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

Po hung Wang, Isseki Yu, Michael Feig, Yuji Sugita

Research output: Contribution to journalArticle

  • 6 Citations

Abstract

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.

LanguageEnglish (US)
Pages63-70
Number of pages8
JournalChemical Physics Letters
Volume671
DOIs
StatePublished - Mar 1 2017

Profile

crowding
Hydration
hydration
proteins
Proteins
Water
water
Volume fraction
deoxyribonucleic acid
simulation
Atoms
Molecules
Kinetics
DNA
kinetics
atoms
molecules

Keywords

  • Diffusion coefficient
  • Hydration
  • Macromolecular crowding
  • Protein crowders
  • Solvent accessible surface area

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding. / Wang, Po hung; Yu, Isseki; Feig, Michael; Sugita, Yuji.

In: Chemical Physics Letters, Vol. 671, 01.03.2017, p. 63-70.

Research output: Contribution to journalArticle

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AB - 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.

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