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Amyloid fibrils and prefibrillar aggregates : molecular and biological properties /

Summing up almost a decade of biomedical research, this topical handbook is a reference on the topic which incorporates recent breakthroughs in amyloid research. The first part covers the structural biology of amyloid fibrils and pre-fibrillar assemblies. The second part looks at the diagnosis and b...

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Detalles Bibliográficos
Clasificación:	Libro Electrónico
Otros Autores:	Otzen, Daniel Erik, 1969-
Formato:	Electrónico eBook
Idioma:	Inglés
Publicado:	Weinheim : Wiley-VCH, [2013]
Temas:	Amyloid. Amyloid > chemistry Amyloid > pharmacokinetics Amyloid Amyloïde. SCIENCE > Life Sciences > Biochemistry. Bioquímica. Llibres electrònics.
Acceso en línea:	Texto completo

Tabla de Contenidos:

Amyloid Fibrils and Prefibrillar Aggregates
Contents
Preface
List of Contributors
1 The Amyloid Phenomenon and Its Significance
1.1 Introduction
1.2 The Nature of the Amyloid State of Proteins
1.3 The Structure and Properties of Amyloid Species
1.4 The Kinetics and Mechanism of Amyloid Formation
1.5 The Link between Amyloid Formation and Disease
1.6 Strategies for Therapeutic Intervention
1.7 Looking to the Future
1.8 Summary
Acknowledgments
References
2 Amyloid Structures at the Atomic Level: Insights from Crystallography
2.1 Atomic Structures of Segments of Amyloid-Forming Proteins
2.1.1 Protein Segments That Form Amyloid-Related Crystals
2.1.2 Atomic Structures of Fiber-Like Microcrystals
2.2 Stability of Amyloid Fibers
2.3 Which Proteins Enter the Amyloid State?
2.4 Molecular Basis of Amyloid Polymorphism and Prion Strains
2.5 Atomic Structures of Steric Zippers Suggest Models for Amyloid Fibers of Parent Proteins
2.6 Atomic Structures of Steric Zippers Offer Approaches for Chemical Interventions against Amyloid Formation
2.7 Summary
Acknowledgments
References
3 What Does Solid-State NMR Tell Us about Amyloid Structures?
3.1 Introduction
3.2 Principles of Solid-State NMR Spectroscopy and Experiments for Structural Constraints
3.2.1 Isotope Labeling, Magic Angle Spinning, Dipolar Coupling, and Resonance Assignment
3.2.2 De.ning the Amyloid Core by Magnetization Transfer from Water
3.2.3 Determining the Fibril Registry
3.2.4 Seeded versus Unseeded Fibrils
3.3 Amyloid Fibrils Investigated by Solid-State NMR Spectroscopy
3.3.1 AÝ peptides of Different Length
3.3.2 Islet Amyloid Polypeptide (IAPP/Amylin): Parallel and Antiparallel Steric Zippers
3.3.3 Ü-Synuclein: Polymorphism with Flexible Terminal Regions.
3.3.4 PrP: Rearrangements to Maintain a Fibrillar Core Region
3.3.5 Yeast Prions with Glutamine/Asparagine-Rich Prion Domains: Sup35p, Ure2p, and Rnq1p
3.3.6 Functional Amyloid: the Yeast Prion HET-s
3.4 Summary
References
4 From Molecular to Supramolecular Amyloid Structures: Contributions from Fiber Diffraction and Electron Microscopy
4.1 Introduction
4.2 History
4.2.1 The Historical Use of X-ray Fiber Diffraction
4.2.2 The Historical Use of Transmission Electron Microscopy
4.3 Methodology
4.3.1 X-Ray Fiber Diffraction
4.3.2 Transmission Electron Microscopy
4.4 Recent Advances in Amyloid Structure Determination
