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.
Table of Contents
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 ?-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