PROTEIN AND PEPTIDE FOLDING, MISFOLDING, AND NON-FOLDING -- CONTENTS -- INTRODUCTION TO THE WILEY SERIES ON PROTEIN AND PEPTIDE SCIENCE -- PREFACE -- CONTRIBUTORS -- INTRODUCTION -- 1: WHY ARE WE INTERESTED IN THE UNFOLDED PEPTIDES AND PROTEINS? Vladimir N. Uversky and A. Keith Dunker -- 1.1. INTRODUCTION -- 1.2. WHY STUDY IDPS? -- 1.3. LESSON 1: DISORDEREDNESS IS ENCODED IN THE AMINO ACID SEQUENCE AND CAN BE PREDICTED -- 1.4. LESSON 2: DISORDERED PROTEINS ARE HIGHLY ABUNDANT IN NATURE -- 1.5. LESSON 3: DISORDERED PROTEINS ARE GLOBALLY HETEROGENEOUS -- 1.6. LESSON 4: HYDRODYNAMIC DIMENSIONS OF NATIVELY UNFOLDED PROTEINS ARE CHARGE DEPENDENT -- 1.7. LESSON 5: POLYMER PHYSICS EXPLAINS HYDRODYNAMIC BEHAVIOR OF DISORDERED PROTEINS -- 1.8. LESSON 6: NATIVELY UNFOLDED PROTEINS ARE PLIABLE AND VERY SENSITIVE TO THEIR ENVIRONMENT -- 1.9. LESSON 7: WHEN BOUND, NATIVELY UNFOLDED PROTEINS CAN GAIN UNUSUAL STRUCTURES -- 1.10. LESSON 8: IDPS CAN FORM DISORDERED OR FUZZY COMPLEXES -- 1.11. LESSON 9: INTRINSIC DISORDER IS CRUCIAL FOR RECOGNITION, REGULATION, AND SIGNALING -- 1.12. LESSON 10: PROTEIN POSTTRANSLATIONAL MODIFICATIONS OCCUR AT DISORDERED REGIONS -- 1.13. LESSON 11: DISORDERED REGIONS ARE PRIMARY TARGETS FOR AS -- 1.14. LESSON 12: DISORDERED PROTEINS ARE TIGHTLY REGULATED IN THE LIVING CELLS -- 1.15. LESSON 13: NATIVELY UNFOLDED PROTEINS ARE FREQUENTLY ASSOCIATED WITH HUMAN DISEASES -- 1.16. LESSON 14: NATIVELY UNFOLDED PROTEINS ARE ATTRACTIVE DRUG TARGETS -- 1.17. LESSON 15: BRIGHT FUTURE OF FUZZY PROTEINS -- ACKNOWLEDGMENTS -- REFERENCES -- I: CONFORMATIONAL ANALYSISOF UNFOLDED STATES -- 2: EXPLORING THE ENERGY LANDSCAPE OF SMALL PEPTIDES AND PROTEINS BY MOLECULAR DYNAMICS SIMULATIONS Gerhard Stock, Abhinav Jain, Laura Riccardi, and Phuong H. Nguyen -- 2.1. INTRODUCTION: FREE ENERGY LANDSCAPES AND HOW TO CONSTRUCT THEM.

2.2. DIHEDRAL ANGLE PCA ALLOWS US TO SEPARATE INTERNAL AND GLOBAL MOTION -- 2.3. DIMENSIONALITY OF THE FREE ENERGY LANDSCAPE -- 2.4. CHARACTERIZATION OF THE FREE ENERGY LANDSCAPE: STATES, BARRIERS, AND TRANSITIONS -- 2.5. LOW-DIMENSIONAL SIMULATION OF BIOMOLECULAR DYNAMICS TO CATCH SLOW AND RARE PROCESSES -- 2.6. PCA BY PARTS: THE FOLDING PATHWAYS OF VILLIN HEADPIECE -- 2.7. THE ENERGY LANDSCAPE OF AGGREGATING Aβ-PEPTIDES -- 2.8. CONCLUDING REMARKS -- ACKNOWLEDGMENTS -- REFERENCES -- 3: LOCAL BACKBONE PREFERENCES AND NEAREST-NEIGHBOR EFFECTS IN THE UNFOLDED AND NATIVE STATES Joe DeBartolo, Abhishek Jha, Karl F. Freed, and Tobin R. Sosnick -- 3.1. INTRODUCTION -- 3.2. EARLY DAYS: RANDOM COIL-THEORY AND EXPERIMENT -- 3.3. DENATURED PROTEINS AS SELF-AVOIDING RANDOM COILS -- 3.4. MODELING THE UNFOLDED STATE -- 3.5. NN EFFECTS IN PROTEIN STRUCTURE PREDICTION -- 3.6. UTILIZING FOLDING PATHWAYS FORSTRUCTURE PREDICTION -- 3.7. NATIVE STATE MODELING -- 3.8. SECONDARY-STRUCTURE PROPENSITIES: NATIVE BACKBONES IN UNFOLDED PROTEINS -- 3.9. CONCLUSIONS -- ACKNOWLEDGMENTS -- REFERENCES -- 4: SHORT-DISTANCE FRET APPLIED TO THE POLYPEPTIDE CHAIN Maik H. Jacob and Werner M. Nau -- 4.1. A SHORT TIMELINE OF RESONANCE ENERGY TRANSFER APPLIED TO THE POLYPEPTIDE CHAIN -- 4.2. A SHORT THEORY OF FRET APPLIED TO THE POLYPEPTIDE CHAIN -- 4.3. DBO AND Dbo -- 4.4. SHORT-DISTANCE FRET APPLIED TO THE STRUCTURED POLYPEPTIDE CHAIN -- 4.5. SHORT-DISTANCE FRET TO MONITOR CHAIN-STRUCTURAL TRANSITIONS UPON PHOSPHORYLATION -- 4.6. SHORT-DISTANCE FRET APPLIED TO THE STRUCTURELESS CHAIN -- 4.7. THE FUTURE OF SHORT-DISTANCE FRET -- ACKNOWLEDGMENTS -- DEDICATION -- REFERENCES -- 5: SOLVATION AND ELECTROSTATICS AS DETERMINANTS OF LOCAL STRUCTURAL ORDER IN UNFOLDED PEPTIDES AND PROTEINSFranc Avbelj -- 5.1. LOCAL STRUCTURAL ORDER IN UNFOLDED PEPTIDES AND PROTEINS -- 5.2. ESM.

