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 PKAcat(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.

The internal dynamics of proteins inside of cells may be affected by the crowded intracellular environments. Here, we test a novel approach to simulations of crowding, in which simulations in the absence of crowders are postprocessed to predict crowding effects, against the direct approach of simulations in the presence of crowders. The effects of crowding on the flap dynamics of HIV-1 protease predicted by the postprocessing approach are found to agree well with those calculated by the direct approach. The postprocessing approach presents distinct advantages over the direct approach in terms of accuracy and speed and is expected to have broad impact on atomistic simulations of macromolecular crowding.