Protein Families (eBook)

Relating Protein Sequence, Structure, and Function

Christine A. Orengo, Alex Bateman (Herausgeber)

eBook Download: PDF

2013 | 1. Auflage
536 Seiten
John Wiley & Sons (Verlag)
978-1-118-74285-3 (ISBN)

Infos

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.

Autor

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.

Inhalt

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

Produkt-Details

• Erscheint lt. Verlag: 11.11.2013
• Reihe/Serie: Wiley Series in Protein and Peptide Science
• Reihe/Serie: Wiley Series in Protein and Peptide Science
• Mitarbeit: Herausgeber (Serie): Vladimir Uversky
• Sprache: englisch
• Themenwelt: Mathematik / Informatik ► Informatik ► Theorie / Studium
• Themenwelt: Naturwissenschaften ► Biologie ► Biochemie
• Themenwelt: Naturwissenschaften ► Chemie ► Organische Chemie
• Schlagworte: Bioinformatics & Computational Biology • Bioinformatik • Bioinformatik u. Computersimulationen in der Biowissenschaften • Biowissenschaften • Chemie • Chemistry • Life Sciences • Proteine • Protein Science • structural biology • Strukturbiologie
• ISBN-10: 1-118-74285-0 / 1118742850
• ISBN-13: 978-1-118-74285-3 / 9781118742853