NAGPKin

NAGPKin analyzes and quantifies nucleation-and-growth (NAG) kinetics of protein phase separation to characterize formation of biomolecular condensates in eukaryotic cells and accumulation of amyloid deposits in neurons.

Key Features:

• Quantitative Analysis: Performs quantitative estimation of NAG rates from mass-based or size-based progress curves, enabling mechanistic kinetic modeling without relying on empirical or untestable assumptions.
• Parameter Fitting and Reporting: Fits NAG parameters to input progress-curve data and generates reports that elucidate mechanisms of liquid-liquid phase separation (LLPS) and protein aggregation.
• Predictive Capabilities: Uses fitted NAG parameters to predict particle size distributions for protein droplets formed by LLPS and for amyloid fibrils arising from aggregation.

Scientific Applications:

• Drug Discovery: Supports evaluation of candidates that modulate protein phase separation or aggregation by providing kinetic parameters and predicted size distributions relevant to therapeutic targeting of amyloid deposits.
• Fundamental Research: Enables mechanistic studies of LLPS and protein self-assembly by quantifying nucleation and growth kinetics underlying biomolecular condensate formation.

Methodology:

Fits nucleation-and-growth parameters to mass-based or size-based progress curves and analyzes fitted parameters to predict particle size distributions.