Protein and Peptide Folding, Misfolding, and Non-Folding

Reinhard Schweitzer-Stenner, PhD, is Professor and currently the Head of the Chemistry Department at Drexel University. Dr. Schweitzer-Stenner also heads the biospectroscopy research group. His research investigates peptide structure and functionally relevant heme distortions as well as ligand-receptor binding on the surface of mast cells. With more than 150 published research articles, Dr. Schweitzer-Stenner is widely recognized as a leader and pioneer in the study of the conformational properties of unfolded peptides.

Introduction to the Wiley Series on Protein and Peptide Science xiii Preface xv

Contributors xix

INTRODUCTION 1

1 Why Are We Interested in the Unfolded Peptides and Proteins? 3
Vladimir N. Uversky and A. Keith Dunker

1.1 Introduction, 3

1.2 Why Study IDPs?, 4

1.3 Lesson 1: Disorderedness Is Encoded in the Amino Acid Sequence and Can Be Predicted, 5

1.4 Lesson 2: Disordered Proteins Are Highly Abundant in Nature, 7

1.5 Lesson 3: Disordered Proteins Are Globally Heterogeneous, 9

1.6 Lesson 4: Hydrodynamic Dimensions of Natively Unfolded Proteins Are Charge Dependent, 14

1.7 Lesson 5: Polymer Physics Explains Hydrodynamic Behavior of Disordered Proteins, 16

1.8 Lesson 6: Natively Unfolded Proteins Are Pliable and Very Sensitive to Their Environment, 18

1.9 Lesson 7: When Bound, Natively Unfolded Proteins Can Gain Unusual Structures, 20

1.10 Lesson 8: IDPs Can Form Disordered or Fuzzy Complexes, 25

1.11 Lesson 9: Intrinsic Disorder Is Crucial for Recognition, Regulation, and Signaling, 25

1.12 Lesson 10: Protein Posttranslational Modifi cations Occur at Disordered Regions, 28

1.13 Lesson 11: Disordered Regions Are Primary Targets for AS, 30

1.14 Lesson 12: Disordered Proteins Are Tightly Regulated in the Living Cells, 31

1.15 Lesson 13: Natively Unfolded Proteins Are Frequently Associated with Human Diseases, 33

1.16 Lesson 14: Natively Unfolded Proteins Are Attractive Drug Targets, 35

1.17 Lesson 15: Bright Future of Fuzzy Proteins, 38

Acknowledgments, 39

References, 40

I CONFORMATIONAL ANALYSIS OF UNFOLDED STATES 55

2 Exploring the Energy Landscape of Small Peptides and Proteins by Molecular Dynamics Simulations 57
Gerhard Stock, Abhinav Jain, Laura Riccardi, and Phuong H. Nguyen

2.1 Introduction: Free Energy Landscapes and How to Construct Them, 57

2.2 Dihedral Angle PCA Allows Us to Separate Internal and Global Motion, 61

2.3 Dimensionality of the Free Energy Landscape, 62

2.4 Characterization of the Free Energy Landscape: States, Barriers, and Transitions, 65

2.5 Low-Dimensional Simulation of Biomolecular Dynamics to Catch Slow and Rare Processes, 67

2.6 PCA by Parts: The Folding Pathways of Villin Headpiece, 69

2.7 The Energy Landscape of Aggregating Aβ-Peptides, 73

2.8 Concluding Remarks, 74

Acknowledgments, 75

References, 75

3 Local Backbone Preferences and Nearest-Neighbor Effects in the Unfolded and Native States 79
Joe DeBartolo, Abhishek Jha, Karl F. Freed, and Tobin R. Sosnick

