NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation

• DOI: 10.1091/mbc.e23-07-0289
• Publication Date: 2023-12-20T17:18:51Z
• Authors: Zsuzsa Sárkány; Francisco Figueiredo; Sandra Macedo-Rib...; Pedro M. Martins
• Keywords: Phase Separation; Amyloid; 0303 health sciences; 03 medical and health sciences; Special Issue on Biomolecular Condensates

The assembly of biomolecular condensate in eukaryotic cells and the accumulation amyloid deposits neurons are processes involving nucleation growth (NAG) new protein phases. To therapeutically target phase separation, drug candidates tested vitro assays that monitor increase mass or size phase. Limited mechanistic insight is, however, provided if empirical untestable kinetic models fitted to these progress curves. Here we present web server NAGPKin quantifies NAG rates using mass-based size-based curves as input data. A report is generated containing parameters elucidating separation mechanisms at play. can be used predict particle distributions of, for example, droplets formed by liquid-liquid (LLPS) fibrils aggregation. Because minimal intervention required from user, a good platform standardized reporting LLPS self-assembly useful discovery well fundamental studies on separation. freely available (no login required) https://nagpkin.i3s.up.pt.