By Ronald Wetzel, Indu Kheterpal
The facility of polypeptides to shape however folded, polymeric constructions comparable to amyloids and similar aggregates is being more and more famous as a tremendous new frontier in protein study. This new quantity of equipment in Enzymology in addition to half B (volume 412) on Amyloid, Prions and different Protein Aggregates proceed within the culture of the 1st quantity (309) in containing unique protocols and methodological insights, supplied by way of leaders within the box, into the newest equipment for investigating the constructions, mechanisms of formation, and organic actions of this significant category of protein assemblies.
* provides exact protocols
* contains troubleshooting assistance
* offers assurance on structural biology, computational tools, and biology
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Extra resources for Amyloid, Prions, and Other Protein Aggregates, Part C
Poorman, R. , Lutzke, B. , Kappenman, A. , Buhl, A. , and Epps, D. E. (2003). Spontaneous aggregation and cytotoxicity of the ‐amyloid A1–40: A kinetic model. J. Prot. Chem. 22, 31–40. Teplow, D. B. (1998). Structural and kinetic features of amyloid ‐protein fibrillogenesis. Amyloid 5, 121–142. , Klimov, D. , and Dima, R. I. (2003). Emerging ideas on the molecular basis of protein and peptide aggregation. Curr. Opin. Struct. Biol. 13, 146–159. , and Langen, R. (2002). Structural and dynamic features of Alzheimer’s A peptide in amyloid fibrils studied by site‐directed spin labeling.
The centrifugation buffer can also be adjusted to minimize the possibility of aggregation during centrifugation; for example, if aggregation is greatly favored by salt, the centrifugation can be conducted in low‐salt conditions and the buffer adjusted to the desired salt concentration after the supernatant has been harvested. Using this protocol, we obtain reproducible spontaneous aggregation kinetics for various A(1–40) molecules and for polyGln peptides of various repeat lengths. Difficult peptides, such as A(1–42), IAPP, and  kinetics and thermodynamics of amyloid assembly 41 polyGln peptides of repeat lengths in the range of 50, have also been successfully treated.
Evaporate the HFIP in tubes under a stream of argon in a chemical fume hood. 9. Immediately further dry the peptide under vacuum (a standard lyophilizer is fine) for 30–60 min to ensure that all of the TFA and HFIP has been removed from the peptide. It is critical to move without delay from step 8 to step 9 and from step 9 to step 10. Delays can lead to aggregate formation upon addition of the 2 mM NaOH. This is probably attributable to the adsorption of water from the atmosphere by the dry peptide films, leading to essentially very concentrated aqueous solutions of peptide that are prone to aggregate.
Amyloid, Prions, and Other Protein Aggregates, Part C by Ronald Wetzel, Indu Kheterpal