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.
Innehållsförteckning
Introduction vii
Contributors xiii
SECTION I. CONCEPTS UNDERLYING PROTEIN FAMILY CLASSIFICATION
1
1 Automated Sequence-Based Approaches for Identifying Domain
Families 3
Liisa Holm and Andreas Heger
2 Sequence Classification of Protein Families: Pfam and other
Resources 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 Gene3D
69
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-Chain
Dehydrogenase/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 IMPORTANT
BIOLOGICAL SYSTEMS 237
10 Functional Adaptation and Plasticity in Cytoskeletal Protein
Domains: Lessons from the Erythrocyte Model 239
Anthony J. Baines
11 Unusual Species Distribution and Horizontal Transfer of
Peptidases 285
Neil D. Rawlings
12 Deducing Transport Protein Evolution Based on Sequence,
Structure, and Function 315
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
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 in
Transcription Factors across the Tree of Life 383
Varodom Charoensawan and Sarah Teichmann
15 Evolution of Eukaryotic Chromatin Proteins and Transcription
Factors 421
L. Aravind, Vivek Anantharaman, Saraswathi Abhiman, and
Lakshminarayan M. Iyer
Index 503
Om författaren
CHRISTINE ORENGO, Ph D, 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, Ph D, is Senior Investigator at Wellcome
Trust Sanger Institute, where he leads the Pfam database project.
Dr. Bateman also participates in the European Inter Pro project,
which seeks to merge the annotations from Pfam, PRINTS, Prosite,
and other domain databases.
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