Protein and Peptide Folding, Misfolding, and Non-Folding E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: Wiley Series in Protein and Peptide Science
• Sprache: Englisch

Seitenzahl: 1089

Veröffentlichungsjahr: 2012

Beschreibung

Sheds new light on intrinsically disordered proteins and peptides, including their role in neurodegenerative diseases With the discovery of intrinsically disordered proteins and peptides (IDPs), researchers realized that proteins do not necessarily adopt a well defined secondary and tertiary structure in order to perform biological functions. In fact, IDPs play biologically relevant roles, acting as inhibitors, scavengers, and even facilitating DNA/RNA-protein interactions. Due to their propensity for self-aggregation and fibril formation, some IDPs are involved in neurodegenerative diseases such as Parkinson's and Alzheimer's. With contributions from leading researchers, this text reviews the most recent studies, encapsulating our understanding of IDPs. The authors explain how the growing body of IDP research is building our knowledge of the folding process, the binding of ligands to receptor molecules, and peptide self-aggregation. Readers will discover a variety of experimental, theoretical, and computational approaches used to better understand the properties and function of IDPs. Moreover, they'll discover the role of IDPs in human disease and as drug targets. Protein and Peptide Folding, Misfolding, and Non-Folding begins with an introduction that explains why research on IDPs has significantly expanded in the past few years. Next, the book is divided into three sections: * Conformational Analysis of Unfolded States * Disordered Peptides and Molecular Recognition * Aggregation of Disordered Peptides Throughout the book, detailed figures help readers understand the structure, properties, and function of IDPs. References at the end of each chapter serve as a gateway to the growing body of literature in the field. With the publication of Protein and Peptide Folding, Misfolding, and Non-Folding, researchers now have a single place to discover IDPs, their diverse biological functions, and the many disciplines that have contributed to our evolving understanding of them.

