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Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments.

ABSTRACT: The rotational diffusion of a protein in the presence of protein crowder molecules was analyzed via computer simulations. Cluster formation as a result of transient intermolecular contacts was identified as the dominant effect for reduced rotational diffusion upon crowding. The slow-down in diffusion was primarily correlated with direct protein-protein contacts rather than indirect interactions via shared hydration layers. But increased solvent viscosity due to crowding contributed to a lesser extent. Key protein-protein contacts correlated with a slow-down in diffusion involve largely interactions between charged and polar groups suggesting that the surface composition of a given protein and the resulting propensity for forming interactions with surrounding proteins in a crowded cellular environment may be the major determinant of its diffusive properties.

SUBMITTER: Nawrocki G

PROVIDER: S-EPMC6322922 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments.

Nawrocki Grzegorz G Karaboga Alp A Sugita Yuji Y Feig Michael M

Physical chemistry chemical physics : PCCP 20190101 2

The rotational diffusion of a protein in the presence of protein crowder molecules was analyzed via computer simulations. Cluster formation as a result of transient intermolecular contacts was identified as the dominant effect for reduced rotational diffusion upon crowding. The slow-down in diffusion was primarily correlated with direct protein-protein contacts rather than indirect interactions via shared hydration layers. But increased solvent viscosity due to crowding contributed to a lesser e ...[more]

PMID: 30560249

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