The ability of polypeptides to form alternatively folded, polymeric structures such as amyloids and related aggregates is being increasingly recognized as a major new frontier in protein research. This new volume of "Methods in Enzymology" along with Part B (volume 412) on Amyloid, Prions and other Protein Aggregates continue in the tradition of the first volume (309) in containing detailed protocols and methodological insights, provided by leaders in the field, into the latest methods for investigating the structures, mechanisms of formation, and biological activities of this important class of protein assemblies. It presents detailed protocols and includes troubleshooting tips. It provides coverage on structural biology, computational methods, and biology.
Characterization of protein deposition in vitro. Chapter 1: Purification of Polyglutamine Proteins Chapter 2: Preparation of amyloid beta-protein for structural and functional studies. Chapter 3: Kinetics and thermodynamics of amyloid assembly using an HPLC-based sedimentation assay. Chapter 4: Protein aggregation starting from the native, globular stete. Chapter 5: Direct observation of amyloid growth monitored by total internal reflection fluorescence microscopy. Chapter 6: Characterization of Amyloid Structures at the Molecular Level by Solid State Nuclear Magnetic Resonance Spectroscopy. Chapter 7: Spin Labeling Analysis of Amyloids and other Protein Aggregates. Chapter 8: Hydrogen-Deuterium Exchange Mass Spectrometry of Protein Aggregates. Chapter 9: Hydrogen-Deuterium Exchange analyzed by Matrix Assisted Laser Desorption-Ionisation Mass Spectrometry and the HET-s prion model. Chapter 10: Analysis of amyloid fibril structure by scanning cysteine mutagenesis. Chapter 11: Sedimentation velocity analysis of amyloid oligomers and fibrils. Chapter 12: Structural study of metastable amyloidogenic protein oligomers by Photo-Induced Cross-linking of Unmodified Proteins (PICUP). Chapter 13: High Pressure Studies on Protein Aggregates and Amyloid Fibrils. Chapter 14: Phage Display Screening for Peptides that Inhibit Polyglutamine Aggegation. Chapter 15: Peptide Based Inhibitors of Amyloid Assembly. Chapter 16: Screening for Modulators of Aggregation with a Microplate Elongation Assay. Chapter 17: Conformation-dependent anti-amyloid oligomer antibodies.