15.3 The Ubiquitin-interacting Motif.
15.4 The UEV Domain.
15.5 The PAZ and NZF Domains.
15.6 Ubiquitin-based Networks.
15.7 Conclusions.
References.
16 The Calponin Homology (CH) Domain (Mario Gimona and Steven J. Winder).
16.1 Introduction and Brief History.
16.2 Structure of the Domain – The CH Domain Fold.
16.3 Molecular and Signaling Function.
16.4 Emerging Research Directions and Recent Developments.
16.5 Concluding Remarks.
References.
17 PH Domains (Mark A. Lemmon and David Keleti).
17.1 Introduction.
17.2 PH Domain Structure and Phosphoinositide Binding.
17.3 Molecular and Signaling Function of PH Domains.
17.4 Emerging Research Directions and Recent Developments.
References.
18 ENTH and VHS Domains (Vimal Parkash, Olli Lohi, Ismo Virtanen, and Veli-Pekka Lehto).
18.1 Introduction.
18.2 History of ENTH.
18.3 Structure of ENTH Domains.
18.4 Signaling and Molecular Functions of ENTH.
18.5 History of VHS.
18.6 Structure of VHS Domains.
18.7 Function of GGA-VHS Domains.
18.8 Function of Non-GGA VHS Domains.
18.9 Involvement of ENTH and VHS Domains in Human Disease.
18.10 Emerging Research Directions.
18.11 Concluding Remarks.
References.
19 PX Domains (Matthew L. Cheever and Michael Overduin).
19.1 Introduction and History of the PX Domain Discovery.
19.2 Structure of the PX Domain.
19.3 Biological Function of the PX Domain.
19.4 Emerging Research Directions and Recent Developments.
References.
20 Peptide and Protein Repertoires for Global Analysis of Modules (Krzysztof Bialek, Andrzej Swistowski, and Ronald Frank).
20.1 Introduction.
20.2 Repertoires from Cell Extracts.
20.3 Repertoires of Proteins Based on Expression Cloning of DNA Libraries.
20.4 Repertoires of Peptide Ligands Based on Expression Cloning of Oligonucleotide Libraries.
20.5 Synthetic Peptide Repertoires.
References.
21 Computational Analysis of Modular Protein Architectures (Rune Linding, Ivica Letunic, Toby J. Gibson, and Peer Bork).
21.1 Introduction.
21.2 Protein Architecture: Sequence, Structure, and Function.
21.3 Analyzing Globular Domains.
21.4 Analyzing Nonglobular Protein Segments.
21.5 URLs.
21.6 Concluding Remarks.
References.
22 Nomenclature for Protein Modules and Their Cognate Motifs (Pål Puntervoll and Rein Aasland).
22.1 Introduction.
22.2 Protein Modules.
22.3 Functional Sites and Their Recognition Modules.
22.4 Representation of Motifs and Functional Sites.
22.5 Application of the Seefeld Convention to a Complex Example.
22.6 New Directions.
References.
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 (Harel Weinstein).
Subject Index.

Gianni Cesareni is a Full Professor of Genetics at the University of Rome Tor Vergata (Italy). After obtaining a degree in physics at the University of Rome La Sapienza he spent three years in Cambridge in the laboratory of Sidney Brenner. He then moved to the EMBL in Heidelberg where he led a group working on the mechanisms controlling plasmid DNA replication. Since 1989 he teaches and works in Rome. He is interested in the interplay between specificity and promiscuity in the protein interaction network mediated by protein recognition modules.

Mario Gimona is laboratory head at the Consorzio Mario Negri Sud in Santa Maria Imbaro (Italy) and reader for molecular cell biology at the University of Salzburg (Austria). He was born in Salzburg where he also received his degrees in genetics and biochemistry, after completing his Ph.D. work in the lab of Vic Small at the Austrian Academy of Sciences. Following his post-doctoral time at the CSHL, New York (USA) with David Helfman he set up his own laboratory in Salzburg at the OeAW in 1996. His research interests revolve around the linguistic variation of functional protein modules and their role in the regulation of the actin cytoskeleton.

Marius Sudol has been an Associate Professor at the Mount Sinai School of Medicine in New York since 1995. He was instrumental in the delineation and characterization of one of the smallest protein modules, the WW domain. His work also implicated the WW domain in signaling pathways underlying several human diseases including Alzheimer's disease, hypertension and cancer. He earned a Ph.D. at The Rockefeller University in New York in 1983 and stayed at his Alma Mater as a postdoctoral fellow and faculty member until his move to Mount Sinai. Dr.Sudol has published 95 research articles and is credited as inventor on two biotechnology patents.

Michael B. Yaffe is Associate Professor of Biology at the Center for Cancer Research, Massachusetts Institute of Technology. He earned his MD and PhD degrees at Case Western Reserve University, and did residency training in general surgery, trauma and critical care medicine at Harvard Medical School. He was a post-doctoral fellow in Cell Biology at Harvard under Lewis C. Cantley, where he remained as junior faculty until moving to MIT in 2000. He is interested in signal transduction, protein phosphorylation, and phosphopeptide-binding domains, with a focus on cell cycle control, DNA damage responses, and inflammation.

All editors are members of the "Protein Module Consortium", a world-wide organization to support researchers interested in protein modules.