Protein Families: Relating Protein Sequence, Structure, and Function

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: 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.

Introduction. Christine Orengo and Alex Bateman Section 1. Concepts underlying protein family classification 1. Automated sequence based approaches for identifying domain families Liisa Holm and Andreas Heger 2. Sequence classification of protein families: Pfam and other resources Alex Bateman 3. Classifying proteins into domain structure families Alison Cuff, Alexey G. Murzin and Christine Orengo 4. Structural annotations of genomes with SUPERFAMILY and Gene3D Julian Gough, Corin Yeats and Christine Orengo 5. Phylogenomic databases and orthology prediction Kimmen Sjölander Section 2. In depth reviews of protein families 6. The Nucleophilic Attack 6–bladed β–Propeller (N6P) Superfamily Michael A. Hicks, Alan E. Barber II, and Patricia C. Babbitt 7. Structural elaboration of the HUP domain superfamily Benoit H. Dessailly and Christine A. Orengo 8. The NAD Binding Domain And The Short–Chain Dehydrogenase/Reductase (SDR) Superfamily Nicholas Furnham, Gemma L. Holliday & Janet M. Thornton 9. The Globin Family Arthur M. Lesk and Juliette T.J. Lecomte Section 3. Review of protein families in important biological systems 10. Functional adaptation and plasticity in cytoskeletal protein domains: Lessons from the erythrocyte model Anthony J. Baines 11. Unusual species distribution and horizontal transfer of peptidases Neil D. Rawlings 12. Deducing Transport Protein Evolution Based on Sequence, Structure, and Function 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, Jr 13. CRISPR–Cas systems and Cas protein families Kira S. Makarova, Daniel H. Haft, Eugene V. Koonin 14. Families of sequence–specific DNA–binding Domains in Transcription Factors across the Tree of Life Varodom Charoensawan and Sarah Teichmann 15. Evolution of Eukaryotic chromatin proteins and transcription factors L.Aravind, Vivek Anantharaman, Saraswathi Abhiman and Lakshminarayan M. Iyer

CHRISTINE ORENGO, PhD, is Professor of Bioinformatics at University College London. Dr. Orengo's research focuses on protein structure comparison, classification, and analysis. Her group develops the CATH domain family classification and algorithms for predicting protein functions and functional networks. ALEX BATEMAN, PhD, is Senior Investigator at Wellcome Trust 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.