Protein and Peptide Folding, Misfolding, and Non–F olding

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 A beta -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 beta -Strands, 141 5.7 The ESM and beta -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, Jurgen 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 alpha -Helix --> beta -Sheet Conformational Transition and hCT Fibrillation, 377 12.13 Concluding Remarks, 378 Acknowledgments, 378 References, 379 13 Solution NMR Studies of A beta Monomers and Oligomers 389 Chunyu Wang 13.1 Introduction, 389 13.2 Overexpression and Purifi cation of Recombinant A beta , 390 13.3 A beta Monomers, 393 13.4 A beta 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