Leseprobe

Table of Contents

Cover

Series page

Title page

Copyright page

INTRODUCTION TO THE WILEY SERIES ON PROTEIN AND PEPTIDE SCIENCE

PREFACE

CONTRIBUTORS

INTRODUCTION

1 WHY ARE WE INTERESTED IN THE UNFOLDED PEPTIDES AND PROTEINS?

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

I: CONFORMATIONAL ANALYSIS OF UNFOLDED STATES

2 EXPLORING THE ENERGY LANDSCAPE OF SMALL PEPTIDES AND PROTEINS BY MOLECULAR DYNAMICS SIMULATIONS

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

3 LOCAL BACKBONE PREFERENCES AND NEAREST-NEIGHBOR EFFECTS IN THE UNFOLDED AND NATIVE STATES

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 FOR STRUCTURE PREDICTION

3.7. NATIVE STATE MODELING

3.8. SECONDARY-STRUCTURE PROPENSITIES: NATIVE BACKBONES IN UNFOLDED PROTEINS

3.9. CONCLUSIONS

ACKNOWLEDGMENTS

4 SHORT-DISTANCE FRET APPLIED TO THE POLYPEPTIDE CHAIN

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

5 SOLVATION AND ELECTROSTATICS AS DETERMINANTS OF LOCAL STRUCTURAL ORDER IN UNFOLDED PEPTIDES AND PROTEINS

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

6 EXPERIMENTAL AND COMPUTATIONAL STUDIES OF POLYPROLINE II PROPENSITY

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

7 MAPPING CONFORMATIONAL DYNAMICS IN UNFOLDED POLYPEPTIDE CHAINS USING SHORT MODEL PEPTIDES BY NMR SPECTROSCOPY

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

8 SECONDARY STRUCTURE AND DYNAMICS OF A FAMILY OF DISORDERED PROTEINS

8.1. INTRODUCTION

8.2. MATERIALS AND METHODS

8.3. RESULTS AND DISCUSSION

ACKNOWLEDGMENTS

II: DISORDERED PEPTIDES AND MOLECULAR RECOGNITION

9 BINDING PROMISCUITY OF UNFOLDED PEPTIDES

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

10 INTRINSIC FLEXIBILITY OF NUCLEIC ACID CHAPERONE PROTEINS FROM PATHOGENIC RNA VIRUSES

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

III: AGGREGATION OF DISORDERED PEPTIDES

11 SELF-ASSEMBLING ALANINE-RICH PEPTIDES OF BIOMEDICAL AND BIOTECHNOLOGICAL RELEVANCE

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

12 STRUCTURAL ELEMENTS REGULATING INTERACTIONS IN THE EARLY STAGES OF FIBRILLOGENESIS: A HUMAN CALCITONIN MODEL SYSTEM

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

13 SOLUTION NMR STUDIES OF Aβ MONOMERS AND OLIGOMERS

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

14 THERMODYNAMIC AND KINETIC MODELS FOR AGGREGATION OF INTRINSICALLY DISORDERED PROTEINS

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

15 MODIFIERS OF PROTEIN AGGREGATION—FROM NONSPECIFIC TO SPECIFIC INTERACTIONS

15.1. INTRODUCTION

15.2. NONSPECIFIC MODIFIERS

15.3. SPECIFIC MODIFIERS

ACKNOWLEDGMENTS

16 COMPUTATIONAL STUDIES OF FOLDING AND ASSEMBLY OF AMYLOIDOGENIC PROTEINS

16.1. INTRODUCTION

16.2. AMYLOIDS

16.3. COMPUTER SIMULATIONS

16.4. SUMMARY

Index

Color plates

WILEY SERIES IN PROTEIN AND PEPTIDE SCIENCE

VLADIMIR N. UVERSKY, Series Editor

Metalloproteomics • Eugene A. Permyakov

Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation • Vladimir Uversky and Sonia Longhi

Protein Misfolding Diseases: Current and Emerging Principles and Therapies• Marina Ramirez-Alvarado, Jeffery W. Kelly, Christopher M. Dobson

Calcium Binding Proteins• Eugene A. Permyakov and Robert H. Kretsinger

Protein Chaperones and Protection from Neurodegenerative Diseases • Stephan Witt

Transmembrane Dynamics of Lipids • Philippe Devaux and Andreas Herrmann

Flexible Viruses: Structural Disorder in Viral Proteins • Vladimir Uversky and Sonia Longhi

Protein and Peptide Folding, Misfolding, and Non-Folding • Reinhard Schweitzer-Stenner

Copyright © 2012 by John Wiley & Sons, Inc. All rights reserved

Published by John Wiley & Sons, Inc., Hoboken, New Jersey

Published simultaneously in Canada

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Library of Congress Cataloging-in-Publication Data:

Protein and peptide folding, misfolding, and non-folding / edited by Reinhard Schweitzer-Stenner.

p. cm. – (Wiley series in protein and peptide science ; 13)

Includes bibliographical references and index.

 ISBN 978-0-470-59169-7

 ISBN 978-1-118-18334-2 (epdf)

 ISBN 978-1-118-18335-9 (epub)

 ISBN 978-1-118-18336-6 (mobi)

 1. Protein folding. 2. Peptides. I. Schweitzer-Stenner, Reinhard.

 QP551.P75 2012

 572'.633–dc23

2011044305

INTRODUCTION TO THE WILEY SERIES ON PROTEIN AND PEPTIDE SCIENCE

Proteins and peptides are the major functional components of the living cell. They are involved in all aspects of the maintenance of life. Their structural and functional repertoires are endless. They may act alone or in conjunction with other proteins, peptides, nucleic acids, membranes, small molecules, and ions during various stages of life. Dysfunction of proteins and peptides may result in the development of various pathological conditions and diseases. Therefore, the protein/peptide structure–function relationship is a key scientific problem lying at the junction point of modern biochemistry, biophysics, genetics, physiology, molecular and cellular biology, proteomics, and medicine.

The Wiley Series on Protein and Peptide Science is designed to supply a complementary perspective from current publications by focusing each volume on a specific protein- or peptide-associated question and endowing it with the broadest possible context and outlook. The volumes in this series should be considered required reading for biochemists, biophysicists, molecular biologists, geneticists, cell biologists, and physiologists as well as those specialists in drug design and development, proteomics, and molecular medicine, with an interest in proteins and peptides. I hope that each reader will find in the volumes within this book series interesting and useful information.

