Molecular Biology of Protein Folding, Part B

by Conn

• ISBN13: 9780123745958
• ISBN10: 0123745950
• Format: Hardcover
• Copyright: 2008-12-03
• Publisher: Elsevier Science

Summary

Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes. Increased understanding of nucleic acids and their role in molecular biology will further many of the biological sciences including genetics, biochemistry, and cell biology. Progress in Nucleic Acid Research and Molecular Biology is intended to bring to light the most recent advances in these overlapping disciplines with a timely compilation of reviews comprising each volume.

Table of Contents

Self-Organizing Dynamics in Protein Folding	p. 1
Introduction	p. 2
Protein Structure and Folding	p. 3
Self-Organization and Nonlinear Processes	p. 7
Self-Organization in Protein Folding	p. 11
Summary	p. 31
References	p. 31
Toward Reliable Simulations of Protein Folding, Misfolding and Aggregation	p. 39
Introduction	p. 39
Protein Models	p. 40
Algorithms for Optimizing Protein Configurations	p. 42
Algorithms for Simulating the Thermodynamics of Configurations	p. 43
Folding Simulations of Small Proteins	p. 48
Misfolding and Aggregation	p. 50
Conclusion	p. 51
References	p. 52
Use of Protein Engineering Techniques to Elucidate Protein Folding Pathways	p. 57
Introduction	p. 58
Early Protein Engineering Studies of Folding Pathways	p. 59
Single Point Mutations and [phi]-Value Analysis	p. 61
[Psi]-Value Analysis	p. 80
Proline Isomerization	p. 82
Repeat Proteins	p. 83
Circular Permutants	p. 87
Multidomain Proteins	p. 91
Engineering Probes of Folding into Proteins	p. 95
Single-Molecule Studies of Protein Folding Pathways	p. 97
Summary	p. 100
References	p. 101
Principles of Protein Misfolding	p. 115
Protein Folding and Misfolding	p. 116
Protein Misfolding: Amyloid Diseases	p. 136
Light Chain Amyloidosis	p. 145
Conclusions	p. 151
References	p. 152
Protein Folding Revisited	p. 161
Introduction	p. 162
Perspectives on the Folding Problem	p. 171
Wormholes in More Detail	p. 186
Conclusions	p. 194
References	p. 197
Minimal Models for Proteins and RNA: From Folding to Function	p. 203
Introduction	p. 204
Rationale for Developing Structure-Based CG Models	p. 206
Protein Folding	p. 209
RNA Folding	p. 231
Concluding Remarks	p. 242
References	p. 243
The Folding Pathway of Triosephosphate Isomerase	p. 251
Introduction	p. 252
The Denaturation of TIM	p. 254
The Reversibility of TIM Denaturation	p. 254
Models Describing TIM Denaturation	p. 257
The Monomeric Intermediate	p. 257
The Folding Pathway of ([beta]/[alpha])[subscript 8] Proteins	p. 259
The Dimeric Intermediate	p. 260
Energetic of the TIM Unfolding	p. 261
Final Remarks	p. 262
References	p. 263
Index	p. 269
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