Protein Modules and Protein-Protein Interactions
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Table of contents
- Contentsv
- Chapter 1.Introduction1
- I. Protein Modules and Protein–Protein Interaction: Towards a Global View1
- Web Sites5
- References6
- Chapter 2. Structural Basis of Macromolecular Recognition9
- I. Introduction9
- II. Geomatric and Chemical Features of Macromlecular Recognition11
- III. Classification of Protein–Protein and Protein–DNA Complexes32
- IV. Energetics of Magromolecular Recognition40
- V. Computational Approaches for Predicting and Simulating Protein–Protein Interaction50
- VI. Concluding Remarks64
- Web Sites65
- References66
- Chapter 3. Sequences Analysis of Multidomain Proteins: Past Perspectives and Future Directions75
- I. Identification of Novel Protein Domain Families75
- II. Methods for Classifying Protein Domain Families81
- III. From Domain Classification to Domain context85
- IV. Genome-Wide Analysis: New Quality in Domain Resarch89
- V. Conclusion96
- References96
- Chapter 4. Identification of Transiently Interacting Proteins and of Stable Protein Complexes99
- I. Introduction99
- II. Genetic Approaches100
- III. Biological Methods103
- IV. Biochemical Methods105
- V. Validation of Interactions113
- VI. Characterization of Interacting Subunits and Dissection of Interaction Domain114
- References115
- Chapter 5. Molecular Recognition in Antibody–Antigen Complexes119
- I. Introduction119
- II. Structure of Antibody-Antigen Interfaces121
- III. Antibody Cross-Reactivity and Molecular Mimicry125
- IV. Thermodynamic Mapping of Antigen–Antibody Interfaces132
- V. Dissection of Binding Energetics in Antigen–Antibody Interfaces Using Dobule-Mutant Cycles136
- VI. Accommodation of Mutations in Antigen–Antibody Interfaces144
- VII. Functional Roles for Protein Plasticity in Antigen Recognition148
- VIII. Conclusions156
- References157
- Chapter 6. Molecular Recognition by SH2 Domains161
- I. Introduction161
- II. Single SH2 Domain Structure164
- III. Functional Analysis of Single SH2 Domain Binding172
- IV. Structure and Function of SH2 Domain in the Context of Other Protein Modules184
- V. Unusual SH2 Domain Interactions197
- VI. SH2 Domain as Drugs Targets202
- VII. Summary204
- References205
- Chapter 7. How SH3 Domain Recognize Proline211
- I. Introduction211
- II. Proline and Polyproline Type II Helices212
- III. The SH3 Domain: A Model System to Understand Interactions Mediated by Proline-Rich PPH Helices215
- References255
- Chapter 8. Structural Biology of elF4F: mRNA Recognition and Preparation in Eukaryotic Translation I269
- I. Introduction269
- II. Structural Features of Eukaryotic mRNAs271
- III. General Mechanisms of Cellular, Cap-Dependent Translation Initiation274
- IV. HEAT Repeats within eIF4G Direct Assembly of Translation Machinery283
- V. Preparation of the mRNA 5'-UTR for Small Ribosomal Subunit Binding288
- VI. Conclusion and Perspectives293
- References294
- AUTHOR INDEX299
- SUBJECT INDEX327
Protein modules engage in a multitude of interactions with one another and with other cellular components, notably with DNA. These interactions are a central aspect of protein function of great relevance in the post-genomic era. This volume describes a panel of approaches for analyzing protein modules and their interactions, ranging from bioinformatics to physical chemistry, to biochemistry, with an emphasis on the structure-function relationship in protein-protein complexes involved in cellular processes including signal transduction.
Key Features
* Comprehensive overview of different facets of macromolecule interactions
* Computational and bioinformatics aspects of analyzing protein modules and their interactions
* Emphasis on structure-function relationship in protein-protein complexes involved in cellular processes
Key Features
* Comprehensive overview of different facets of macromolecule interactions
* Computational and bioinformatics aspects of analyzing protein modules and their interactions
* Emphasis on structure-function relationship in protein-protein complexes involved in cellular processes