First and foremost I would like to acknowledge the assistance of Anita Lekhwani of John Wiley & Sons, Inc. throughout this project. She has guided me through countless difficulties in the preparation of this book series and her enthusiasm, input, suggestions, and efforts were indispensable in bringing the Wiley Series on Protein and Peptide Science into existence. I would like to take this opportunity to thank everybody whose contribution in one way or another has helped and supported this project. Finally, a special thank you goes to my wife, sons, and mother for their constant support, invaluable assistance, and continuous encouragement.

VLADIMIR UVERSKY

September 9, 2008

PREFACE

The unfolded state of peptides and proteins has attracted a considerable interest over the last 10–15 years for a variety of reasons. First, the discovery of the existence of so-called intrinsically disordered proteins and (IDPs) peptides indicated that in contrast to a central dogma of modern biochemistry proteins do not necessarily have to adopt a well-defined secondary and tertiary structure in order to perform biological functions [1]. IDPs are known to play biologically relevant roles, acting as inhibitors, scavengers, and even facilitating DNA/RNA–protein interaction [2–5]. Some IDPs such as α-synuclein, τ-protein, and β-amyloid are involved in neurodegenerative diseases, for example, Parkinson’s and Alzheimer’s because of their propensity for self-aggregation and fibril formation [6–9]. Moreover, experimental and theoretical evidence has been provided for the notion that the unfolded state is structurally less disordered as predicted by the statistical (or random) coil model, which is built on the assumption that all amino acid residues besides proline can sample the entire sterically accessible region of the Ramachandran plot [10]. In this book, all these issue are addressed in detail by the contributing authors.

The introductory chapter describes the reasons why research on IDPs and peptides has so significantly expanded over the last years. The authors briefly describe the difference between structured (folded) and disordered (unstructured, unfolded) proteins and list the different functions such proteins and peptides can perform. Their chapter is subdivided into “lessons,” which show that (1) disorder is encoded in the amino acid sequence; (2) IDPs are highly abundant in nature and globally heterogeneous; (3) their hydrodynamic properties are charge dependent and describable in terms of polymer physics concepts; (4) IDPs are very pliable and therefore convert into (partially) folded systems upon binding to specific targets (other proteins, peptides, or membrane surfaces) and/or can become involved in multiple processes such as recognition, regulation, and signaling; and (5) IDP-type segments of proteins and peptides can be involved in posttranslational modifications, such as phosphorylation or methylation (to name only a few), and in alternative splicing. The authors also emphasize the role of IDPs in human diseases and their role as drug targets.

Part I of the book deals with the conformational analysis of unfolded peptides and proteins. Chapter 2 describes recent efforts to explore the energy landscape of small peptides and proteins with molecular dynamics simulations. It delineates how a principal component analysis can be employed to obtain an accurate, artifact-free energy landscape. While the results suggest that the landscape of unfolded systems is very complex, they are at variance with the classical random coil model in that they suggest the existence of a countable number of metastable states. Chapter 3 describes research on coil libraries of a large set of proteins, the results of which have led the authors to conclude that conformational ensembles sampled in the unfolded state depend on the amino acid sequence and that the 20 natural amino acids exhibit different conformational preferences, which are modified by their nearest neighbors. In their chapter the authors provide evidence for the notion that these conformational preferences bias the folding pathway. They refer to a suite of web-based applications that graphically display the individual conformational preferences of amino acids and the nearest-neighbor effects. The authors of Chapter 4 have pioneered the use of very special donor–acceptor pairs for measuring the end-to-end distance by fluorescence resonance energy transfer. In their chapter they describe the basic aspects of their method and provide several examples to demonstrate its applicability. Chapter 5 summarizes recent work on how solvation and electrostatic interactions determine the backbone conformation of unfolded peptides and proteins. One very important conclusion for nuclear magnetic resonance (NMR) spectroscopists is that chemical shift values cannot be used as indicators of conformations in the same way for solvated and non-solvated residues. In Chapter 6 the authors investigate different polyproline II (PPII) propensity scales of amino acid residues reported in the literature. Their results led them to the conclusion that PPII propensities do not correlate, for example, with secondary-structure propensities. This notion will certainly ignite some debate in the future. In Chapter 7, the authors show how different types of NMR experiments can be used to determine a set of J-coupling constants that depend differently on the dihedral angles of residues. These coupling constants can be used to determine the conformational ensembles of unfolded peptides. Part I of the book concludes with Chapter 8, which reports the results of NMR measurements on an intrinsically unstructured linker domain in a subunit of a Replication Protein A.

