Protein and Peptide Folding, Misfolding, and Non-Folding

, by Schweitzer-Stenner, Reinhard; Uversky, Vladimir

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ISBN: 9780470591697 | 0470591692
Cover: Hardcover
Copyright: 3/27/2012

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This book provides an overview on what researchers have learned about unfolded peptides and how this knowledge facilitates the understanding of (a) the folding process, (b) the binding of ligands to receptor molecules and (c) peptide self-aggregation. In this context different experimental, theoretical and computational concepts and approaches are introduced. This book can become a very useful addition for graduate level courses on protein folding for the education of undergraduate and graduate students in research groups, which are exploring peptide self-aggregation for biomedical and biotechnological purposes.

Introduction to the Wiley Series on Protein and Peptide Science	p. xiii
Preface	p. xv
Contributors	p. xix
Introduction	p. 1
Why Are We Interested in the Unfolded Peptides and Proteins?	p. 3
Introduction	p. 3
Why Study IDPs?	p. 4
Lesson 1: Disorderedness Is Encoded in the Amino Acid Sequence and Can Be Predicted	p. 5
Lesson 2: Disordered Proteins Are Highly Abundant in Nature	p. 7
Lesson 3: Disordered Proteins Are Globally Heterogeneous	p. 9
Lesson 4: Hydrodynamic Dimensions of Natively Unfolded Proteins Are Charge Dependent	p. 14
Lesson 5: Polymer Physics Explains Hydrodynamic Behavior of Disordered Proteins	p. 16
Lesson 6: Natively Unfolded Proteins Are Pliable and Very Sensitive to Their Environment	p. 18
Lesson 7: When Bound, Natively Unfolded Proteins Can Gain Unusual Structures	p. 20
Lesson 8: IDPs Can Form Disordered or Fuzzy Complexes	p. 25
Lesson 9: Intrinsic Disorder Is Crucial for Recognition, Regulation, and Signaling	p. 25
Lesson 10: Protein Posttranslational Modifications Occur at Disordered Regions	p. 28
Lesson 11: Disordered Regions Are Primary Targets for AS	p. 30
Lesson 12: Disordered Proteins Are Tightly Regulated in the Living Cells	p. 31
Lesson 13: Natively Unfolded Proteins Are Frequently Associated with Human Diseases	p. 33
Lesson 14: Natively Unfolded Proteins Are Attractive Drug Targets	p. 35
Lesson 15: Bright Future of Fuzzy Proteins	p. 38
Acknowledgments	p. 39
References	p. 40
Conformational Analysis of Unfolded States	p. 55
Exploring the Energy Landscape of Small Peptides and Proteins by Molecular Dynamics Simulations	p. 57
Introduction: Free Energy Landscapes and How to Construct Them	p. 57
Dihedral Angle PCA Allows Us to Separate Internal and Global Motion	p. 61
Dimensionality of the Free Energy Landscape	p. 62
Characterization of the Free Energy Landscape: States, Barriers, and Transitions	p. 65
Low-Dimensional Simulation of Biomolecular Dynamics to Catch Slow and Rare Processes	p. 67
PCA by Parts: The Folding Pathways of Villin Headpiece	p. 69
The Energy Landscape of Aggregating Aß-Peptides	p. 73
Concluding Remarks	p. 74
Acknowledgments	p. 75
References	p. 75
Local Backbone Preferences and Nearest-Neighbor Effects in the Unfolded and Native States	p. 79
Introduction	p. 79
Early Days: Random Coil-Theory and Experiment	p. 80
Denatured Proteins as Self-Avoiding Random Coils	p. 82
Modeling the Unfolded State	p. 82
NN Effects in Protein Structure Prediction	p. 86
Utilizing Folding Pathways for Structure Prediction	p. 87
Native State Modeling	p. 88
Secondary-Structure Propensities: Native Backbones in Unfolded Proteins	p. 92
Conclusions	p. 92
Acknowledgments	p. 93
References	p. 94
Short-Distance FRET Applied to the Polypeptide Chain	p. 99
A Short Timeline of Resonance Energy Transfer Applied to the Polypeptide Chain	p. 99
A Short Theory of FRET Applied to the Polypeptide Chain	p. 101
DBO and Dbo	p. 105
Short-Distance FRET Applied to the Structured Polypeptide Chain	p. 107
Short-Distance FRET to Monitor Chain-Structural Transitions upon Phosphorylation	p. 116
Short-Distance FRET Applied to the Structureless Chain	p. 120
The Future of Short-Distance FRET	p. 125
Acknowledgments	p. 125
Dedication	p. 126
References	p. 126
Solvation and Electrostatics as Determinants of Local Structural Order in Unfolded Peptides and Proteins	p. 131
Local Structural Order in Unfolded Peptides and Proteins	p. 131
ESM	p. 134
The ESM and Strand-Coil Transition Model	p. 137
The ESM and Backbone Conformational Preferences	p. 138
The Nearest-Neighbor Effect	p. 141
The ESM and Cooperative Local Structures-Fluctuating ß-Strands	p. 141
