Atomistic Modeling of Excluded-Volume and Soft Interactions in Crowded Environments

Abstract

In cellular environments the total macromolecule concentrations can exceed 300 g/l. Such crowded conditions can significantly affect stability, kinetics, and function of proteins. Previous studies on the effects of crowding have focused on the excluded-volume interaction. Recent studies with protein crowders and cell lysates suggested that, in addition to excluded-volume interaction, these crowding agents also have a soft interaction with the test protein chymotrypsin inhibitor 2 (CI2). The latter interaction has a comparable, or even greater effect on CI2 folding stability than the former interaction. We have developed a postprocessing method for modeling crowding [1, 2]. In this method we simulate the end states (e.g., folded and unfolded states) of a protein in a dilute solution and then calculate the free energies of transferring these end-state conformations to a crowded solution. We thus bypass the slow transitions between end states, which have necessitated coarse-grained representations by others. The postprocessing method was applied previously [1-3] to treat excluded-volume interaction, by either an insertion algorithm [1] or a theory involving numerically calculated radius, area, and volume [4], with the test proteins represented at the all-atom level. Here we treat the additional soft interaction, by using a fast Fourier transform based algorithm. We use the new method to study the total effects of protein crowders on CI2 folding stability and compare the results to experimental data. The success in modeling both excluded-volume and soft interactions of protein crowders is an important step toward understanding the total impact of cellular environments.[1] Qin & Zhou (2009) Biophys. J. 97, 12.[2] Qin, Minh, McCammon & Zhou (2010) J. Phys. Chem. Lett. 1, 107.[3] Dong, Qin & Zhou (2010) PLoS Comput. Biol. 6, e1000833.[4] Qin & Zhou (2010) Phys. Rev. E 81, 031919.