4.4.1 X-ray Fiber Diffraction
4.4.2 Transmission Electron Microscopy
4.5 Summary
Acknowledgments
References
5 Structures of Aggregating Species by Small-Angle X-Ray Scattering
5.1 Introduction
5.2 Theoretical and Experimental Aspects
5.3 Data Analysis and Modeling Methods
5.4 Studying Protein Aggregation and Fibrillation Using SAXS
5.4.1 Some General Considerations
5.4.2 SAXS Studies of Insulin, Glucagon, and Ü-Synuclein
5.4.3 SDS-Induced Aggregation of Ü-Synuclein
5.4.4 Multi-Component Fitting and Analysis of SAXS Data
5.5 General Strategies for Modeling SAXS Data from Protein Complexes
5.6 Summary and Final Remarks
Acknowledgments
References
6 Structural and Compositional Information about Pre-Amyloid Oligomers
6.1 General Introduction
6.2 Biophysical Techniques to Study Amyloid Oligomers
6.2.1 Fluorescence Spectroscopy
6.2.1.1 Ensemble Spectroscopy
6.2.1.2 Single-Molecule Spectroscopy
6.2.2 Atomic Force Microscopy
6.2.3 Absorbance and Circular Dichroism Spectroscopy
6.2.4 Small-Angle X-Ray Scattering
6.2.5 Mass Spectrometry
6.3 The Structure and Composition of Amyloid Oligomers
6.3.1 Ü-Synuclein Oligomers.
6.3.1.1 Morphology
6.3.1.2 Oligomer Structure
6.3.1.3 Oligomer Composition
6.3.2 AÝ Peptide Oligomers
6.3.2.1 Morphology
6.3.2.2 Composition
6.4 Concluding Remarks
Acknowledgments
References
7 The Oligomer Species: Mechanistics and Biochemistry
7.1 Introduction
7.2 The Structure-Toxicity Relation of Early Amyloids
7.2.1 Antibodies Define Different Structural Classes of Oligomers and Fibrils
7.2.2 Proteins May Form Different Kinds of Oligomers with Different Structural and Biological Activities
7.3 The Oligomer-Membrane Complex
7.3.1 The Effect of Surfaces on Protein Misfolding and Aggregation
7.3.2 The Membrane Composition Affects Binding and Aggregation Processes
7.3.3 Complex Roles of Cholesterol and Gangliosides in Oligomer Cytotoxicity
7.4 Biochemical Modifications Underlying Amyloid Toxicity
7.4.1 A New View of the Amyloid Cascade Hypothesis
7.4.2 Amyloid Pores: a Mechanism for Cytotoxicity?
7.4.3 Other Mechanisms for Oligomer Cytotoxicity
7.4.3.1 Oxidative Stress and Amyloid Aggregates
7.4.3.2 Lipid Modification and Ca2+ Entry
7.4.3.3 The Complexity of Amyloid and Oligomer Polymorphism
7.5 Summary
References
8 Pathways of Amyloid Formation
8.1 Introduction
8.2 Nomenclature of the Various Conformational States
8.3 Graphical Representations of the Mechanisms Leading to Amyloid
8.3.1 Time Course of Amyloid Content
8.3.2 Energy Landscapes of Amyloid Fibril Formation
8.3.3 Reaction Equilibria Involved in Amyloid Fibril Formation
8.4 Pathways of Amyloid Fibril Formation
8.5 Nucleation Growth versus Nucleated Conformational Conversion
8.6 Summary
References
9 Sequence-Based Prediction of Protein Behavior
9.1 Introduction
9.2 The Strategy of the Zyggregator Predictions.
9.2.1 Prediction of the Effects of Amino Acid Substitutions on Protein Aggregation Rates
9.2.2 Prediction of the Overall Aggregation Rates of Peptides and Proteins
9.2.3 Prediction of Aggregation-Prone Regions in Amino Acid Sequences
9.3 Aggregation Under Other Conditions
9.3.1 Prediction of Protein Aggregation-Prone Regions in the Presence of Denaturants
9.3.2 Prediction of Aggregation-Prone Regions in Native States of Proteins