Chapters 9 and 10 comprise Part II, on “molecular recognition.” Chapter 9 focuses on so-called hub-proteins, which are capable of binding to a variety of different partners. The authors discuss several models designed to rationalize the mediation of protein–protein interactions by intrinsic disorder. The authors of Chapter 10 describe properties of RNA chaperons concerning interactions with nucleic acid that take place during the replication of widespread pathogenic RNA viruses such as retroviruses and flaviviruses. They provide evidence for how mutations of the chaperone can yield replication-defective viral particles, which they relate to unfolding or misfolding.

Part III of the book is dedicated to peptide and protein aggregation. Chapter 11 presents an overview of the aggregation properties of alanine-based polypeptides. Chapter 12 reviews research of human calcitonin, a 32-residue polypeptide synthesized and secreted by the C cells of the thyroid and involved in calcium regulation and bone dynamics. The authors focus on characterizing the early stage of self-aggregation at which metastable aggregates are formed. Chapter 14 is a theoretical contribution. The authors use concepts from colloid and polymer physics to obtain phase diagrams for IDPs, which encompass the state of self-aggregation. Chapter 15 is on modifiers of peptide and protein aggregation, namely salts, ionic liquids, and osmolytes. Chapters 13 and 16 deal with the classical self-aggregating IDP, the β-amyloid peptide Aβ1–41(42). The author of Chapter 13 reviews recent advances in NMR spectroscopy for investigating the early phase of Aβ self-aggregation. This involves the determination of equilibrium and rater constants. Finally, in Chapter 16 the authors show how Aβ self-aggregation can be explored computationally by molecular dynamics simulation techniques. Their review reports the results of simulations aimed at elucidating the influence of inhibitors on the aggregation process.

Altogether, this book provides the interested reader with a rather broad, though certainly still incomplete, overview of the wealth of experimental and theoretical techniques that are currently used to explore IDPs. Moreover, it highlights some most recent discoveries and theories that will certainly stimulate discussions.

I like to thank Dr. Vladimir Uversky for inviting me to serve as an editor of this book. I am indebted to Anita Lekhwani, Senior Commissioning Editor at Wiley-Blackwell, and Stephanie Sakson, Project Manager at Toppan Best-set Premedia, for their valuable assistance at various stages of the editing and publication process. Finally, I gratefully acknowledge the assistance of my son David Stenner, who has helped me to produce the subject index of this book.

REINHARD SCHWEITZER-STENNER

Note: Color versions of selected figures are available atftp://ftp.wiley.com/public/sci_tech_med/protein_peptide.

REFERENCES

1 Uversky, V. N. (2002) What does it mean to be natively unfolded? Eur J Biochem 269, 2–12.

2 Uversky, V. N. (2008) Natively unfolded proteins. In: Creamer, T. P., ed., Unfolded proteins. From denaturated to intrinsically disordered, Nova, Hauppauge, NY.

3 Li, X., Romero, P., Rani, M., Dunker, A. K., and Obradovic, Z. (1999) Predicting protein disorders for N, C, and internal regions, Genome Informatics 10, 30.

4 Romero, P., Obradovic, Z., Li, X., Garner, E. C., Brown, C. J., and Dunker, A. K. (2001) Sequence complexity of disordered proteins, Proteins 42, 38–48.

