Protein Families : Relating Protein Sequence, Structure, and Function.
Title:
Protein Families : Relating Protein Sequence, Structure, and Function.
Author:
Orengo, Christine A.
ISBN:
9781118742815
Personal Author:
Edition:
1st ed.
Physical Description:
1 online resource (577 pages)
Series:
Wiley Series in Protein and Peptide Science Ser.
Contents:
Cover -- Title Page -- Contents -- Introduction -- Contributors -- Part I Concepts Underlying Protein Family Classification -- Chapter 1 Automated Sequence-Based Approaches for Identifying Domain Families -- 1.1 Introduction -- 1.2 Motivation Behind Automated Classification -- 1.3 Clustering the Sequence Space Graph -- 1.4 Historical Overview of Sequence Clustering Algorithms -- 1.5 Related Methods -- 1.6 Quality Assessment -- 1.7 ADDA-The Automatic Domain Delineation Algorithm -- 1.8 Results -- 1.9 Conclusions -- References -- Chapter 2 Sequence Classification of Protein Families: Pfam and other Resources -- 2.1 Introduction -- 2.2 Pfam -- 2.3 Smart, Prosite Profiles, CDD and Tigrfams -- 2.4 Philosophy of Pfam -- 2.5 HMMER3 and Jackhmmer -- 2.6 Sources of New Families -- 2.7 Annotation of Families -- 2.8 The InterPro Collection -- 2.9 The Future of Sequence Classification -- References -- Chapter 3 Classifying Proteins into Domain Structure Families -- 3.1 Introduction -- 3.2 The Classification Hierarchies Adopted by Scop and Cath -- 3.3 Challenges in Identifying Domains in Proteins -- 3.4 Structure-Based Approaches for Identifying Related Folds and Homologs -- 3.5 Approaches to Structure Comparison -- 3.6 The DALI Algorithm -- 3.7 The SSAP Algorithm Used for Fold Recognition in CATH -- 3.8 Fast Approximate Methods Used to Recognize Folds in CATH -- 3.9 Measuring Structural Similarity -- 3.10 Multiple Structure Alignment -- 3.11 Classification Protocols -- 3.12 Population of the Hierarchy -- 3.13 Comparisons Between Scop and CATH -- 3.14 Hierarchical Classifications Versus Structural Continuum -- 3.15 Websites -- References -- Chapter 4 Structural Annotations of Genomes with Superfamily and Gene3D -- 4.1 Introduction -- 4.2 The Importance of Being High Throughput.
4.3 The Use of Structural Information -- 4.4 Applications -- 4.5 History -- 4.6 Technology -- 4.7 Hidden Markov Models -- 4.8 Building Models -- 4.9 Domain Annotations -- 4.10 High Throughput Computation -- 4.11 Development of New Bioinformatics Algorithms -- 4.12 Genomes -- 4.13 e-Value Scores -- 4.14 Other Sequence Sets -- 4.15 Data Access -- 4.16 Analysis Tools -- 4.17 Conclusion -- References -- Chapter 5 Phylogenomic Databases and Orthology Prediction -- 5.1 The Evolution of Novel Functions and Structures in Gene Families -- 5.2 Homologs, Orthologs, Paralogs, and Other Evolutionary Terms -- 5.3 The Standard Functional Annotation Protocol -- 5.4 Orthology Identification Methods and Databases -- 5.5 Challenges in Phylogenetic Methods of Ortholog Identification -- 5.6 Evaluating Ortholog Identification Methods -- 5.7 Orthology Databases -- 5.8 Phylogenomic Databases -- 5.9 PhyloFacts -- 5.10 Subfamily Classification in Phylofacts -- 5.11 PhyloFacts 3.0 -- 5.12 PhylomeDB -- 5.13 Panther -- 5.14 Structural Phylogenomics: Improved Functional Annotation Through Integration of Information from Structure and Evolution -- 5.15 Specific Issues in Phylogenomic Pipelines -- 5.16 Improving Functional Inference using Information from Protein Structure -- 5.17 Example Case Studies -- 5.18 Review of Key Points -- References -- Part II In-Depth Reviews of Protein Families -- Chapter 6 The Nucleophilic Attack Six-Bladed Beta-Propeller (N6P) Superfamily -- 6.1 Introduction -- 6.2 Background, Resources, and Tools Important for Understanding this Chapter -- 6.3 Sequence/Structure/Function Relationships in the Nucleophilic Attack 6-Bladed β-Propeller (N6P) Superfamily -- 6.4 What we Know and Do not Know About the Enzymes of the N6P Superfamily.
