Amyloid Fibrils and Prefibrillar Aggregates: Molecular and Biological Properties / Edition 1

Amyloid Fibrils and Prefibrillar Aggregates: Molecular and Biological Properties / Edition 1

by Daniel Erik Otzen
ISBN-10:
3527332006
ISBN-13:
9783527332007
Pub. Date:
04/01/2013
Publisher:
Wiley
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Overview

Amyloid Fibrils and Prefibrillar Aggregates: Molecular and Biological Properties / Edition 1

Summing up almost a decade of biomedical research, this topical and eagerly awaited handbook is the first reference on the topic to incorporate recent breakthroughs in amyloid research.

The first part covers the structural biology of amyloid fibrils and pre-fibrillar assemblies, including a description of current models for amyloid formation. The second part looks at the diagnosis and biomedical study of amyloid in humans and in animal models, while the final section discusses pharmacological approaches to manipulating amyloid and also looks at its physiological roles in lower and higher organisms. For Biochemists, Molecular Biologists, Neurobiologists, Neurophysiologists and those working in the Pharmaceutical Industry.

Product Details

ISBN-13: 9783527332007
Publisher: Wiley
Publication date: 04/01/2013
Pages: 464
Product dimensions: 6.90(w) x 9.70(h) x 1.10(d)

Table of Contents

Preface XIX

List of Contributors XXIII

1 The Amyloid Phenomenon and Its Significance 1
Christopher M. Dobson

1.1 Introduction 1

1.2 The Nature of the Amyloid State of Proteins 1

1.3 The Structure and Properties of Amyloid Species 5

1.4 The Kinetics and Mechanism of Amyloid Formation 7

1.5 The Link between Amyloid Formation and Disease 9

1.6 Strategies for Therapeutic Intervention 11

1.7 Looking to the Future 14

1.8 Summary 15

Acknowledgments 16

References 16

2 Amyloid Structures at the Atomic Level: Insights from Crystallography 21
Michael R. Sawaya and David Eisenberg

2.1 Atomic Structures of Segments of Amyloid-Forming Proteins 21

2.2 Stability of Amyloid Fibers 25

2.3 Which Proteins Enter the Amyloid State? 26

2.4 Molecular basis of Amyloid Polymorphism and Protein Strains 27

2.5 Atomic Structures of Steric Zippers Suggest Models for Amyloid Fibers of Parent Proteins 28

2.6 Atomic Structures of Steric Zippers Offer Approaches for Chemical Interventions against Amyloid Formation 31

2.7 Summary 34

Acknowledgments 36

References 36

3 What Does Solid-State NMR Tell Us about Amyloid Structures ? 39
Wolfgang Hoyer and Henrike Heise

3.1 Introduction 39

3.2 Principles of Solid-State NMR Spectroscopy and Experiments for Structural Constraints 40

3.3 Amyloid Fibrils Investigated by Solid-State NMR Spectroscopy 45

3.4 Summary 53

References 54

4 From Molecular to Supramolecular Amyloid Structures: Contributions from Fiber Diffraction and Electron Microscopy 63
Kyle L. Morris and Louise C. Serpell

