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.

• 
  
• 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

Preface to the first edition.

Preface to the second edition.

Acknowledgments.

Introduction.

1. Protein-Coding Genes.

1.1 Structure of protein-coding genes.

1.2 Transcription.

1.3 Translation.

References.

Useful internet resources.

2. Protein Structure.

2.1 The polypeptide backbone.

2.2 The amino acids.

2.3 Covalent modifications of amino acid side chains.

2.4 Interactions that govern protein folding and stability.

2.5 Secondary structural elements.

2.6 Supersecondary structures.

2.7 Tertiary structures of proteins.

2.8 Multidomain proteins.

2.9 Multisubunit proteins.

References.

Useful internet resources.

3. Mutations.

3.1 Types of mutations.

3.2 Factors affecting rates of mutation.

3.3 The fate of mutations.

3.4 The molecular clock.

References.

Useful internet resources.

4. Evolution of Protein-Coding Genes.

4.1 Alignment of nucleotide and amino acid sequences.

4.2 Estimating the number of nucleotide substitutions.

4.3 Rates and patterns of nucleotide substitution.

4.4 Variation in substitution rates.

4.5 Molecular phylogeny.

References.

Useful internet resources.

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.

5.8 Detecting sequence homology of protein-coding genes.

References.

Useful internet resources.

6. Formation of Novel Protein-Coding Genes.

6.1 De novo formation of novel protein-coding genes.

6.2 Gene duplications.

References.

Useful internet resources.

7. Evolution of Paralogous Proteins.

7.1 Advantageous duplications.

7.2 Neutral duplications.

7.3 Similarities and differences in the evolution of paralogous and orthologous proteins.

7.4 Predicting the function of proteins by homology.

7.5 Detecting distant homology of protein-coding genes.

References.

Useful internet resources.

8. Protein Evolution by Assembly from Modules.

8.1 Modular assembly by intronic recombination.

8.2 Modular assembly by exonic recombination.

References.

Useful internet resources.

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.

9.7 The genome of the cenancestor.

9.8 Changes in gene number and gene density in different evolutionary lineages.

9.9 Proteome evolution.

References.

Useful internet resources.

Glossary.

Index

Laszlo Patthy is the head of the Extracellular Proteolysis Group of the Institute of Enzymology, Budapest. In the last twenty-five years the main area of his experimental research has been the molecular biology, structure, function, and evolution of multidomain protein components of extracellular proteolytic systems of vertebrates. He is the author of Protein Evolution by Exon-shuffling (1995) and Protein Evolution (Blackwell, 1999). 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/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 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. This second edition, while retaining its accessible style and reader-friendly organization, is completely updated and boasts a new glossary and updated references. The chapter on genome evolution has been significantly expanded in order to cover genomes of model organisms sequenced since the completion of the first edition. Protein Evolution is ideal 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.