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Preface to the first edition ix
Preface to the second edition xi
Acknowledgements xiii
Introduction xv
Protein-Coding Genes 1
A Structure of protein-coding genes 2
Transcription 3
Translation 10
References 14
Useful internet resources 15
Protein Structure 18
The polypeptide backbone 18
The amino acids 18
Covalent modifications of amino acid side chains 23
Enzymatic modifications 23
Nonenzymatic chemical modifications 27
Interactions that govern protein folding and stability 28
Noncovalent interactions 28
The hydrophobic interaction 29
Secondary structural elements 30
The [alpha]-helix 30
[beta]-sheets 31
Reverse turns 32
Supersecondary structures 32
Tertiary structures of proteins 33
Globular proteins 33
Fibrous proteins 35
Unusual structures of internally repeated proteins 36
Secreted proteins and membraneproteins 37
Intrinsically disordered proteins 40
Multidomain proteins 40
Multisubunit proteins 40
References 41
Useful internet resources 41
Mutations 45
Types of mutations 45
Substitutions 45
Deletion, duplication, insertion and fusion 48
Factors affecting rates of mutation 50
The fate of mutations 52
The molecular clock 59
References 61
Useful internet resources 62
Evolution of Protein-Coding Genes 63
Alignment of nucleotide and amino acid sequences 63
Estimating the number of nucleotide substitutions 65
Substitutions in translated regions 67
Substitutions in untranslated regions, introns and 5[prime] and 3[prime] flanking regions of protein-coding genes 68
Rates and patterns of nucleotide substitution 68
Rates of nucleotide substitution 69
Variation in substitution rates 71
Variation among different sites of the translated region 72
Variation among genes 74
Constancy and variation in substitution rates of orthologous genes 75
Nonrandom substitutions at synonymous positions 76
Molecular phylogeny 78
Phylogenetic trees 78
Tree reconstruction 79
Tree-making methods 81
Estimation of species-divergence times 85
References 85
Useful internet resources 87
Evolution of Orthologous Proteins 89
Orthologous proteins with the same function in different species 91
Orthologous proteins with modified function in different species 94
Orthologous proteins with major modification of function 98
Orthologous proteins that have lost their function 98
Orthologous proteins that have gained additional functions 99
Prediction of the function of orthologous proteins 99
The three-dimensional structure of orthologous proteins 100
Prediction of secondary structure of proteins 100
Prediction of the three-dimensional structure of proteins 102
Detecting sequence homology of protein-coding genes 103
References 104
Useful internet resources 105
Formation of Novel Protein-Coding Genes 108
De novo formation of novel protein-coding genes 108
Gene duplications 110
Mechanisms of gene duplication 111
Fate of duplicated genes 117
Fate of genes acquired by lateral gene transfer 121
Dating gene duplications 121
References 124
Useful internet resources 125
Evolution of Paralogous Proteins 126
Advantageous duplications 127
Unprocessed genes 127
Processed genes 127
Neutral duplications 130
Modification of function by point mutations 132
Major change of function by point mutations 140
Major change of function by domain acquisitions 143
Similarities and differences in the evolution of paralogous and orthologous proteins 147
Predicting the function of proteins by homology 150
Nonhomology-based methods for the prediction of the function of proteins 151
Detecting distant homology of protein-coding genes 152
Delecting distant homology by consensus approaches 152
Detecting distant homology by comparing three-dimensional structures 161
Detecting distant homology by comparing exon-intron structures 162
References 163
Useful internet resources 166
Protein Evolution by Assembly from Modules 170
Modular assembly by intronic recombination 171
Introns 173
Internal gene duplications/deletions via recombination in introns 182
Fusion of genes via recombination in introns 183
Exon shuffling via recombination in introns 183
Factors affecting acceptance of mutants created by intronic recombination 192
Classification of modules and mosaic proteins produced by exon shuffling 199
Genome evolution and the evolution of exon shuffling 207
Evolutionary significance of exon shuffling 209
Genome evolution and the evolution of alternative splicing 211
Modular assembly by exonic recombination 211
References 213
Useful internet resources 216
Genome Evolution and Protein Evolution 218
Evolution of genome size 218
The role and survival of nongenic DNA 221
Repetitiveness of genomic DNA 221
Mechanisms responsible for increases in genome size 223
Compositional organization of eukaryotic genomes 224
Genomes of model organisms 225
Viral genomes 226
Cellular genomes 230
Eubacterial genomes 231
Archaeal genomes 238
Organelle genomes 241
Eukaryotic genomes 244
Genome duplications in the evolution of early vertebrates 271
Value of comparative genomics for the identification of functional elements 276
Finding protein-coding genes in genome sequences 277
The genome of the cenancestor 280
Changes in gene number and gene density in different evolutionary lineages 280
Proteome evolution 282
Proteome evolution - classification of proteins by structural features 282
Proteome evolution - classification of proteins by homology 283
Proteome evolution - classification of proteins by function 283
Proteome evolution - evolution of proteome complexity 287
Proteome evolution and organismic complexity 291
References 293
Useful internet resources 302
Glossary 309
Index 367
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Protein Evolution, 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.
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Protein Evolution, 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.
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