5.3. THE ESM AND STRAND-COIL TRANSITION MODEL -- 5.4. THE ESM AND BACKBONE CONFORMATIONAL PREFERENCES -- 5.5. THE NEAREST-NEIGHBOR EFFECT -- 5.6. THE ESM AND COOPERATIVE LOCAL STRUCTURES-FLUCTUATING β-STRANDS -- 5.7. THE ESM AND β-SHEET PREFERENCES IN NATIVE PROTEINS-SIGNIFICANCE OF UNFOLDED STATE -- 5.8. THE ESM AND SECONDARY CHEMICAL SHIFTS OF POLYPEPTIDES -- 5.9. ROLE OF BACKBONE SOLVATION IN DETERMINING HYDROGEN EXCHANGE RATES OF UNFOLDED POLYPEPTIDES -- 5.10. OTHER THEORETICAL MODELS OF UNFOLDED POLYPEPTIDES -- ACKNOWLEDGMENTS -- REFERENCES -- 6: EXPERIMENTAL AND COMPUTATIONAL STUDIES OF POLYPROLINE II PROPENSITY W. Austin Elam, Travis P. Schrank, and Vincent J. Hilser -- 6.1. INTRODUCTION -- 6.2. EXPERIMENTAL MEASUREMENT OF PII PROPENSITIES -- 6.3. COMPUTATIONAL STUDIES OF DENATURED STATE CONFORMATIONAL PROPENSITIES -- 6.4. A STERIC MODEL REVEALS COMMON PII PROPENSITY OF THE PEPTIDE BACKBONE -- 6.5. CORRELATION OF PII PROPENSITY TO AMINO ACID PROPERTIES -- 6.6. SUMMARY -- ACKNOWLEDGMENTS -- REFERENCES -- 7: MAPPING CONFORMATIONAL DYNAMICS IN UNFOLDED POLYPEPTIDE CHAINS USING SHORT MODEL PEPTIDES BY NMR SPECTROSCOPY Daniel Mathieu, Karin Rybka, Jürgen Graf, and Harald Schwalbe -- 7.1. INTRODUCTION -- 7.2. GENERAL ASPECTS OF NMR SPECTROSCOPY -- 7.3. NMR PARAMETERS AND THEIR MEASUREMENT -- 7.4. TRANSLATING NMR PARAMETERS TO STRUCTURAL INFORMATION -- 7.5. CONCLUSIONS -- ACKNOWLEDGMENTS -- REFERENCES -- 8: SECONDARY STRUCTURE AND DYNAMICS OF A FAMILY OF DISORDERED PROTEINS Pranesh Narayanaswami and Gary W. Daughdrill -- 8.1. INTRODUCTION -- 8.2. MATERIALS AND METHODS -- 8.3. RESULTS AND DISCUSSION -- ACKNOWLEDGMENTS -- REFERENCES -- II: DISORDERED PEPTIDES AND MOLECULAR RECOGNITION -- 9: BINDING PROMISCUITY OF UNFOLDED PEPTIDES Christopher J. Oldfield, Bin Xue, A. Keith Dunker, and Vladimir N. Uversky -- 9.1. PROTEIN-PROTEIN INTERACTION NETWORKS.

