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Protein Families
Relating Protein Sequence, Structure, and Function
Christine A. Orengo (Edited by), C Orengo (Author), Alex Bateman (Edited by), Vladimir Uversky (Series edited by)
9780470624227, Wiley
Hardback, published 18 March 2014
576 pages
24.4 x 16.5 x 3.6 cm, 0.962 kg
New insights into the evolution and nature of proteins Exploring several distinct approaches, this book describes the methods for comparing protein sequences and protein structures in order to identify homologous relationships and classify proteins and protein domains into evolutionary families. Readers will discover the common features as well as the key philosophical differences underlying the major protein classification systems, including Pfam, Panther, SCOP, and CATH. Moreover, they'll discover how these systems can be used to understand the evolution of protein families as well as understand and predict the degree to which structural and functional information are shared between relatives in a protein family. Edited and authored by leading international experts, Protein Families offers new insights into protein families that are important to medical research as well as protein families that help us understand biological systems and key biological processes such as cell signaling and the immune response. The book is divided into three sections: All chapters are extensively illustrated, including depictions of evolutionary relationships. References at the end of each chapter guide readers to original research papers and reviews in the field. Covering protein family classification systems alongside detailed descriptions of select protein families, this book offers biochemists, molecular biologists, protein scientists, structural biologists, and bioinformaticians new insight into the evolution and nature of proteins.
Introduction vii Contributors xiii SECTION I. CONCEPTS UNDERLYING PROTEIN FAMILY CLASSIFICATION 1 1 Automated Sequence-Based Approaches for Identifying Domain Families 3 2 Sequence Classification of Protein Families: Pfam and other Resources 25 3 Classifying Proteins into Domain Structure Families 37 4 Structural Annotations of Genomes with Superfamily and Gene3D 69 5 Phylogenomic Databases and Orthology Prediction 99 SECTION II. IN-DEPTH REVIEWS OF PROTEIN FAMILIES 125 6 The Nucleophilic Attack Six-Bladed β-Propeller (N6P) Superfamily 127 7 Functional Diversity of the HUP Domain Superfamily 159 8 The NAD Binding Domain and the Short-Chain Dehydrogenase/Reductase (SDR) Superfamily 191 9 The Globin Family 207 SECTION III. REVIEW OF PROTEIN FAMILIES IN IMPORTANT BIOLOGICAL SYSTEMS 237 10 Functional Adaptation and Plasticity in Cytoskeletal Protein Domains: Lessons from the Erythrocyte Model 239 11 Unusual Species Distribution and Horizontal Transfer of Peptidases 285 12 Deducing Transport Protein Evolution Based on Sequence, Structure, and Function 315 13 Crispr-CAS Systems and CAS Protein Families 341 14 Families of Sequence-Specific DNA-Binding Domains in Transcription Factors across the Tree of Life 383 15 Evolution of Eukaryotic Chromatin Proteins and Transcription Factors 421 Index 503
Liisa Holm and Andreas Heger
Alex Bateman
Alison Cuff, Alexey Murzin, and Christine Orengo
Julian Gough, Corin Yeats, and Christine Orengo
Kimmen Sj¨olander
Michael A. Hicks, Alan E. Barber II, and Patricia C. Babbitt
Benoit H. Dessailly and Christine Orengo
Nicholas Furnham, Gemma L. Holliday, and Janet M. Thornton
Arthur M. Lesk and Juliette T.J. Lecomte
Anthony J. Baines
Neil D. Rawlings
Steven T. Wakabayashi, Maksim A. Shlykov, Ujjwal Kumar, Vamsee S. Reddy, Ankur Malhotra, Erik L. Clarke, Jonathan S. Chen, Rostislav Castillo, Russell De La Mare, Eric I. Sun, and Milton H. Saier
Kira S. Makarova, Daniel H. Haft, and Eugene V. Koonin
Varodom Charoensawan and Sarah Teichmann
L. Aravind, Vivek Anantharaman, Saraswathi Abhiman, and Lakshminarayan M. Iyer
Subject Areas: Chemistry [PN]
