Modeling Amyloid Aggregation Kinetics: A Case Study with Sup35NM.

Area of Science:

• Biochemistry and Molecular Biology
• Biophysics

Background:

• Amyloid protein aggregation, exemplified by Sup35NM, is crucial for understanding amyloid diseases.
• Thioflavin T (ThT) fluorescence is commonly used to monitor amyloid fibril formation due to its red shift upon binding to aggregates.

Purpose of the Study:

• To infer amyloid aggregation mechanisms by monitoring aggregate mass progression under varying conditions.
• To develop a framework for fitting arbitrary amyloid aggregation kinetics using a population balance model (PBM).

Main Methods:

• Monitoring aggregate mass progression using ThT fluorescence for the amyloid-forming fragment Sup35NM.
• Implementing a population balance model (PBM) to resolve aggregate mass and fibril length distribution over time.
• Reanalyzing previously published aggregate size distribution data using the developed PBM framework.

Main Results:

• Analysis of Sup35NM aggregation suggests primary nucleation, elongation, secondary nucleation, and fragmentation are relevant but their relative importance is ambiguous from fluorescence data alone.
• The PBM framework successfully resolves both total aggregate mass and the entire fibril length distribution.
• Reanalysis of prior data indicated secondary nucleation generated fewer Sup35NM fibrils than fragmentation.

Conclusions:

• Discriminating between amyloid fibril generation processes requires additional information beyond total aggregate mass, such as fibril length distribution.
• Combining ThT fluorescence data with experimental fibril length distributions via the PBM framework enhances confidence in inferring aggregation mechanisms.
• The developed PBM strategy offers a robust approach for detailed mechanistic studies of amyloid aggregation.