9.4 Prediction of the Cellular Toxicity of Protein Aggregates
9.5 Relationship to Other Methods of Predicting Protein Aggregation Propensities
9.6 Competition between Folding and Aggregation of Proteins
9.7 Prediction of Protein Solubility from the Competition between Folding and Aggregation
9.7.1 Sequence-Based Prediction of Protein Solubility
9.7.2 Prediction of the Solubility of Proteins Based on Their Cellular Abundance
9.8 Sequence-Based Prediction of Protein Interactions with Molecular Chaperones
9.9 Summary
References
10 The Kinetics and Mechanisms of Amyloid Formation
10.1 Introduction
10.2 Classical Theory of Nucleated Polymerization
10.2.1 From Microscopic Processes to a Master Equation
10.2.2 Kinetic Equations for Experimental Observables
10.2.3 Characteristics of Oosawa-Type Growth
10.2.3.1 Nucleation and Growth Occur Simultaneously
10.2.3.2 The Early Stages of the Reaction Time Course Are Described by Polynomial Growth
10.2.3.3 The Late Stages of the Reaction Time Course are Described by Simple First-Order Kinetics
10.2.3.4 The Integrated Rate Laws Exhibit Scaling Behavior
10.2.4 Global Analysis of Experimental Data Using the Oosawa Theory
10.3 The Theory of Filamentous Growth with Secondary Pathways
10.3.1 Extending the Oosawa Framework to Include Fragmentation and Secondary Nucleation
10.3.2 Early Time Perturbative Solutions.
10.3.3 Characteristics of Exponential-Type Growth
10.3.3.1 The Early Stages of the Reaction Time Course Are Exponential
10.3.3.2 The Solution Exhibits Scaling Behavior
10.3.4 Global Analysis of Experimental Data Using Linearized Solutions
10.4 Self-Consistent Solutions for the Complete Reaction Time Course
10.4.1 The Key Phenomenological Parameters Depend on Combinations of the Microscopic Rate Constants
10.4.2 Reaction Time Course with Depleted Monomer Concentration
10.4.3 Global Analysis of Amyloid Reaction Kinetics Using Self-Consistent Solutions
10.5 Summary
References
11 Fluorescence Spectroscopy as a Tool to Characterize Amyloid Oligomers and Fibrils
11.1 Introduction
11.2 Fluorescence Spectroscopy for Studies of Amyloid Reactions In vitro
11.2.1 Fluorescence Output Formats
11.2.2 Fluorescence Anisotropy
11.2.3 Single Molecule Detection
11.2.4 Conformational Probes
11.3 Cysteine-Reactive Fluorescent Probes
11.3.1 Environmentally Sensitive Probes
Spectrochromic Stokes Shift Assay
11.3.2 Fluorescence Anisotropy Probes for Amyloid Oligomerization
11.3.3 Pyrene Excimer Formation Probes for amyloid Oligomer and Fibril Topology
11.3.4 Bifunctional Cysteine Reagents as Probes for Amyloid Oligomers and Fibrils
11.4 Amyloidotropic Probes for Amyloid Fibrils and Oligomeric States
11.4.1 Are There Selective Probes for Prefibrillar Oligomeric States?
11.4.2 Fluorescence Anisotropy of Small Molecule Probes for Capturing the Intermediate Oligomeric State
11.4.3 In vivo Fluorescent Probes for Amyloid Fibrils
11.5 Luminescent Conjugated Poly and Oligothiophenes LCPs and LCOs
11.5.1 Optical Properties of Chemically Defined LCOs
11.5.2 Bridging the Imaging and Spectroscopy Gap
Microspectroscopy of In vivo Formed Amyloids.

Amyloid fibrils and prefibrillar aggregates : molecular and biological properties /

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