9.2. ROLE OF INTRINSIC DISORDER IN PPI NETWORKS -- 9.3. TRANSIENT STRUCTURAL ELEMENTS IN PROTEIN-BASED RECOGNITION -- 9.4. CHAMELEONS AND ADAPTORS: BINDING PROMISCUITY OF UNFOLDED PEPTIDES -- 9.5. PRINCIPLES OF USING THE UNFOLDED PROTEIN REGIONS FOR BINDING -- 9.6. CONCLUSIONS -- ACKNOWLEDGMENTS -- REFERENCES -- 10: INTRINSIC FLEXIBILITY OF NUCLEIC ACID CHAPERONE PROTEINS FROM PATHOGENIC RNA VIRUSES Roland Ivanyi-Nagy, Zuzanna Makowska, and Jean-Luc Darlix -- 10.1. INTRODUCTION -- 10.2. RETROVIRUSES AND RETROVIRAL NUCLEOCAPSID PROTEINS -- 10.3. CORE PROTEINS IN THE FLAVIVIRIDAE FAMILY OF VIRUSES -- 10.4. CORONAVIRUS NUCLEOCAPSID PROTEIN -- 10.5. HANTAVIRUS NUCLEOCAPSID PROTEIN -- ACKNOWLEDGMENTS -- REFERENCES -- III: AGGREGATION OF DISORDERED PEPTIDES -- 11: SELF-ASSEMBLING ALANINE-RICH PEPTIDES OF BIOMEDICAL AND BIOTECHNOLOGICAL RELEVANCE Thomas J. Measey and Reinhard Schweitzer-Stenner -- 11.1. BIOMOLECULAR SELF-ASSEMBLY -- 11.2. MISFOLDING AND HUMAN DISEASE -- 11.3. EXPLOITATION OF PEPTIDE SELF-ASSEMBLY FOR BIOTECHNOLOGICAL APPLICATIONS -- 11.4. CONCLUDING REMARKS -- ACKNOWLEDGMENTS -- REFERENCES -- 12: STRUCTURAL ELEMENTS REGULATING INTERACTIONS IN THE EARLY STAGES OF FIBRILLOGENESIS: A HUMAN CALCITONIN MODEL SYSTEM Rosa Maria Vitale, Giuseppina Andreotti, Pietro Amodeo, and Andrea Motta -- 12.1. STATING THE PROBLEM -- 12.2. AGGREGATION MODELS: THE STATE OF THE ART -- 12.3. HUMAN CALCITONIN HCT AS A MODEL SYSTEM FOR SELF-ASSEMBLY -- 12.4. THE "PREFIBRILLAR" STATE OF HCT -- 12.5. HOW MANY MOLECULES FOR THE CRITICAL NUCLEUS? -- 12.6. MODELING PREFIBRILLAR AGGREGATES -- 12.7. HCT HELICAL OLIGOMERS -- 12.8. THE ROLE OF AROMATIC RESIDUES IN THE EARLY STAGES OF AMYLOID FORMATION -- 12.9. THE FOLDING OF HCT BEFORE AGGREGATION -- 12.10. MODEL EXPLAINS THE DIFFERENCES IN AGGREGATION PROPERTIES BETWEEN HCT AND SCT -- 12.11. HCT FIBRIL MATURATION.

12.12. α-HELIX →β-SHEET CONFORMATIONAL TRANSITION AND HCT FIBRILLATION -- 12.13. CONCLUDING REMARKS -- ACKNOWLEDGMENTS -- REFERENCES -- 13: SOLUTION NMR STUDIES OF Aβ MONOMERS AND OLIGOMERS Chunyu Wang -- 13.1. INTRODUCTION -- 13.2. OVEREXPRESSION AND PURIFICATION OF RECOMBINANT Aβ -- 13.3. Aβ MONOMERS -- 13.4. Aβ OLIGOMERS AND MONOMER-OLIGOMER INTERACTION -- 13.5. CONCLUSION -- REFERENCES -- 14: THERMODYNAMIC AND KINETIC MODELS FOR AGGREGATION OF INTRINSICALLY DISORDERED PROTEIN SScott L. Crick and Rohit V. Pappu -- 14.1. INTRODUCTION -- 14.2. THERMODYNAMICS OF PROTEIN AGGREGATION-THE PHASE DIAGRAM APPROACH -- 14.3. THERMODYNAMICS OF IDP AGGREGATION (PHASE SEPARATION)-MPM DESCRIPTION -- 14.4. KINETICS OF HOMOGENEOUS NUCLEATION AND ELONGATION USING MPMS -- 14.5. CONCEPTS FROM COLLOIDAL SCIENCE -- 14.6. CONCLUSIONS -- ACKNOWLEDGMENTS -- REFERENCES -- 15: MODIFIERS OF PROTEIN AGGREGATION-FROM NONSPECIFIC TO SPECIFIC INTERACTIONS Michal Levy-Sakin,1 Roni Scherzer-Attali,1 and Ehud Gazit -- 15.1. INTRODUCTION -- 15.2. NONSPECIFIC MODIFIERS -- 15.3. SPECIFIC MODIFIERS -- ACKNOWLEDGMENTS -- REFERENCES -- 16: COMPUTATIONAL STUDIES OF FOLDING AND ASSEMBLY OF AMYLOIDOGENIC PROTEINS J. Srinivasa Rao, Brigita Urbanc, and Luis Cruz -- 16.1. INTRODUCTION -- 16.2. AMYLOIDS -- 16.3. COMPUTER SIMULATIONS -- 16.4. SUMMARY -- REFERENCES -- INDEX -- Colorplate.