6.5 Functional Predictions and Prediction of Misannotation of SSL Subgroup Enzymes -- 6.6 Do the Strictosidine Synthases Really Belong to the N6P Superfamily? -- 6.7 Re-Examination of the Boundaries of the N6P SF in the Context of other β-Propeller Fold Proteins -- 6.8 Using the Superfamily Context to Select Protein Targets for Experimental Characterization -- 6.9 Conclusion -- Access to Data from this Work -- Acknowledgments -- References -- Chapter 7 Functional Diversity of the HUP Domain Superfamily -- 7.1 Introduction -- 7.2 Function Diversity in the HUP Superfamily -- 7.3 Description of Functional Groups -- 7.4 Functional Diversity in Gene3D HUP Domains -- 7.5 Function Diversity and Evolution -- 7.6 Multidomain Architectures in the Different FSGs -- 7.7 Structural Diversity of HUP Domains -- 7.8 Structural Embellishments in the HUP Superfamily and Their Role in Determining the Function Diversity of HUP Domains -- 7.9 Conclusion -- References -- Chapter 8 The NAD Binding Domain and the Short-Chain Dehydrogenase/Reductase (SDR) Superfamily -- 8.1 The NAD Binding Domain -- 8.2 NAD Binding Domain in Multidomain Architectures -- 8.3 Transitions in Function -- 8.4 Characterization and Overview of the SDR Superfamily -- 8.5 The SDRS in Humans -- 8.6 Conclusions -- References -- Chapter 9 The Globin Family -- 9.1 Introduction -- 9.2 Early History of Globin Research -- 9.3 Globin Structures -- 9.4 Species Distribution in Globins -- 9.5 Globin Functions -- 9.6 Hemoglobinopathies-``Molecular Diseases'' Caused by Abnormal Hemoglobins -- 9.7 Conclusions -- References -- Part III Review of Protein Families in Important Biological Systems.
Chapter 10 Functional Adaptation and Plasticity in Cytoskeletal Protein Domains: Lessons from the Erythrocyte Model -- 10.1 Introduction -- 10.2 The Spectrin Superfamily: Common Folding Units Adapted to Varying Functions -- 10.3 Origins of Domains in the Spectrin Lineage -- 10.4 Spectrin Triple Helices-A Common Fold but with Many Functional Adaptations -- 10.5 Function as a Spacer Module -- 10.6 Function as a Protein Binding Module -- 10.7 Lipid Interactions -- 10.8 Accomodating Deformation -- 10.9 Triple Helical Repeats as the Basis for Enzyme Structures -- 10.10 Calponin Homology Domains -- 10.11 Functional Interactions and Regulation -- 10.12 The Calmodulin-Like Domain -- 10.13 Ankyrin -- 10.14 Ankyrin Repeats -- 10.16 Structure and Regulation of the 4.1R Ferm Domain -- 10.17 Summary and Conclusion -- References -- Chapter 11 Unusual Species Distribution and Horizontal Transfer of Peptidases -- 11.1 Introduction -- 11.2 Mechanisms of Horizontal Gene Transfer -- 11.3 Distribution of Peptidases in Bacteria -- 11.4 Unusual Occurrences in Peptidase Families -- 11.5 Conclusions -- References -- Chapter 12 Deducing Transport Protein Evolution Based on Sequence, Structure, and Function -- 12.1 Introduction -- 12.2 Data Input for TCDB -- 12.3 Functional Predictions -- 12.4 Semiautomated Genome Analysis -- 12.5 Conclusions and Perspectives -- Acknowledgment -- References -- Chapter 13 Crispr-CAS Systems and CAS Protein Families -- 13.1 Introduction -- 13.2 Cas Protein Families -- 13.3 The Three Major Groups of RAMPS -- 13.4 The Characteristic Arrangement of RAMPS in CRISPR-Cas Operons -- 13.5 Putative Homology Among the Large and Small Subunits of Diverse Type I and Type III CRISPR-Cas System -- 13.6 Conclusions -- Acknowledgment -- References.
Chapter 14 Families of Sequence-Specific DNA-Binding Domains in Transcription Factors across the Tree of Life -- 14.1 Introduction -- 14.2 Genomic Repertoires of TFs Based on DBD Families -- 14.3 TF Annotation Resources Currently Available -- 14.4 Genomic Repertoires of TFs and their Families Across the Tree of Life -- 14.5 Phylogenetic Distribution of DBD Families is Highly Lineage-Specific -- 14.6 Few DBD Families are Conserved in Multiple Superkingdoms -- 14.7 Prokaryotic DBD Repertoires -- 14.8 Eukaryotic DBD Repertoires -- 14.9 Protein Families Combine to form Complex TF Domain Architectures -- 14.10 Genome-Wide Studies of TFs: What Have we Learned? -- References -- Chapter 15 Evolution of Eukaryotic Chromatin Proteins and Transcription Factors -- 15.1 Introduction -- 15.2 Eukaryotic CPs and TFs -- 15.3 Diversity of Eukaryotic-Specific TFs -- 15.4 The Natural History and Evolution of Major Functional Types of CPs -- 15.5 Interactions Between RNA-Based Regulatory Systems and Chromatin Factors -- 15.6 Domain Architectures of CPs -- 15.7 General Considerations and Conclusions -- Acknowledgments -- References -- Index -- Supplemental Images.
Abstract:
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.
Local Note:
Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2017. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.
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