Protein Amyloid Aggregation: Methods and Protocols

Part I: Labeling Strategies

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

Wojciech Paslawski, Nikolai Lorenzen, and Daniel E. Otzen

10. Fluorescence Methods for Unraveling Oligomeric Amyloid Intermediates

Niels Zijlstra, Nathalie Schilderink, and Vinod

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 -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.