Protein Evolution

Laszlo Patthy

• Publisher: Wiley-Blackwell
• Year: 2009
• Print ISBN: 9781405151665
• eBook ISBN: 9781444308884
• Edition: 2
• Topic: Biological Sciences
• Subtopic: Biochemistry
• Index: Biological Sciences

This book provides an up-to-date summary of the principles of protein evolution and discusses both the methods available to analyze the evolutionary history of proteins as well as those for predicting their structure-function relationships.

• Includes a significantly expanded chapter on genome evolution to cover genomes of model organisms sequenced since the completion of the first edition, and organelle genome evolution
  
• Retains its reader-friendly, accessible style and organization
  
• Contains an updated glossary and new references, including a list of online reference sites

Table of contents

• Preface to the first edition
• Preface to the second edition
• Acknowledgements
• Introduction
• Chapter 1: Protein-coding genes
• 1.1 Structure of protein-coding genes
• 1.2 Transcription
• 1.3 Translation
• References
• Useful internet resources
• Chapter 2: Protein structure
• 2.1 The polypeptide backbone
• 2.2 The amino acids
• 2.3 Covalent modifications of amino acid side chains
• 2.3.1 Enzymatic modifications
• 2.3.2 Nonenzymatic chemical modifications
• 2.4 Interactions that govern protein folding and stability
• 2.4.1 Noncovalent interactions
• 2.4.2 The hydrophobic interaction
• 2.5 Secondary structural elements
• 2.5.1 The α α -helix
• 2.5.2 β β -sheets
• 2.5.3 Reverse turns
• 2.6 Supersecondary structures
• 2.7 Tertiary structures of proteins
• 2.7.1 Globular proteins
• 2.7.2 Fibrous proteins
• 2.7.3 Unusual structures of internally repeated proteins
• 2.7.4 Secreted proteins and membrane proteins
• 2.7.5 Intrinsically disordered proteins
• 2.8 Multidomain proteins
• 2.9 Multisubunit proteins
• References
• Useful internet resources
• Chapter 3: Mutations
• 3.1 Types of mutations
• 3.1.1 Substitutions
• 3.1.2 Deletion, duplication, insertion and fusion
• 3.2 Factors affecting rates of mutation
• 3.3 The fate of mutations
• 3.4 The molecular clock
• References
• Useful internet resources
• Chapter 4: Evolution of protein-coding genes
• 4.1 Alignment of nucleotide and amino acid sequences
• 4.2 Estimating the number of nucleotide substitutions
• 4.2.1 Substitutions in translated regions
• 4.2.2 Substitutions in untranslated regions, introns and 5and 3flanking regions of protein-coding genes
• 4.3 Rates and patterns of nucleotide substitution
• 4.3.1 Rates of nucleotide substitution
• 4.4 Variation in substitution rates
• 4.4.1 Variation among different sites of the translated region
• 4.4.2 Variation among genes
• 4.4.3 Constancy and variation in substitution rates of orthologous genes
• 4.4.4 Nonrandom substitutions at synonymous positions
• 4.5 Molecular phylogeny
• 4.5.1 Phylogenetic trees
• 4.5.2 Tree reconstruction
• 4.5.3 Tree-making methods
• 4.5.4 Estimation of species-divergence times
• References
• Useful internet resources
• Chapter 5: Evolution of orthologous proteins
• 5.1 Orthologous proteins with the same function in different species
• 5.2 Orthologous proteins with modified function in different species
• 5.3 Orthologous proteins with major modification of function
• 5.4 Orthologous proteins that have lost their function
• 5.5 Orthologous proteins that have gained additional functions
• 5.6 Prediction of the function of orthologous proteins
• 5.7 The three-dimensional structure of orthologous proteins
• 5.7.1 Prediction of secondary structure of proteins
• 5.7.2 Prediction of the three-dimensional structure of proteins
• 5.8 Detecting sequence homology of protein-coding genes
• References
• Useful internet resources
• Chapter 6: Formation of novel protein-coding genes
• 6.1 De novo formation of novel protein-coding genes
• 6.2 Gene duplications
• 6.2.1 Mechanisms of gene duplication
• 6.2.2 Fate of duplicated genes
• 6.2.3 Fate of genes acquired by lateral gene transfer
• 6.2.4 Dating gene duplications
• References
• Useful internet resources
• Chapter 7: Evolution of paralogous proteins
• 7.1 Advantageous duplications
• 7.1.1 Unprocessed genes
• 7.1.2 Processed genes
• 7.2 Neutral duplications
• 7.2.1 Modification of function by point mutations
• 7.2.2 Major change of function by point mutations
• 7.2.3 Major change of function by domain acquisitions
• 7.3 Similarities and differences in the evolution of paralogous and orthologous proteins
• 7.4 Predicting the function of proteins by homology
• 7.5 Nonhomology-based methods for the prediction of the function of proteins
• 7.6 Detecting distant homology of protein-coding genes
• 7.6.1 Detecting distant homology by consensus approaches
• 7.6.2 Detecting distant homology by comparing three-dimensional structures
• 7.6.3 Detecting distant homology by comparing exon–intron structures
• References
• Useful internet resources
• Chapter 8: Protein evolution by assembly from modules
• 8.1 Modular assembly by intronic recombination
• 8.1.1 Introns
• 8.1.2 Internal gene duplications/deletions via recombination in introns
• 8.1.3 Fusion of genes via recombination in introns
• 8.1.4 Exon shuffling via recombination in introns
• 8.1.5 Factors affecting acceptance of mutants created by intronic recombination
• 8.1.6 Classification of modules and mosaic proteins produced by exon shuffling
• 8.1.7 Genome evolution and the evolution of exon shuffling
• 8.1.8 Evolutionary significance of exon shuffling
• 8.1.9 Genome evolution and the evolution of alternative splicing
• 8.2 Modular assembly by exonic recombination
• References
• Useful internet resources
• Chapter 9: Genome evolution and protein evolution
• 9.1 Evolution of genome size
• 9.2 The role and survival of nongenic DNA
• 9.3 Repetitiveness of genomic DNA
• 9.4 Mechanisms responsible for increases in genome size
• 9.5 Compositional organization of eukaryotic genomes
• 9.6 Genomes of model organisms
• 9.6.1 Viral genomes
• 9.6.2 Cellular genomes
• 9.6.2.1 Eubacterial genomes
• 9.6.2.2 Archaeal genomes
• 9.6.2.3 Organelle genomes
• 9.6.2.4 Eukaryotic genomes
• 9.6.2.5 Genome duplications in the evolution of early vertebrates
• 9.6.3 Value of comparative genomics for the identification of functional elements
• 9.6.4 Finding protein-coding genes in genome sequences
• 9.7 The genome of the cenancestor
• 9.8 Changes in gene number and gene density in different evolutionary lineages
• 9.9 Proteome evolution
• 9.9.1 Proteome evolution – classification of proteins by structural features
• 9.9.2 Proteome evolution – classification of proteins by homology
• 9.9.3 Proteome evolution – classification of proteins by function
• 9.9.4 Proteome evolution – evolution of proteome complexity
• 9.9.5 Proteome evolution and organismic complexity
• References
• Useful internet resources
• Glossary
• Index