Orengo / Bateman Protein Families

Relating Protein Sequence, Structure, and Function
1. Auflage 2013
ISBN: 978-1-118-74285-3
Verlag: John Wiley & Sons
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 536 Seiten, E-Book

Reihe: Wiley Series in Protein and Peptide Science

New insights into the evolution and nature of proteins
Exploring several distinct approaches, this book describes themethods for comparing protein sequences and protein structures inorder to identify homologous relationships and classify proteinsand protein domains into evolutionary families. Readers willdiscover the common features as well as the key philosophicaldifferences underlying the major protein classification systems,including Pfam, Panther, SCOP, and CATH. Moreover, they'll discoverhow these systems can be used to understand the evolution ofprotein families as well as understand and predict the degree towhich structural and functional information are shared betweenrelatives in a protein family.
Edited and authored by leading international experts, ProteinFamilies offers new insights into protein families that areimportant to medical research as well as protein families that helpus understand biological systems and key biological processes suchas cell signaling and the immune response. The book is divided intothree sections:
* Section I: Concepts Underlying Protein FamilyClassification reviews the major strategies for identifyinghomologous proteins and classifying them into families.
* Section II: In-Depth Reviews of Protein Families focuseson some fascinating super protein families for which we havesubstantial amounts of sequence, structural and functional data,making it possible to trace the emergence of functionally diverserelatives.
* Section III: Review of Protein Families in ImportantBiological Systems examines protein families associated with aparticular biological theme, such as the cytoskeleton.
All chapters are extensively illustrated, including depictionsof evolutionary relationships. References at the end of eachchapter guide readers to original research papers and reviews inthe field.
Covering protein family classification systems alongsidedetailed descriptions of select protein families, this book offersbiochemists, molecular biologists, protein scientists, structuralbiologists, and bioinformaticians new insight into the evolutionand nature of proteins.

Autoren/Hrsg.

Orengo, Christine A.

Bateman, Alex

Weitere Mitwirkende

Uversky, Vladimir

Inhaltsverzeichnis

Introduction vii
Contributors xiii
SECTION I. CONCEPTS UNDERLYING PROTEIN FAMILY CLASSIFICATION1
1 Automated Sequence-Based Approaches for Identifying DomainFamilies 3
Liisa Holm and Andreas Heger
2 Sequence Classification of Protein Families: Pfam and otherResources 25
Alex Bateman
3 Classifying Proteins into Domain Structure Families 37
Alison Cuff, Alexey Murzin, and Christine Orengo
4 Structural Annotations of Genomes with Superfamily and Gene3D69
Julian Gough, Corin Yeats, and Christine Orengo
5 Phylogenomic Databases and Orthology Prediction 99
Kimmen Sj¨olander
SECTION II. IN-DEPTH REVIEWS OF PROTEIN FAMILIES 125
6 The Nucleophilic Attack Six-Bladed beta-Propeller (N6P)Superfamily 127
Michael A. Hicks, Alan E. Barber II, and Patricia C.Babbitt
7 Functional Diversity of the HUP Domain Superfamily 159
Benoit H. Dessailly and Christine Orengo
8 The NAD Binding Domain and the Short-ChainDehydrogenase/Reductase (SDR) Superfamily 191
Nicholas Furnham, Gemma L. Holliday, and Janet M.Thornton
9 The Globin Family 207
Arthur M. Lesk and Juliette T.J. Lecomte
SECTION III. REVIEW OF PROTEIN FAMILIES IN IMPORTANTBIOLOGICAL SYSTEMS 237
10 Functional Adaptation and Plasticity in Cytoskeletal ProteinDomains: Lessons from the Erythrocyte Model 239
Anthony J. Baines
11 Unusual Species Distribution and Horizontal Transfer ofPeptidases 285
Neil D. Rawlings
12 Deducing Transport Protein Evolution Based on Sequence,Structure, and Function 315
Steven T. Wakabayashi, Maksim A. Shlykov, Ujjwal Kumar, VamseeS. Reddy, Ankur Malhotra, Erik L. Clarke, Jonathan S. Chen,Rostislav Castillo, Russell De La Mare, Eric I. Sun, and Milton H.Saier
13 Crispr-CAS Systems and CAS Protein Families 341
Kira S. Makarova, Daniel H. Haft, and Eugene V. Koonin
14 Families of Sequence-Specific DNA-Binding Domains inTranscription Factors across the Tree of Life 383
Varodom Charoensawan and Sarah Teichmann
15 Evolution of Eukaryotic Chromatin Proteins and TranscriptionFactors 421
L. Aravind, Vivek Anantharaman, Saraswathi Abhiman, andLakshminarayan M. Iyer
Index 503

Über Autor(innen)

CHRISTINE ORENGO, PhD, is Professor of Bioinformatics atUniversity College London. Dr. Orengo's research focuses on proteinstructure comparison, classification, and analysis. Her groupdevelops the CATH domain family classification and algorithms forpredicting protein functions and functional networks.
ALEX BATEMAN, PhD, is Senior Investigator at WellcomeTrust Sanger Institute, where he leads the Pfam database project.Dr. Bateman also participates in the European InterPro project,which seeks to merge the annotations from Pfam, PRINTS, Prosite,and other domain databases.