Protein Engineering and Design
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Table of contents
- Contentsv
- Contributorsxi
- Prefacexiii
- Part I: PREDICTIONxv
- Chapter 1. Strategies for the Design of Novel Proteins1
- I. Introduction1
- II. Strategies for the Design of Structure2
- III. Strategies for the Design of Function28
- IV. Conclusion45
- References46
- Chapter 2. Computer Methods in Protein Modeling: An Overview51
- I. Introduction51
- II. Early Methods of Computer Modeling "by Hand"52
- III. Hardware and Computational Workstyles54
- IV. Molecular Mechanics, a Controversial Paradigm of Protein Folding55
- V. What Do We Know about Folding?57
- VI. Electrostatics of Protein Structures58
- VII. De Novo Design of Proteins: Folding in the Computer60
- VIII. Secondary Structure Prediction61
- IX. Surfaces and Volumes62
- X. Molecular Dynamics Simulations63
- XI. Free Energy Perturbation64
- XII. Knowledge-Based Approaches to Model Building65
- XIII. Conformational Searches66
- XIV. The Free Energy Problem67
- XV. Future Trends68
- References69
- Part II: PRODUCTION74
- Chapter 3. The Art of Expression: Sites and Strategies for Heterologous Expression75
- I. Why Escherichia coli?75
- II. Genetic Considerations in Expression77
- III. Post-translational Manipulations: Form of the Expressed Protein90
- IV. Sites of Expression96
- V. Conclusion101
- References102
- Chapter 4. Methods for Expressing Recombinant Proteins in Yeast105
- I. Introduction105
- II. Materials and Methodology for Protein Expression in Saccharomyces cerevisiae110
- III. Summary145
- References146
- Chapter 5. In Vitro Mutagenesis155
- I. Introduction155
- II. In Vitro Mutagenesis: Principle and Variations157
- Ill. Examples of Applications172
- IV. Conclusions174
- Appendix: Some Key Literature References and Commercial Products for Those Wishing to Use in Vitro S175
- References176
- Part III: CHARACTERIZATION180
- Chapter 6. Determination of Structures of Larger Proteins in Solution by Three- and Four-Dimensional181
- I. Introduction181
- II. The Nature of the Structural Data Derived from NMR Measurements183
- III. General Principles Involved in Deriving Experimental Restraints from NMR Data186
- IV. Basics of 3D and 4D NMR189
- V. Heteronuclear 3D and 4D NMR in Practice192
- VI. Application of 3D and 4D NMR to the Determination of Larger Protein Structures197
- VII. Concluding Remarks202
- References203
- Chapter 7. A Consumer's Guide to Protein Crystallography205
- I. Crystallization210
- II. Data Collection215
- III. Phase Determination219
- IV. Electron Density Map Interpretation221
- V. Refinement223
- VI. Exploiting the Structure226
- VII. Some Final Comments227
- Appendix: Some Useful Articles and Addresses227
- References228
- Chapter 8. Spectroscopic and Calorimetric Methods for Characterizing Proteins and Peptides231
- I. Introduction231
- II. Circular Dichroism232
- III. Fourier-Transform Infrared Spectroscopy240
- IV. Raman and Resonance Raman Spectroscopies247
- V. Differential Scanning Calorimetry254
- References260
- Part IV: APPLICATIONS264
- Chapter 9. The Design of Polymeric Biomaterials from Natural α-L-Amino Acids265
- I. Introduction265
- II. Poly(amino acids) as Biomaterials267
- III. Disadvantages of Poly(amino acids) as Biomaterials269
- IV. Strategies for the Modification of Conventional Poly(amino acids)270
- V. Pseudo-poly(amino acids)273
- VI. Conclusions283
- References284
- Chapter 10. The Nicotinic Acetylcholine Receptor as a Model for a Superfamily of Ligand-Gated Ion Ch289
- I. The Similar Sequence and Multisubunit Structure of the Nicotinic Acetylcholine Receptor and Other289
- II. Structure of Cholinergic Ligand Binding Sites on the AChR α Subunit309
- III. Structure of Ligand Binding Sites of Other Members of the AChR Superfamily326
- IV. Multiplicity of Ligand Binding Sites on the AChR and Other Related Receptors328
- V. Molecular Approaches for the Identification of the Ion Channel337
- VI. Summary340
- References341
- Index353
The design and production of novel peptides and proteins occupy pivotal positions in science and technology and will continue to do so in the 21st century. Protein Engineering and Design outlines the rapid advances in computer-based modeling, protein engineering, and methods needed for protein and peptide preparation and characterization. This indispensable reference lays the groundwork for understanding this multidisciplinary activity while providing an introduction for researchers and students to the field of protein design.
Key Features
* Introduces and defines the techniques involved in protein engineering and design
* Provides a concise overview of key technologies involved and demonstrates their contributions to the specialized design and production of novel proteins and peptides
Key Features
* Introduces and defines the techniques involved in protein engineering and design
* Provides a concise overview of key technologies involved and demonstrates their contributions to the specialized design and production of novel proteins and peptides