4.1 Introduction 63

4.2 History 65

4.3 Methodology 68

4.4 Recent Advances in Amyloid Structure Determination 73

4.5 Summary 78

Acknowledgments 79

References 79

5 Structures of Aggregating Species by Small-Angle X-Ray Scattering 85
Cristiano L. P. Oliveira and Jan Skov Pedersen

5.1 Introduction 85

5.2 Theoretical and Experimental Aspects 85

5.3 Data Analysis and Modeling Methods 88

5.4 Studying Protein Aggregation and Fibrillation Using SAXS 91

5.5 General Strategies for Modeling SAXS Data from Protein Complexes 98

5.6 Summary and Final Remarks 100

Acknowledgments 101

References 101

6 Structural and Compositional Information about Pre-Amyloid Oligomers 103
Niels Zijstra and Vinod Subramaniam

6.1 General Introduction 103

6.2 Biophysical Techniques to Study Amyloid Oligomers 104

6.3 The Structure and Composition of Amyloid Oligomers 109

6.4 Concluding Remarks 116

Acknowledgments 118

References 118

7 The Oligomer Species: Mechanistics and Biochemistry 127
Massimo Stefani

7.1 Introduction 127

7.2 The Structure-Toxicity Relation of Early Amyloids 128

7.3 The Oligomer-Membrane complex 131

7.4 Biochemical Modification Underlying Amyloid Toxicity 134

7.5 Summary 141

References 141

8 Pathways of Amyloid Formation 151
Francesco Bemporad and Fabrizio Chiti

8.1 Introduction 151

8.2 Nomenclature of the Various Conformational States 152

8.3 Graphical Representations of the Mechanisms Leading to Amyloid 153

8.4 Pathways of Amyloid Fibril Formation 159

8.5 Nucleation Growth versus Nucleated Conformational Conversion 161

8.6 Summary 163

References 163

9 Sequence-Based Prediction of Protein Behavior 167
Gian Gaetano Tartagli and Michele Vendruscolo

9.1 Introduction 167

9.2 The Strategy of Zyggregator Predictions 167

9.3 Aggregation Under Other Conditions 173

9.4 Prediction of the Cellular Toxicity of Protein Aggregates 174

9.5 Relationship to Other Methods of Predicting Protein Aggregation Propensities 175

9.6 Competition between Folding and Aggregation of Proteins 177

9.7 Prediction of Protein Solubility from the Competition between Folding and Aggregation 177

9.8 Sequence-Based Prediction of Protein Interactions with Molecular Chaperones 179

9.9 Summary 179

References 180

10 The Kinetics and Mechanisms of Amyloid Formation 183
Samuel I. A. Cohen, Michele Vendruscolo, Christopher M. Dobson and Tuomas P. J. Knowles

10.1 Introduction 183

10.2 Classical Theory of Nucleated Polymerization 184

10.3 The Theory of Filamentous Growth with Secondary Pathways 193

10.4 Self-Consistent Solutions for the Complete Reaction Time Course 200

10.5 Summary 205

References 205

11 Fluorescence Spectroscopy as a Tool to Characterize Amyloid Oligomers and Fibrils 211
Per Hammarström, Mikael Lindgren and K. Peter R. Nilson

11.1 Introduction 211

11.2 Fluorescence Spectroscopy for Studies of Amyloid Reactions In vitro 212

11.3 Cysteine-Reactive Fluorescent Probes 214

11.4 Amyloidotropic Probes for Amyloid Fibrils and Oligomeric States 218

11.5 Luminescent Conjugated Poly and Oligothiophenes LCPs and LCOs 228

11.6 Summary 236

Acknowledgments 237

References 239

12. Animal Models of Amyloid Diseases 245
Stanislav Ott and Damian C. Crowther

12.1 Introduction 245

12.2 Some Big Questions Regarding Amyloid Diseases and Some Answers from Animal Models 247

12.3 Identifying the Toxic Species in the Systemic Amyloidoses 248

12.4 Identifying the Toxic Species in Alzheimer’s Disease 250

12.5 Infectious Protein Misfolding 252

12.6 Conclusions 256

References 257

13 The Role of Aβ in Alzheimer’s Disease 263
Timothy M. Ryan, Blaine R. Roberts, Victor A. Streltsov, Stewart D. Nuttall and Colin L. Masters