3.1 Introduction, 79

3.2 Early Days: Random Coil—Theory and Experiment, 80

3.3 Denatured Proteins as Self-Avoiding Random Coils, 82

3.4 Modeling the Unfolded State, 82

3.5 NN Effects in Protein Structure Prediction, 86

3.6 Utilizing Folding Pathways for Structure Prediction, 87

3.7 Native State Modeling, 88

3.8 Secondary-Structure Propensities: Native Backbones in Unfolded Proteins, 92

3.9 Conclusions, 92

Acknowledgments, 93

References, 94

4 Short-Distance FRET Applied to the Polypeptide Chain 99
Maik H. Jacob and Werner M. Nau

4.1 A Short Timeline of Resonance Energy Transfer Applied to the Polypeptide Chain, 99

4.2 A Short Theory of FRET Applied to the Polypeptide Chain, 101

4.3 DBO and Dbo, 105

4.4 Short-Distance FRET Applied to the Structured Polypeptide Chain, 107

4.5 Short-Distance FRET to Monitor Chain-Structural Transitions upon Phosphorylation, 116

4.6 Short-Distance FRET Applied to the Structureless Chain, 120

4.7 The Future of Short-Distance FRET, 125

Acknowledgments, 125

Dedication, 126

References, 126

5 Solvation and Electrostatics as Determinants of Local Structural Order in Unfolded Peptides and Proteins 131
Franc Avbelj

5.1 Local Structural Order in Unfolded Peptides and Proteins, 131

5.2 ESM, 134

5.3 The ESM and Strand-Coil Transition Model, 137

5.4 The ESM and Backbone Conformational Preferences, 138

5.5 The Nearest-Neighbor Effect, 141

5.6 The ESM and Cooperative Local Structures—Fluctuating β-Strands, 141

5.7 The ESM and β-Sheet Preferences in Native Proteins—Significance of Unfolded State, 144

5.8 The ESM and Secondary Chemical Shifts of Polypeptides, 145

5.9 Role of Backbone Solvation in Determining Hydrogen Exchange Rates of Unfolded Polypeptides, 148

5.10 Other Theoretical Models of Unfolded Polypeptides, 148

Acknowledgments, 149

References, 149

6 Experimental and Computational Studies of Polyproline II Propensity 159
W. Austin Elam, Travis P. Schrank, and Vincent J. Hilser

6.1 Introduction, 159

6.2 Experimental Measurement of PII Propensities, 161

6.3 Computational Studies of Denatured State Conformational Propensities, 168

6.4 A Steric Model Reveals Common PII Propensity of the Peptide Backbone, 172

6.5 Correlation of PII Propensity to Amino Acid Properties, 175

6.6 Summary, 180

Acknowledgments, 180

References, 180

7 Mapping Conformational Dynamics in Unfolded Polypeptide Chains Using Short Model Peptides by NMR Spectroscopy 187
Daniel Mathieu, Karin Rybka, Jürgen Graf, and Harald Schwalbe

7.1 Introduction, 187

7.2 General Aspects of NMR Spectroscopy, 189

7.3 NMR Parameters and Their Measurement, 191

7.4 Translating NMR Parameters to Structural Information, 202

7.5 Conclusions, 213

Acknowledgments, 215

References, 215

8 Secondary Structure and Dynamics of a Family of Disordered Proteins 221
Pranesh Narayanaswami and Gary W. Daughdrill

8.1 Introduction, 221

8.2 Materials and Methods, 223

8.3 Results and Discussion, 226

Acknowledgments, 235

References, 235

II DISORDERED PEPTIDES AND MOLECULAR RECOGNITION 239

9 Binding Promiscuity of Unfolded Peptides 241
Christopher J. Oldfi eld, Bin Xue, A. Keith Dunker, and Vladimir N. Uversky

9.1 Protein–Protein Interaction Networks, 241

9.2 Role of Intrinsic Disorder in PPI Networks, 242

9.3 Transient Structural Elements in Protein-Based Recognition, 243

9.4 Chameleons and Adaptors: Binding Promiscuity of Unfolded Peptides, 256

9.5 Principles of Using the Unfolded Protein Regions for Binding, 262

9.6 Conclusions, 266

Acknowledgments, 266

References, 266

10 Intrinsic Flexibility of Nucleic Acid Chaperone Proteins from Pathogenic RNA Viruses 279
Roland Ivanyi-Nagy, Zuzanna Makowska, and Jean-Luc Darlix

