Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins

Abstract

Due to their conformational malleability, intrinsically disordered proteins (IDPs) are particularly susceptible to influences of crowded cellular environments. Here we report a computational study of the effects of macromolecular crowding on the conformational ensemble of a coarse-grained IDP model, by using two approaches. In one, the IDP is simulated along with the crowders; in the other, crowder-free simulations are postprocessed to predict the conformational ensembles under crowding. We found significant decreases in the radius of gyration of the IDP under crowding, and suggest repulsive interactions with crowders as a common cause for chain compaction in a number of experimental studies. The postprocessing approach accurately reproduced the conformational ensembles of the IDP in the direct simulations here, and holds enormous potential for realistic modeling of IDPs under crowding, by permitting thorough conformation sampling for the proteins even when they and the crowders are both represented at the all-atom level.

Keywords: Intrinsically disordered proteins; macromolecular crowding; postprocessing approach.

Figure 1

Illustrative conformations of the IDP sampled without and with crowders present (ξ = 0.8). (A) Four conformations in crowder-free simulations. The values of R_g are listed. (B) A snapshot from a simulation at ø = 0.18. The IDP has R_g= 27 Å.

Figure 2

Histograms of R_g from four sets of trajectories (ξ = 0.5). Each set consists of 36 repeat trajectories. Two sets are for ø = 0 and two sets are for ø = 0.31. In each set, the trajectories were started either from a compact or an extended conformation for the IDP.

Figure 3

Histograms of R_gfrom direct simulations at ø = 0.31 and predicted by postprocessing the crowder-free simulations (with ø= 0). Hard sphere: Δμ calculated by approximating the crowders as hard spheres; Inverse r12: Δμ calculated by exact treatment of the inverse r¹² form of protein-crowder interactions. Results are for ξ = 0.7.

Figure 4

R_g;rms values obtained from direct simulations (symbols with error bars representing standard deviations among 36 repeat trajectories) and predicted by the postprocessing approach, with Δμ calculated either by approximating the crowders as hard spheres (dashed curves) or by exact treatment of the inverse r¹² form of protein-crowder interactions (red arrows at ø = 0.31).