The ESM and ß-Sheet Preferences in Native Proteins- Significance of Unfolded State	p. 144
The ESM and Secondary Chemical Shifts of Polypeptides	p. 145
Role of Backbone Solvation in Determining Hydrogen Exchange Rates of Unfolded Polypeptides	p. 148
Other Theoretical Models of Unfolded Polypeptides, 148 Acknowledgments	p. 149
References	p. 149
Experimental and Computational Studies of Polyproline II Propensity	p. 159
Introduction	p. 159
Experimental Measurement of PII Propensities	p. 161
Computational Studies of Denatured State Conformational Propensities	p. 168
A Steric Model Reveals Common PII Propensity of the Peptide Backbone	p. 172
Correlation of PII Propensity to Amino Acid Properties	p. 175
Summary	p. 180
Acknowledgments	p. 180
References	p. 180
Mapping Conformational Dynamics in Unfolded Polypeptide Chains Using Short Model Peptides by NMR Spectroscopy	p. 187
Introduction	p. 187
General Aspects of NMR Spectroscopy	p. 189
NMR Parameters and Their Measurement	p. 191
Translating NMR Parameters to Structural Information	p. 202
Conclusions	p. 213
Acknowledgments	p. 215
References	p. 215
Secondary Structure and Dynamics of a Family of Disordered Proteins	p. 221
Introduction	p. 221
Materials and Methods	p. 223
Results and Discussion	p. 226
Acknowledgments	p. 235
References	p. 235
Disordered Peptides and Molecular Recognition	p. 239
Binding Promiscuity of Unfolded Peptides	p. 241
Protein-Protein Interaction Networks	p. 241
Role of Intrinsic Disorder in PPI Networks	p. 242
Transient Structural Elements in Protein-Based Recognition	p. 243
Chameleons and Adaptors: Binding Promiscuity of Unfolded Peptides	p. 256
Principles of Using the Unfolded Protein Regions for Binding	p. 262
Conclusions	p. 266
Acknowledgments	p. 266
References	p. 266
Intrinsic Flexibility of Nucleic Acid Chaperone Proteins from Pathogenic RNA Viruses	p. 279
Introduction	p. 279
Retroviruses and Retroviral Nucleocapsid Proteins	p. 280
Core Proteins in the Flaviviridae Family of Viruses	p. 288
Coronavirus Nucleocapsid Protein	p. 290
Hantavirus Nucleocapsid Protein	p. 291
Acknowledgments	p. 293
References	p. 293
Aggregation of Disordered Peptides	p. 307
Self-Assembling Alanine-Rich Peptides of Biomedical and Biotechnological Relevance	p. 309
Biomolecular Self-Assembly	p. 309
Misfolding and Human Disease	p. 310
Exploitation of Peptide Self-Assembly for Biotechnological Applications	p. 326
Concluding Remarks	p. 340
Acknowledgments	p. 340
References	p. 340
Structural Elements Regulating Interactions in the Early Stages of Fibrillogenesis: A Human Calcitonin Model System	p. 351
Stating the Problem	p. 351
Aggregation Models: The State of The Art	p. 354
Human Calcitonin hCT as a Model System for Self-Assembly	p. 356
The "Prefibrillar" State of hCT	p. 358
How Many Molecules for the Critical Nucleus?	p. 361
Modeling Prefibrillar Aggregates	p. 366
hCT Helical Oligomers	p. 366
The Role of Aromatic Residues in the Early Stages of Amyloid Formation	p. 372
The Folding of hCT before Aggregation	p. 373
Model Explains the Differences in Aggregation Properties between hCT and sCT	p. 374
hCT Fibril Maturation	p. 375
¿-Helix →ß-Sheet Conformational Transition and hCT Fibrillation	p. 377
Concluding Remarks	p. 378
Acknowledgments	p. 378
References	p. 379
Solution NMR Studies of Aß Monomers and Oligomers	p. 389
Introduction	p. 389
Overexpression and Purification of Recombinant Aß	p. 390
Aß Monomers	p. 393
Aß Oligomers and Monomer-Oligomer Interaction	p. 403
Conclusion	p. 406
References	p. 406
Thermodynamic and Kinetic Models for Aggregation of Intrinsically Disordered Proteins	p. 413
Introduction	p. 413
Thermodynamics of Protein Aggregation-the Phase Diagram Approach	p. 415
Thermodynamics of IDP Aggregation (Phase Separation)- MPM Description	p. 420
Kinetics of Homogeneous Nucleation and Elongation Using MPMs	p. 425
Concepts from Colloidal Science	p. 427
Conclusions	p. 433
Acknowledgments	p. 433
References	p. 434
Modifiers of Protein Aggregation-From Nonspecific to Specific Interactions	p. 441
Introduction	p. 441
Nonspecific Modifiers	p. 442
Specific Modifiers	p. 454
Acknowledgments	p. 465
References	p. 466
Computational Studies of Folding and Assembly of Amyloidogenic Proteins	p. 479
Introduction	p. 479
Amyloids	p. 480
Computer Simulations	p. 485
Summary	p. 514
References	p. 515
Index	p. 529
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Protein and Peptide Folding, Misfolding, and Non-Folding

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