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arXiv · 2009.06829

Universal relation between instantaneous diffusivity and radius of gyration of proteins in aqueous solution

Eiji Yamamoto·Takuma Akimoto·Ayori Mitsutake·Ralf Metzler
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Abstract

Protein conformational fluctuations are highly complex and exhibit long-term correlations. Here, molecular dynamics simulations of small proteins demonstrate that these conformational fluctuations directly affect the protein's instantaneous diffusivity $D_I$. We find that the radius of gyration $R_g$ of the proteins exhibits $1/f$ fluctuations, that are synchronous with the fluctuations of $D_I$. Our analysis demonstrates the validity of the local Stokes-Einstein type relation $D_I\propto1/(R_g + R_0)$, where $R_0\sim0.3$ nm is assumed to be a hydration layer around the protein. From the analysis of different protein types with both strong and weak conformational fluctuations the validity of the Stokes-Einstein type relation appears to be a general property.

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Eiji Yamamoto, Takuma Akimoto, Ayori Mitsutake, Ralf Metzler. 2021-03-04. Universal relation between instantaneous diffusivity and radius of gyration of proteins in aqueous solution. https://doi.org/10.1103/physrevlett.126.128101

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