(Ebook) Protein Families: Relating Protein Sequence, Structure, and Function by Christine Orengo, Alex Bateman, Vladimir Uversky ISBN 9780470624227, 9781118743089, 0470624221, 1118743083

(Ebook) Protein Families: Relating Protein Sequence, Structure, and Function by Christine Orengo, Alex Bateman, Vladimir Uversky ISBN 9780470624227, 9781118743089, 0470624221, 1118743083

New insights into the evolution and nature of proteinsExploring 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: Section I: Concepts Underlying Protein Family Classification reviews the major strategies for identifying homologous proteins and classifying them into families.Section II: In-Depth Reviews of Protein Families focuses on some fascinating super protein families for which we have substantial amounts of sequence, structural and functional data, making it possible to trace the emergence of functionally diverse relatives.Section III: Review of Protein Families in Important Biological Systems examines protein families associated with a particular biological theme, such as the cytoskeleton.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.Content: Chapter 1 Automated Sequence‐Based Approaches for Identifying Domain Families (pages 1–24): Liisa Holm and Andreas HegerChapter 2 Sequence Classification of Protein Families: Pfam and other Resources (pages 25–36): Alex BatemanChapter 3 Classifying Proteins into Domain Structure Families (pages 37–68): Alison Cuff, Alexey Murzin and Christine OrengoChapter 4 Structural Annotations of Genomes with Superfamily and G3D (pages 69–97): Julian Gough, Corin Yeats and Christine OrengoChapter 5 Phylogenomic Databases and Orthology Prediction (pages 99–124): Kimmen SjölanderChapter 6 The Nucleophilic Attack Six‐Bladed β‐Propeller (N6P) Superfamily (pages 125–158): Michael A. Hicks, Alan E. Barber and Patricia C. BabbittChapter 7 Functional Diversity of the HUP Domain Superfamily (pages 159–189): Benoit H. Dessailly and Christine OrengoChapter 8 The NAD Binding Domain and the Short‐Chain Dehydrogenase/Reductase (SDR) Superfamily (pages 191–206): Nicholas Furnham, Gemma L. Holliday and Janet M. ThorntonChapter 9 The Globin Family (pages 207–235): Arthur M. Lesk and Juliette T.J. LecomteChapter 10 Functional Adaptation and Plasticity in Cytoskeletal Protein Domains: Lessons from the Erythrocyte Model (pages 237–284): Anthony J. BainesChapter 11 Unusual Species Distribution and Horizontal Transfer of Peptidases (pages 285–314): Neil D. RawlingsChapter 12 Deducing Transport Protein Evolution Based on Sequence, Structure, and Function (pages 315–339): 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. SaierChapter 14 Families of Sequence‐Specific DNA‐Binding Domains in Transcription Factors across the Tree of Life (pages 383–420): Varodom Charoensawan and Sarah TeichmannChapter 15 Evolution of Eukaryotic Chromatin Proteins and Transcription Factors (pages 421–502): L. Aravind, Vivek Anantharaman, Saraswathi Abhiman and Lakshminarayan M. IyerChapter 13 CRISPR‐Cas Systems and Cas Protein Families (pages 341–381): Kira S. Makarova, Daniel H. Haft and Eugene V. Koonin