5 Dunker, A. K., Lawson, J. D., Brown, C. J., Williams, R. M., Romero, P., Oh, J. S., Oldfield, C. J., Campen, A. M., Ratliff, C. M., Hipps, K. W., Ausio, J., Nissen, M. S., Reeves, R., Kang, C., Kissinger, C. R., Bailey, R. W., Griswold, M. D., Chiu, W., Garner, E. C., and Obradovic, Z. (2001) Intrinsically disordered protein., J Mol Graphics and Modelling 19, 26–59.

6 Dobson, C. M. (1999) Protein misfolding, evolution and disease, Trends Biochem Sci 24, 329–332.

7 Hamley, I. W. (2007) Peptide fibrillization, Angewandte Chemie-International Edition 46, 8128–8147.

8 Mukrasch, M. D., Markwick, P., Biernat, J., ]von Bergen, M., Bernado, P., Greisinger, C., Mandelkow, E., Zweckstetter, M., and Blackledge, M. (2007) Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation, J Am Chem Soc 129, 5235–5243.

9 Bernado., P., Bertoncini, C. W., Griesinger, C., Zweckstetter, M., and Blackledge, M. (2005) Defining long-range order and local disorder in native α-synuclein using residual dipolar couplings, J Am Chem Soc 127, 17968–17969.

10 Flory, P. J. (1969) Statistical mechanics of chain molecules, Wiley & Sons, New York.

CONTRIBUTORS

Pietro Amodeo, Istituto di Chimica Biomolecolare de Consiglio Nazionale delle Ricerche, Compensario Olivetti, Pozzuoli, Italy.

Giuseppina Andreotti, Istituto di Chimica Biomolecolare de Consiglio Nazionale delle Ricerche, Compensario Olivetti, Pozzuoli, Italy.

Franc Avbelj, National Institute of Chemistry, Ljubljana SI 1115, Slowenia.

Scott L. Crick, Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA.

Luis Cruz, Department of Physics, Drexel University, Philadelphia, PA 19104, USA.

Jean-Luc Darlix, Unitè de Virologie Humaine (412), Ecole Normale Supéieure de Lyon et Institut National de la Santé et de la Recherche Médicale, IRF 128, 46 allé d’Italie, 69364 Lyon, France.

Joe DeBartolo, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.

Gary Daughdrill, Department of Cell Biology, Microbiology, and Molecular Biology and the Center for Biomolecular Identification and Targeted Therapeutics, University of South Florida, 3720 Spectrum Blvd., Tampa, FL 33612, USA.

A. Keith Dunker, Center for Computational Biology and Bioinformatics, Institute for Intrinsically Disordered Protein Research, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

W. Austin Elam, T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.

Karl F. Freed, Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.

Ehud Gazit, Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel.

Jrgen Graf, Institut fr Organische Chemie, Ruprecht Karls-University, Im Neuenhainer Feld 270, D-69120 Heidelberg, Germany.

Vincent J. Hilser, T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.

Roland Ivanyi-Nagy, Molecular Parasitology Group, The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom.

Maik H. Jacob, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.

Abhishek Jha, Agios Pharmaceuticals, Cambridge, MA 02139, USA.

Abhinav Jain, Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany.

Michal Levy-Sakin, Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel.

Zuzanna Makowska, Department of Biomedicine, University of Basel, CH-4031 Basel, Switzerland.

Daniel Mathieu, Institut fr Organische und Biologische Chemie, Johann Wolfgang Goethe Universität, 60439 Frankfurt, Germany.

Thomas J. Measey, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.

Andrea Motta, Istituto di Chimica Biomolecolare de Consiglio Nazionale delle Ricerche, Compensario Olivetti, Pozzuoli, Italy.

Pranesh Narayanaswami, Department of Chemistry, PO Box 644630, Washington State University, Pullman, WA 99164-4630, USA.

Werner Nau, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.

Phuong H. Nguyen, Institut fr Physikalische und Theoretische Chemie, Johann Wolfgang Goethe Universität, 60439 Frankfurt, Germany.

Christopher J. Oldfield, Center for Computational Biology and Bioinformatics, Institute for Intrinsically Disordered Protein Research, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

Rohit V. Pappu, Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA.

J. Srinivasa Rao, Department of Physics, Drexel University, Philadelphia, PA 19104, USA.

Laura Riccardi, Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany.

