UC San Diego

Researchers developed a method called fast Fourier transform (FFT)-based modeling of atomistic protein–protein interactions applied to cross second virial coefficient B23(FMAPB23) to characterize protein kinase A (PKA) subunits as macromolecular regulators of PKA RIα liquid-liquid phase separation. The cross second virial coefficient B23 was calculated for Mg²⁺-bound PKAcat [denoted as PKA^cat(Mg²⁺)] and cAMP-bound RIα [denoted as RIa(cAMP)]. Five structures for the first molecule were taken from PDB: 6NO7 chains E and G, 3O7L chain B, and 4NTT chains A and B, while two structures for the second molecule were taken from 4MX3 chains A and B. The results from the total of ten runs were used to calculate a mean value and a standard error of the mean.