Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

Abstract

For a long time the effect of crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse much slower in a living cell than in a diluted solution and further studies suggest that the diffusion depends on the local surrounding. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin head piece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. While internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with increasing protein concentrations. Weighting diffusion coefficients estimated for different clusters extracted from the simulations with the distribution of clusters largely reproduces the overall observed diffusion rates, suggesting that transient cluster formation is a primary cause for a slow-down in diffusion upon crowding with other proteins.

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

“…Further work on additional proteins is needed to assess whether such 6-8% increase of the protein-water interaction strength is also applicable to other systems simulated with the Martini force field. Although perhaps fortuitous, the rescaling is similar in magnitude to the adjustments seen for some all-atom force field adjusted to simulate proteins with intrinsically disordered regions (36)(37)(38). For the TIA-1 system, reliable distribution for collective variables such as " and $& could be obtained from several nonperfect force fields by reweighting against experiments.…”

“…Tuning protein-water interaction strength in the Martini model As described in more detail in the results section, we find that simulations using the unperturbed Martini force field yielded structures that were too compact and thus did not fit the experimental SAXS and SANS data. Several atomistic force fields have likewise failed to describe flexible and disordered proteins, but increasing the proteinwater interaction strength has in several cases been shown to improve the fit to experimental data (36)(37)(38). Inspired by this work and a previous modification to Martini force field v.2.2 (39) we examined whether a similar solution could be applied here, and thus varied (increased) the protein-water interaction strength.…”

“…To improve the fit between the ensemble from the MD simulations and SAXS, we explored a rescaling of the protein-water interaction strength similar to what has previously been done for all-atomic force fields (36)(37)(38) and Martini v.2.2 (39,50,51). By changing the solvent properties towards a better solvent (i.e.…”

Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom MD Simulations, Confirming a Step-wise Association Process for Native PPIs

“…Despite early successes in Brownian and coarse grained molecular dynamics simulations of (mostly tightly bound) complexes, 2,6-10 there have, as yet, been very few simulations of protein association processes using unrestrained all-atom simulations. [11][12][13][14][15][16] In many cases it remains difficult to computationally predict the correct protein complexes structures ab initio. 17 Only relatively recently have computational protein docking programs started to incorporate main chain (or even side chain) flexibility; [18][19] also the role of local, as well as global dynamics in protein complexes and in complex formation is now becoming well appreciated.…”

“…14,31 In case of the former, many proteins -even those having only non-specific non-covalent self-association (such as ubiquitin)-showed a strong and unphysical aggregation. 14,32 Similarly, IDPs became too compact in the simulations. 33,34 Both effects arise from an underestimation of protein solvation and both are in disagreement with experimental observations.…”