Karin Rybka, Institut fr Organische und Biologische Chemie, Johann Wolfgang Goethe Universität, 60439 Frankfurt, Germany.

Roni Scherzer-Attali, Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel.

Travis P. Schrank, Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.

Harald Schwalbe, Institut fr Organische und Biologische Chemie, Johann Wolfgang Goethe Universität, 60439 Frankfurt, Germany.

Reinhard Schweitzer-Stenner, Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA.

Tobin R. Sosnick, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.

Gerhard Stock, Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany.

Brigita Urbanc, Department of Physics, Drexel University, Philadelphia, PA 19104, USA.

Vladimir N. Uversky, Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA.

Rosa Maria Vitale, Istituto di Chimica Biomolecolare de Consiglio Nazionale delle Ricerche, Compensario Olivetti, Pozzuoli, Italy.

Chunyu Wang, Biology Department Rm 2229, Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180-3590, USA.

Bin Xue, Center for Computational Biology and Bioinformatics, Institute for Intrinsically Disordered Protein Research, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

INTRODUCTION

1

WHY ARE WE INTERESTED IN THE UNFOLDED PEPTIDES AND PROTEINS?

Vladimir N. Uversky and A. Keith Dunker

1.1. INTRODUCTION

In addition to transmembrane, globular, and fibrous proteins, it is becoming increasingly recognized that the protein universe includes intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs). These IDPs and IDRs are biologically active and yet fail to form specific three-dimensional (3-D) structures, existing instead as collapsed or extended dynamically mobile conformational ensembles [1–7]. These floppy proteins and regions are known as pliable, rheomorphic [8], flexible [9], mobile [10], partially folded [11], natively denatured [12], natively unfolded [3, 13], natively disordered [6], intrinsically unstructured [2, 5], intrinsically denatured [12], intrinsically unfolded [13], intrinsically disordered [4], vulnerable [14], chameleon [15], malleable [16], four-dimensional (4D) [17], protein-clouds [18], and dancing proteins [19], among several other terms. The variability of terms used to describe such proteins and regions is a simple reflection of their highly dynamic nature and the lack of the unique 3-D structure. None of these terms or their combinations is completely appropriate, as the majority of them have been borrowed from the fields such as protein folding or crystallography, which are not directly related to the biologically active proteins that normally exist as structural ensembles.

Since these proteins are highly abundant in any given proteome [20], the role of disorder in determining protein functionality in organisms can no longer be ignored. Native biologically active proteins were conceptualized as parts of the “protein trinity” [21] or the “protein quartet” [22], models where functional protein might exist in one of the several conformations—ordered, collapsed–disordered (molten globule-like), partially collapsed–disordered (pre-molten globule-like), or extended–disordered (coil-like)—and protein function might be derived from any one of these states and/or from the transitions between them. Disordered proteins are typically involved in regulation, signaling, and control pathways [23–25], which complement the functional repertoire of ordered proteins, which have evolved mainly to carry out efficient catalysis [26].

1.2. WHY STUDY IDPS?

Ordered globular proteins are characterized by rigid 3-D structures. The presence of such rigid structures implies that the Ramachandran angles and backbone atoms of each residue undergo non-isotropic small-amplitude motions relative to their local neighborhood and are characterized by the equilibrium positions defined by their time-averaged values. The atom fluctuations are caused by two factors, random thermal motion and small cooperative conformational changes of the local sequence neighborhood, and are known to be correlated with local residue packing [27]. Contrarily to this very static behavior, intrinsically disordered or natively unfolded proteins exist as dynamic ensembles in which atom positions and backbone Ramachandran angles vary significantly over time with no specific equilibrium values and typically involve non-cooperative conformational changes [6].

The kindred of proteins and protein domains, which have been shown in vitro to have little or no ordered structure under physiological conditions, is rapidly amplifying. In fact, over the past decade there has been an exponential increase in the amount of studies dedicated to intrinsically disordered or natively unfolded proteins, starting from a few papers in the early 1990s, and ending with about 300 papers in 2011. A special database, DisProt, was created to keep information about these proteins [28]. There are currently more than 620 proteins in this database.