Protein Folding

1st Edition - December 28, 1982
Author: Charis Ghelis
Language: English
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 1 4 0 9 2 - 8

Protein Folding aims to collect the most important information in the field of protein folding and probes the main principles that govern formation of the three-dimensional… Read more

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Protein Folding aims to collect the most important information in the field of protein folding and probes the main principles that govern formation of the three-dimensional structure of a protein from a nascent polypeptide chain, as well as how the functional properties appear. This text is organized into three sections and consists of 15 chapters. After an introductory chapter where the main problems of protein folding are considered at the cellular level in the context of protein biosynthesis, the discussion turns to the conformation of native globular proteins. Definitions and rules of nomenclature are given, including the structural organization of globular proteins deduced from X-ray crystallographic data. Folding mechanisms are tentatively deduced from the observation of invariants in the architecture of folded proteins. The next chapters focus on the energetics of protein conformation and structure, indicating the principles of thermodynamic stability of the native structure, along with theoretical computation studies of protein folding, structure prediction, and folding simulation. The reader is also introduced to various experimental approaches; the reversibility of the unfolding-folding process; equilibrium and kinetic studies; and detection and characterization of intermediates in protein folding. This text concludes with a chapter dealing with problems specific to oligomeric proteins. This book is intended for research scientists, specialists, biochemists, and students of biochemistry and biology.

Preface

Acknowledgments

Introduction: Cellular Environment and Significance of Folding Processes

1 Folding and Processing : The Last Events in Protein Biosynthesis

1.1. Evolution of the Main Concepts of Protein Folding

1.2. Structure of Folded Proteins in the Biological Environment

1.3. Posttranslational and Cotranslational Processes

I Considerations of Protein Folding Deduced from Characteristics of Folded Proteins

2 Structural Characteristics of Folded Proteins

2.1. Definition of the Levels of Protein Structure

2.2. Primary Structure

2.3. Description of Protein Conformation

2.4. Backbone Conformation

2.5. Supersecondary Structures

2.6. Structural Domains

2.7. Overall Conformation of Proteins

2.8. Quaternary Structure of Proteins

2.9. Localization of Water Molecules Interacting with Proteins

2.10. Structural Similarities between Monomeric and Oligomeric Proteins

2.11. Evolutionary Aspect of Protein Structures

3 Energetics of Protein Conformation: Conditions Restricting the Allowed Conformations

3.1. Introduction: The Random Search for the Native Structure

3.2. Intramolecular Interactions Arising from Factors Intrinsic to the Protein Molecule

3.3. Intramolecular Interactions Influenced by the Solvent

3.4. Intramolecular Interactions Determined Mainly by the Solvent

3.5. Interactions between Solvent and Protein Molecules

3.6. Total Conformational Energy of the Polypeptide Chain

4 Theoretical Approach to Protein Folding

4.1. Introduction: Problems in Computation of Protein Conformation

4.2. Methods for Evaluation of Conformational Preferences of a Single Peptide Unit

4.3. Methods for Evaluation of Conformational Preferences of a Polypeptide Chain

4.4. Prediction of Ordered Structures in Proteins

4.5. Prediction of Supersecondary Structures

4.6. Simulation of Protein Folding

4.7. Analysis of Prediction and Simulation Results

4.8. Conformational Fluctuations of Proteins

4.9. Comments on Theoretical Approaches to Protein Folding

II Experimental Approaches

5 Simulation of Protein Folding: Studies of In Vitro Denaturation-Renaturation

5.1. Protein Unfolding Induced by Physicochemical Perturbations

5.2. Characterization of the Unfolded State

5.3. Spontaneous Refolding of Proteins without Disulfide Bridges

5.4. Spontaneous Refolding of Proteins with Disulfide Bridges

5.5. Influence of Various Factors on Protein Folding

5.6. Spontaneous Refolding of Oligomeric Proteins

5.7. Apparent Irreversibility of the Unfolding-Folding Process under Critical Conditions

5.8. Comments on the Validity of the in Vitro Denaturation-Renaturation Model

6 Physicochemical Studies of the Unfolding-Folding Equilibrium

6.1. Studies of the Unfolding-Folding Transition at Equilibrium

6.2. The Two-State Approximation

6.3. Energetics of the Transition Deduced from Equilibrium Studies

6.4. Interpretation of Experimental Studies of the Unfolding-Folding Transition

6.5. Calorimetric Studies of the Transition

7 Kinetic Studies of Unfolding and Folding Processes

7.1. Kinetics of Reversible First-Order Transitions

7.2. Analysis of the Kinetics

7.3. Kinetic Studies by Fast Reaction Techniques

7.4. Occurrence of Abortive Intermediates

7.5. Nature of Fast and Slow Refolding Reactions

8 Detection and Characterization of Intermediates

8.1. Detection of Structured Segments during Unfolding or Refolding Processes

8.2. Detection of Intermediates by Nuclear Magnetic Resonance Studies

8.3. Trapping of Intermediates during Refolding of Unfolded and Reduced Proteins by Blocking the SH Groups

8.4. Detection of Intermediates in Protein Folding by Differential Labeling

8.5. Detection of Intermediates by Accessibility of Peptide Bonds to Proteolytic Enzymes

8.6. Detection of Intermediates by Use of Nonspecific Surface-Labeling Reagents

8.7. Use of Extrinsic Probes Attached to Side Chains for Detection of Intermediates in Protein Folding

8.8. Detection of Intermediates in Protein Folding by Other Methods

9 Immunochemical Approaches to Protein Folding

9.1. Antibody Probe as a Tool to Study Protein Structure

9.2. Immunochemical Approaches using Monospecific Antibodies

9.3. Immunochemical Approaches using Unfractionated Antibodies against the Entire Protein

10 Folding and Assembly of Building Blocks

10.1. Folding of Polypeptide Fragments

10.2. Folding of Fragments Corresponding to Structural Domains

10.3. Nucleation and Folding

10.4. In Vitro Complementation of Fragments

10.5. In Vitro Complementation of Fragments Corresponding to Structural Domains

10.6. Role of Domains and of Smaller Substructures in Protein Folding

11 Folding-Unfolding of Oligomeric Proteins

11.1. Specific Problems Concerning Folding of Oligomeric Proteins

11.2. Kinetics of Unfolding-Folding of Oligomeric Proteins

11.3. Trapping of Intermediates during Refolding of Oligomeric Proteins

11.4. Activity of Isolated Subunits

11.5. Conformational Changes on Subunit Assembly

11.6. Effects of Ligands in Refolding of Oligomeric Proteins

III Concluding Comments

12 Mechanisms of Protein Folding

12.1. Pathway(s) of Folding

12.2. Stability of the Native Structure

12.3. Conformational Fluctuations of Native Proteins

12.4. Proteins Achieve Their Folding upon a Specific Binding Process or during Catalysis

12.5. Concluding Remarks on the Development of Studies on Protein Folding

References

Index