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Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation
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    Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation
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    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
    RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
    § RIKEN iTHES, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
    RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minaotojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
    RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
    *E-mail: [email protected]. Phone: +1 (517) 432-7439. Fax: +1 (517) 353-9334.
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    The Journal of Physical Chemistry B

    Cite this: J. Phys. Chem. B 2017, 121, 49, 11072–11084
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    https://doi.org/10.1021/acs.jpcb.7b08785
    Published November 20, 2017
    Copyright © 2017 American Chemical Society

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    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.

    Copyright © 2017 American Chemical Society

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpcb.7b08785.

    • Details of MD and coarse-grained simulations, details of the analysis (translational diffusion correction term, correlation function of contact formation, minimum distance for contact map), comparison of translational diffusion obtained with different thermostats, generalized internal order parameter, Sl2, RMSD, cluster distributions, conformational sampling of villin (PMF plots), representative transient cluster structures, translational and rotational diffusion coefficients of MD-derived cluster structures estimated using HYDROPRO, contact map (32 mM, 64 villin copies system) (PDF)

    • Movie showing center-of-mass motion of selected villin molecules (MPG)

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    The Journal of Physical Chemistry B

    Cite this: J. Phys. Chem. B 2017, 121, 49, 11072–11084
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    https://doi.org/10.1021/acs.jpcb.7b08785
    Published November 20, 2017
    Copyright © 2017 American Chemical Society

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