Protein and Peptide Folding, Misfolding, and Non–Folding

Sheds new light on intrinsically disordered proteins andpeptides, including their role in neurodegenerative diseases

With the discovery of intrinsically disordered proteins andpeptides (IDPs), researchers realized that proteins do notnecessarily adopt a well defined secondary and tertiary structurein order to perform biological functions. In fact, IDPs playbiologically relevant roles, acting as inhibitors, scavengers, andeven facilitating DNA/RNA–protein interactions. Due to theirpropensity for self–aggregation and fibril formation, some IDPs areinvolved in neurodegenerative diseases such as Parkinson′s andAlzheimer′s.

With contributions from leading researchers, this text reviewsthe most recent studies, encapsulating our understanding of IDPs.The authors explain how the growing body of IDP research isbuilding our knowledge of the folding process, the binding ofligands to receptor molecules, and peptide self–aggregation.Readers will discover a variety of experimental, theoretical, andcomputational approaches used to better understand the propertiesand function of IDPs. Moreover, they′ll discover the role of IDPsin human disease and as drug targets.

Protein and Peptide Folding, Misfolding, and Non–Folding beginswith an introduction that explains why research on IDPs hassignificantly expanded in the past few years. Next, the book isdivided into three sections:

Conformational Analysis of Unfolded States

Disordered Peptides and Molecular Recognition

Aggregation of Disordered Peptides

Throughout the book, detailed figures help readers understandthe structure, properties, and function of IDPs. References at theend of each chapter serve as a gateway to the growing body ofliterature in the field.

With the publication of Protein and Peptide Folding, Misfolding,and Non–Folding, researchers now have a single place to discoverIDPs, their diverse biological functions, and the many disciplinesthat have contributed to our evolving understanding of them.

Preface xv

Contributors xix

INTRODUCTION 1

1 Why Are We Interested in the Unfolded Peptides andProteins? 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 theAmino Acid Sequence and Can Be Predicted, 5

1.4 Lesson 2: Disordered Proteins Are HighlyAbundant in Nature, 7

1.5 Lesson 3: Disordered Proteins Are GloballyHeterogeneous, 9

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

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

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

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

1.10 Lesson 8: IDPs Can Form Disordered or FuzzyComplexes, 25

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

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

1.13 Lesson 11: Disordered Regions Are Primary Targetsfor AS, 30

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

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

1.16 Lesson 14: Natively Unfolded Proteins Are AttractiveDrug 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 andProteins by Molecular Dynamics Simulations 57
Gerhard Stock, Abhinav Jain, Laura Riccardi, and Phuong H.Nguyen

2.1 Introduction: Free Energy Landscapes and How to ConstructThem, 57

2.2 Dihedral Angle PCA Allows Us to Separate Internal and GlobalMotion, 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 CatchSlow and Rare Processes, 67

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

2.7 The Energy Landscape of Aggregating A –Peptides,73

2.8 Concluding Remarks, 74

Acknowledgments, 75

References, 75

3 Local Backbone Preferences and Nearest–Neighbor Effects inthe 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 inUnfolded Proteins, 92

3.9 Conclusions, 92

Acknowledgments, 93

References, 94

4 Short–Distance FRET Applied to the Polypeptide Chain99
Maik H. Jacob and Werner M. Nau

4.1 A Short Timeline of Resonance Energy Transfer Applied to thePolypeptide 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 PolypeptideChain, 107

4.5 Short–Distance FRET to Monitor Chain–Structural Transitionsupon 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 LocalStructural 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 –Strands, 141

5.7 The ESM and –Sheet Preferences in NativeProteins 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 ExchangeRates of Unfolded Polypeptides, 148

5.10 Other Theoretical Models of Unfolded Polypeptides, 148

Acknowledgments, 149

References, 149

6 Experimental and Computational Studies of Polyproline IIPropensity 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 ConformationalPropensities, 168

6.4 A Steric Model Reveals Common PII Propensity of the PeptideBackbone, 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 PolypeptideChains Using Short Model Peptides by NMR Spectroscopy 187
Daniel Mathieu, Karin Rybka, Jürgen Graf, and HaraldSchwalbe

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 DisorderedProteins 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, andVladimir 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 UnfoldedPeptides, 256

9.5 Principles of Using the Unfolded Protein Regions forBinding, 262

9.6 Conclusions, 266

Acknowledgments, 266

References, 266

10 Intrinsic Flexibility of Nucleic Acid Chaperone Proteinsfrom Pathogenic RNA Viruses 279
Roland Ivanyi–Nagy, Zuzanna Makowska, and Jean–LucDarlix

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 andBiotechnological 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 BiotechnologicalApplications, 326

11.4 Concluding Remarks, 340

Acknowledgments, 340

References, 340

12 Structural Elements Regulating Interactions in the EarlyStages of Fibrillogenesis: A Human Calcitonin Model System351
Rosa Maria Vitale, Giuseppina Andreotti, Pietro Amodeo, andAndrea 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 ofAmyloid Formation, 372

12.9 The Folding of hCT before Aggregation, 373

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

12.11 hCT Fibril Maturation, 375

12.12 –Helix –SheetConformational Transition and hCT Fibrillation, 377

12.13 Concluding Remarks, 378

Acknowledgments, 378

References, 379

13 Solution NMR Studies of A Monomers andOligomers 389
Chunyu Wang

13.1 Introduction, 389

13.2 Overexpression and Purifi cation of RecombinantA , 390

13.3 A Monomers, 393

13.4 A Oligomers and Monomer OligomerInteraction, 403

13.5 Conclusion, 406

References, 406

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

14.1 Introduction, 413

14.2 Thermodynamics of Protein Aggregation the PhaseDiagram Approach, 415

14.3 Thermodynamics of IDP Aggregation (PhaseSeparation) MPM Description, 420

14.4 Kinetics of Homogeneous Nucleation and Elongation UsingMPMs, 425

14.5 Concepts from Colloidal Science, 427

14.6 Conclusions, 433

Acknowledgments, 433

References, 434

15 Modifiers of Protein Aggregation From Nonspecific toSpecific Interactions 441
Michal Levy–Sakin, Roni Scherzer–Attali, and EhudGazit

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 ofAmyloidogenic 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

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.