Protein Amyloid Aggregation: Methods and Protocols

ISBN-13: 9781493929771 / Angielski / Twarda / 2015 / 314 str.

David Eliezer

Opis

This detailed volume focuses on methods for the characterization of aggregation processes that lead to the formation of amyloid fibrils and amyloid oligomers which feature in the etiology of a variety of human disorders collectively known as amyloidoses. The scope of the collection includes techniques for visualizing early steps on the amyloid formation pathway, methods for capturing and characterizing oligomeric, potentially toxic, intermediates, strategies for preparing and characterizing mature amyloid fibrils and approaches for understanding templating and transmission of amyloid aggregates. Written in the highly successful "Methods in Molecular Biology" series format, the chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, "Protein Amyloid Aggregation: Methods and Protocols" serves as an ideal guide for biochemists and biophysicists with an interest in elucidating the mechanisms of protein amyloid formation, as well as chemists, pharmacologists and clinicians with an interest in leveraging an understanding of such mechanisms for the purpose of therapeutic development.

Spis treści

Part I: Labeling Strategies

 

1. Semisynthesis and Enzymatic Preparation of Post-Translationally Modified α-Synuclein

            Bruno Fauvet and Hilal A. Lashuel

 

2. Isotope-Labeled Amyloids Via Synthesis, Expression, and Chemical Ligation for Use in FTIR, 2D IR, and NMR Studies

            Tianqi O. Zhang, Maksim Grechko, Sean D. Moran, and Martin T. Zanni

 

Part II: Kinetics/Mechanism

 

3. Inter-Molecular Paramagnetic Relaxation Enhancement (PRE) Studies of Transient Complexes in Intrinsically Disordered Proteins

            Maria K. Janowska and Jean Baum

 

4. Detection of Helical Intermediates During Amyloid Formation by Intrinsically Disordered Polypeptides and Proteins

            Andisheh Abedini, Ping Cao, and Daniel P. Raleigh

 

5. Fluorescence Correlation Spectroscopy: A Tool to Study Protein Oligomerization and Aggregation In Vitro and In Vivo

            Bankanidhi Sahoo, Kenneth W. Drombosky, and Ronald Wetzel

 

6. Deep UV Resonance Raman Spectroscopy for Characterizing Amyloid Aggregation

            Joseph D. Handen and Igor K. Lednev

 

7. Analyzing Tau Aggregation with Electron Microscopy

            Carol J. Huseby and Jeff Kuret

 

Part III: Oligomers

 

8. Characterization of Amyloid Oligomers by Electrospray Ionization-Ion Mobility Spectrometry-Mass Spectrometry (ESI-IMS-MS)

            Charlotte A. Scarff, Alison E. Ashcroft, and Sheena E. Radford

 

9. Formation and Characterization of α-Synuclein Oligomers

            Wojciech Paslawski, Nikolai Lorenzen, and Daniel E. Otzen

 

10. Fluorescence Methods for Unraveling Oligomeric Amyloid Intermediates

            Niels Zijlstra, Nathalie Schilderink, and Vinod

Subramaniam

 

Part IV: Fibrils

 

11. Preparation of Amyloid Fibrils for Magic-Angle Spinning Solid-State NMR Spectroscopy

            Marcus D. Tuttle, Joseph M. Courtney, Alexander M. Barclay, and Chad M. Rienstra

 

12. Spin Labeling and Characterization of Tau Fibrils Using Electron Paramagnetic Resonance (EPR)

            Virginia Meyer and Martin Margittai

 

13. Preparation of Crystalline Samples of Amyloid Fibrils and Oligomers

            Asher Moshe, Meytal Landau, and David Eisenberg

 

14. Quenched Hydrogen Exchange NMR of Amyloid Fibrils

            Andrei T. Alexandrescu

 

Part V: Computational Approaches

 

15. Studying the Early Stages of Protein Aggregation Using Replica Exchange Molecular Dynamics Simulations

            Joan-Emma Shea and Zachary A. Levine

 

16. Computational Methods for Structural and Functional Studies of Alzheimer’s Amyloid Ion Channels

            Hyunbum Jang, Fernando Teran Arce, Joon Lee, Alan L. Gillman, Srinivasan Ramachandran, Bruce L. Kagan, Ratnesh Lal, and Ruth Nussinov

 

17. Analyzing Ensembles of Amyloid Proteins Using Bayesian Statistics

            Thomas Gurry, Charles K. Fisher, Molly Schmidt, and Collin M. Stultz

 

Part VI: Toxicity and Pathology

 

18. In Vitro Studies of Membrane Permeability Induced by Amyloidogenic Polypeptides Using Large Unilamellar Vesicles

            Ping Cao and Daniel P. Raleigh

 

19. Cell Models to Study Cell-to-Cell Transmission of α-Synuclein

            Eun-Jin Bae, He-Jin Lee, and Seung-Jae Lee

 

20. Preparation of Amyloid Fibrils Seeded from Brain and Meninges

            Kathryn P. Scherpelz, Jun-Xia Lu, Robert Tycko, and Stephen C.

Meredith