10.1 Introduction, 279

10.2 Retroviruses and Retroviral Nucleocapsid Proteins, 280

10.3 Core Proteins in the Flaviviridae Family of Viruses, 288

10.4 Coronavirus Nucleocapsid Protein, 290

10.5 Hantavirus Nucleocapsid Protein, 291

Acknowledgments, 293

References, 293

III AGGREGATION OF DISORDERED PEPTIDES 307

11 Self-Assembling Alanine-Rich Peptides of Biomedical and Biotechnological Relevance 309
Thomas J. Measey and Reinhard Schweitzer-Stenner

11.1 Biomolecular Self-Assembly, 309

11.2 Misfolding and Human Disease, 310

11.3 Exploitation of Peptide Self-Assembly for Biotechnological Applications, 326

11.4 Concluding Remarks, 340

Acknowledgments, 340

References, 340

12 Structural Elements Regulating Interactions in the Early Stages of Fibrillogenesis: A Human Calcitonin Model System 351
Rosa Maria Vitale, Giuseppina Andreotti, Pietro Amodeo, and Andrea Motta

12.1 Stating the Problem, 351

12.2 Aggregation Models: The State of The Art, 354

12.3 Human Calcitonin hCT as a Model System for Self-Assembly, 356

12.4 The “Prefi brillar” State of hCT, 358

12.5 How Many Molecules for the Critical Nucleus?, 361

12.6 Modeling Prefi brillar Aggregates, 366

12.7 hCT Helical Oligomers, 366

12.8 The Role of Aromatic Residues in the Early Stages of Amyloid Formation, 372

12.9 The Folding of hCT before Aggregation, 373

12.10 Model Explains the Differences in Aggregation Properties between hCT and sCT, 374

12.11 hCT Fibril Maturation, 375

12.12 α-Helix →β-Sheet Conformational Transition and hCT Fibrillation, 377

12.13 Concluding Remarks, 378

Acknowledgments, 378

References, 379

13 Solution NMR Studies of Aβ Monomers and Oligomers 389
Chunyu Wang

13.1 Introduction, 389

13.2 Overexpression and Purifi cation of Recombinant Aβ, 390

13.3 Aβ Monomers, 393

13.4 Aβ Oligomers and Monomer–Oligomer Interaction, 403

13.5 Conclusion, 406

References, 406

14 Thermodynamic and Kinetic Models for Aggregation of Intrinsically Disordered Proteins 413
Scott L. Crick and Rohit V. Pappu

14.1 Introduction, 413

14.2 Thermodynamics of Protein Aggregation—the Phase Diagram Approach, 415

14.3 Thermodynamics of IDP Aggregation (Phase Separation)—MPM Description, 420

14.4 Kinetics of Homogeneous Nucleation and Elongation Using MPMs, 425

14.5 Concepts from Colloidal Science, 427

14.6 Conclusions, 433

Acknowledgments, 433

References, 434

15 Modifiers of Protein Aggregation—From Nonspecific to Specific Interactions 441
Michal Levy-Sakin, Roni Scherzer-Attali, and Ehud Gazit

15.1 Introduction, 441

15.2 Nonspecific Modifi ers, 442

15.3 Specific Modifiers, 454

Acknowledgments, 465

References, 466

16 Computational Studies of Folding and Assembly of Amyloidogenic Proteins 479
J. Srinivasa Rao, Brigita Urbanc, and Luis Cruz

16.1 Introduction, 479

16.2 Amyloids, 480

16.3 Computer Simulations, 485

16.4 Summary, 514

References, 515

INDEX 529