Dataset Information

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

ABSTRACT: For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece 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. Although 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.

SUBMITTER: Nawrocki G

PROVIDER: S-EPMC5951686 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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

Nawrocki Grzegorz G Wang Po-Hung PH Yu Isseki I Sugita Yuji Y Feig Michael M

The journal of physical chemistry. B 20171130 49

For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece solutions. After for ...[more]

PMID: 29151345

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Project description:The effects of macromolecular crowding on the thermodynamic properties of test proteins are determined by the latter's transfer free energies from a dilute solution to a crowded solution. The transfer free energies in turn are determined by effective protein-crowder interactions. When these interactions are modeled at the all-atom level, the transfer free energies may defy simple predictions. Here we investigated the dependence of the transfer free energy (Δμ) on crowder concentration. We represented both the test protein and the crowder proteins atomistically, and used a general interaction potential consisting of hard-core repulsion, non-polar attraction, and solvent-screened electrostatic terms. The chemical potential was rigorously calculated by FMAP (Qin and Zhou, 2014), which entails expressing the protein-crowder interaction terms as correlation functions and evaluating them via fast Fourier transform (FFT). To high accuracy, the transfer free energy can be decomposed into an excluded-volume component (Δμe-v), arising from the hard-core repulsion, and a soft-attraction component (Δμs-a), arising from non-polar and electrostatic interactions. The decomposition provides physical insight into crowding effects, in particular why such effects are very modest on protein folding stability. Further decomposition of Δμs-a into non-polar and electrostatic components does not work, because these two types of interactions are highly correlated in contributing to Δμs-a. We found that Δμe-v fits well to the generalized fundamental measure theory (Qin and Zhou, 2010), which accounts for atomic details of the test protein but approximates the crowder proteins as spherical particles. Most interestingly, Δμs-a has a nearly linear dependence on crowder concentration. The latter result can be understood within a perturbed virial expansion of Δμ (in powers of crowder concentration), with Δμe-v as reference. Whereas the second virial coefficient deviates strongly from that of the reference system, higher virial coefficients are close to their reference counterparts, thus leaving the linear term to make the dominant contribution to Δμs-a.

Dataset Information

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

Publications

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

Similar Datasets

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