13.1 History of Amyloidsis 263

13.2 Biochemistry of Aβ 264

13.3 Amyloid Fibrils 268

13.4 The Soluble Oligomer Theory of AD 269

13.5 Other Factors Involved in Amyloid Plaque Formation in AD 274

12.6 Metal Ions 278

13.7 Other Potential Aβ Interactions 280

13.8 Other Neurodegenerative Diseases 280

13.9 Conclusion 280

References 281

14 Experimental Approaches to Inducing Amyloid Aggregate 295
Lise Giehm and Daniel Otzen

14.1 The Need for Reproducible Fibrillation Assays 295

14.2 Setting Up an Assay to Monitor Fibrillation 296

14.3 Conditions That Promote Protein Aggregation 298

14.4 Processing and Batch Differences 312

14.5 Toward High-Throughput Assays 313

14.6 Summary 314

References 314

15 Fibrillar Polymorphism 321
Marcus Fändrick, Melanie Wulff, Jesper Søndergaard Pedersen and Daniel Otzen

15.1 Detection of Fibrillar Polymorphism 321

15.2 The Structural Definition of Fibril Polymorphism 322

15.3 The Two Classes of Fibril Polymorphism 328

15.4 How Does Fibrilliar Polymorphism Arise? 332

15.5 The Interconversion of Fibril Polymorphs 334

15.6 The Biological Implications of Fibril Polymorphism 335

15.7 Summary 337

Acknowledgments 338

References 338

16 Inhibitors of Amyloid and Oligomer Formation 345
Nikolai Lorenzen, Erich E. Wanker and Daniel Otzen

16.1 Introduction: Amyloidoses versus Neurodegenerative Diseases 345

16.2 Summary 362

References 363

17 Development of Therapeutic Strategies for the Transthyretin Amyloidoses 373
Colleen Fearns, Stephen Connelly, Evan T. Powers and Jeffrey W. Kelly

17.1 Introduction to Transthyretin Structure and Function 373

17.2 Introduction to Amyloid Diseases in General 373

17.3 Mechanism of Transthyretin Amyloidogenesis 378

17.4 Kinetic Stabilization of the Transthyretin Tetramer Ameliorates Amyloid Disease – Genetic Evidence 379

17.5 Assessment of Diflunisal for Treatment of Transthyretin Amyloidosis 385

17.6 Tafamidis, the First Approved Drug for Treatment of a Transthyretin Amyloidosis 385

17.7 Summary 387

References 387

18 Hormone Amyloids in Sickness and in Health 395
Carolin Seuring, Nadezhda Nespovitaya, Jonas Rutishauser, Martin Spies and Roland Riek

18.1 Introduction 395

18.2 Constitutive vs. Regulated Secretory Pathways 395

18.3 Secretory Granules Contain Aggregated Cargo 396

18.4 Secretory Granule Aggregation by Functional Amyloid Formation 401

18.5 Hormone Amyloids in Disease: Diabetes Insipidus 402

18.6 conclusions 405

References 405

19 Functional Amyloids in Bacteria 411
Morten S. Dueholm, Per Halkjaer Nielsen, Matthew Chapman and Daniel Otzen

19.1 Introduction 411

19.2 Functional Amyloids are Common in Nature 412

19.3 Identification and Characterization of Functional Amyloids 413

19.4 Functional Bacterial Amyloids Play Many Roles 415

19.5 Biogenesis and Regulation of Functional Bacterial Amyloids 418

19.6 Structural Composition of Functional Amyloids 421

19.7 Assembly Properties of Functional Amyloid In Vitro 425

19.8 Diversity and Distribution of Functional Amyloid Genes 426

19.9 Summary 431

References 433

20 Structural Properties and Applications of Self-Assembling Peptides 439
Zhongli Luo and Shuguang Zhang

20.1 Introduction to Self-Assembling Peptides 439

20.2 The Principles of Self-Assembling Peptides 439

20.3 Self-Assembling Peptide Nanofibers 443

20.4 Diverse Applications of Self-Assembling Peptide Nanofibers Scaffolds 446

20.5 Summary 451

Acknowledgments 452

References 452

21 Harnessing the Self-Assembling Properties of Proteins in Spider Silk and Lung Surfactant 455
Jan Johansson

21.1 Introduction 455

21.2 Amino Acid Sequences and Amyloid Formation 455

21.3 Spider Silk and How the Spiders Make It 458

21.4 Harnessing the Properties of Spider Silk and Its Constituent Proteins 461

21.5 Biosynthesis of an ɑ-Helix from One of the Most β-Prone Sequences Known 462

21.6 Anti-Amyloid Properties of the BRICHOS Domain 464

21.7 Summary 465

Acknowledgments 465

References 466

Index 471

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