Protein Evolution

The flood of information on gene and protein sequences from the genome projects has revolutionised molecular and evolutionary biology and has led to the rapid development of the science called genomics. Reliable prediction of the function of a novel gene/protein requires complex computational analysis of genomic and protein sequence information which exploit the principles governing the evolution of protein structure and function. This book aims to provide an up-to-date summary of the principles of protein evolution and discusses both the methods available to analyse the evolutionary history of proteins as well as those for predicting their structure-function relationships. Protein Evolution is intended for senior undergraduates and graduate students taking courses in protein structure and evolution, as well as bioinformatics. it will also be a useful supplement for students taking wider courses in molecular evolution, as well as a valuable resource for professionals in the area of functional genomics.

Table of Contents:
Preface Introduction 1. Protein-Coding Genes Structure Of Protein-Coding Genes Transcription Translation 2. Protein Structure The Polypeptide Backbone The Amino Acids Covalent Modifications Of Amino Acid Side Chains Enzymatic Modifications Nonenzymatic Chemical Modifications Interactions Governing Protein-Folding And Stability Noncovalent Interactions The Hydrophobic Interaction Secondary Structural Elements Supersecondary Structures Tertiary Structures Of Proteins Globular Proteins Fibrous Proteins Unusual Structures Of Internally Repeated Proteins Membrane Proteins Multidomain Proteins Multisubunit Proteins 3. Mutations Types Of Mutations Substitutions Deletion, Duplication, Insertion, Fusion; Factors Affecting Rates Of Mutation The Fate Of Mutations The Molecular Clock 4. Evolution Of Protein-Coding Genes Alignment Of Nucleotide And Amino Acid Sequences Estimating The Number Of Nucleotide Substitutions Substitutions In Translated Regions Substitutions In Untranslated Regions, Introns And 5' And 3' Flanking Regions Of Protein-Coding Genes Rates And Patterns Of Nucleotide Substitution Rates Of Nucleotide Substitution Variation In Substitution Rates Variation Among Different Sites Of Translated Regions Variation Among Genes Constancy And Variation In Substitution Rates Of Orthologous Genes Nonrandom Substitutions In Synonymous Positions Molecular Phylogeny Phylogenetic Trees Tree Reconstruction Tree-Making Methods Estimation Of Species-Divergence Times 5. Evolution Of Orthologous Proteins Orthologous Proteins With The Same Function In Different Species Orthologous Proteins With Modified Function In Different Species Orthologous Proteins With Major Modification Of Function Orthologous Proteins That Lost Their Function Orthologous Proteins That Gained Additional Functions The Three-Dimensional Structure Of Orthologous Proteins Prediction Of Secondary Structure Of Proteins Prediction Of The Three-Dimensional Structure Of Proteins Detecting Sequence Homology Of Protein-Coding Genes 6. Formation Of Novel Protein-Coding Genes De Novo Formation Of Novel Protein-Coding Genes Gene Duplications Mechanisms Of Gene Duplications Fate Of Duplicated Genes Dating Gene Duplications 7. Evolution Of Paralogous Proteins Advantageous Duplications Unprocessed Genes Processed Genes Neutral Duplications Modification Of Function By Point Mutations Major Change Of Function By Point Mutations Major Change Of Function By Domain Acquisition Similarities And Differences In The Evolution Of Paralogous And Orthologous Proteins Prediction Of The Function Of Proteins Detecting Distant Homology Of Protein-Coding Genes Detecting Distant Homology By Consensus Approaches Detecting Distant Homology By Comparison Of Three-Dimensional Structures Detecting Distant Homology By Comparison Of Exon-Intron Structures 8. Protein Evolution By Assembly From Modules Modular Assembly By Intronic Recombination Introns; Internal Gene Duplications/Deletions Via Recombination In Introns Exon-Shuffling Via Recombination In Introns Factors Affecting Acceptance Of Mutants Created By Intronic Recombination Classifications Of Module And Mosaic Proteins Produced By Exon-Shuffling Evolution Of Exon-Shuffling Evolutionary Significance Of Exon-Shuffling Modular Assembly Of Proteins By Exonic Recombination 9. Genome Evolution And Protein Evolution Evolution Of Genome Size The Role And Survival Of Nongenic DNA Repetitiveness Of Genomic DNA Mechanisms Responsible For Increases In Genome Size Compositional Organization Of The Eukaryotic Genomes Genomes Of Model Organisms Eubacterial Genomes Archaeal Genomes Eukaryotic Genomes The Genome Of The Cenancestor Changes In Gene Number And Gene Density In Different Evolutionary Lineages Proteome Evolution Classification Of Proteins By Structural Features Classification Of Proteins By Homology Classification Of Proteins By Function