Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding

[Display omitted] •The effects of protein crowder sizes on hydration are investigated by MD simulations.•Significant slow down of water diffusion in the presence of small protein crowders is observed.•Crowder size is found to be another factor to determine the effect of macromolecular crowding. We i...

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Published inChemical physics letters Vol. 671; pp. 63 - 70
Main Authors Wang, Po-hung, Yu, Isseki, Feig, Michael, Sugita, Yuji
Format Journal Article
LanguageEnglish
Published Elsevier B.V 01.03.2017
Subjects
Diffusion coefficient
Hydration
Macromolecular crowding
Protein crowders
Solvent accessible surface area
Macromolecular crowding
Protein crowders
Hydration
Diffusion coefficient
Solvent accessible surface area
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Summary:[Display omitted] •The effects of protein crowder sizes on hydration are investigated by MD simulations.•Significant slow down of water diffusion in the presence of small protein crowders is observed.•Crowder size is found to be another factor to determine the effect of macromolecular crowding. We investigate the effects of protein crowder sizes on hydration structure and dynamics in macromolecular crowded systems by all-atom MD simulations. The crowded systems consisting of only small proteins showed larger total surface areas than those of large proteins at the same volume fractions. As a result, more water molecules were trapped within the hydration shells, slowing down water diffusion. The simulation results suggest that the protein crowder size is another factor to determine the effect of macromolecular crowding and to explain the experimental kinetic data of proteins and DNAs in the presence of crowding agents.
ISSN:0009-2614
1873-4448
DOI:10.1016/j.cplett.2017.01.012