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Protein Evolution Book

Protein Evolution
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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  • Protein Evolution
  • Written by author Laszlo Patthy
  • Published by Wiley, John & Sons, Incorporated, January 2008
  • 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.
  • The flood of information on gene and protein sequences from the genome projects has revolutionized molecular and evolutionary biology and led to the rapid development of the science called genomics. Reliable prediction of the function of a novel gene/prot
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Authors

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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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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