Recently, we reported 14 amyloid protein aggregation kinetic data sets that were fit using the "Ockham's razor"/minimalistic Finke-Watzky (F-W) two-step model of slow nucleation (A --> B, rate constant k 1) and fast autocatalytic growth (A + B --> 2B, rate constant k 2), yielding quantitative (average) rate constants for nucleation ( k 1) and growth ( k 2), where A is the monomeric protein and B is the polymeric protein [Morris, A. M., et al. (2008) Biochemistry 47, 2413-2427]. Herein, we apply the F-W model to 27 representative prion aggregation kinetic data sets obtained from the literature. Each prion data set was successfully fit with the F-W model, including three different yeast prion proteins (Sup35p, Ure2p, and Rnq1p) as well as mouse and human prions. These fits yield the first quantitative rate constants for the steps of nucleation and growth in prion aggregation. Examination of a Sup35p system shows that the same rate constants are obtained for nucleation and for growth within experimental error, regardless of which of six physical methods was used, a unique set of important control experiments in the protein aggregation literature. Also provided herein are analyses of several factors influencing the aggregation of prions such as glutamine/asparagine rich regions and the number of oligopeptide repeats in the prion domain. Where possible, verification or refutation of previous correlations to glutamine/asparagine regions, or the number of repeat sequences, in literature aggregation kinetics is given in light of the quantitative rate constants obtained herein for nucleation and growth during prion aggregation. The F-W model is then contrasted to four literature mechanisms that address the molecular picture of prion transmission and propagation. Key limitations of the F-W model are listed to prevent overinterpretation of the data being analyzed, limitations that derive ultimately from the model's simplicity. Finally, possible avenues of future research are suggested.
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Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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Site | Modification | Modifier | Source | Reference |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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