Publication

Abstract : The rotational diffusion coefficient is an essential parameter in determining the mechanistic features of biomolecules in both crowded and confined environments. Understanding the influence of nanoconfinement on rotational diffusion is vital in conceptualizing dynamics of biomolecules (such as proteins) in nanopores. The control of the translational movement of biomolecules is practiced widely in nanopore experiments. However, the restrictions on the translational movement may affect other dynamic properties such as rotational diffusion. In this paper, we use a coarse-grained molecular dynamics approach to study the rotational dynamics of a sample protein under the influence of cylindrical nanopore confinement. Our simulation reveals a 2-fold reduction in magnitude from the bulk rotational diffusion coefficient value as the confinement radius reaches double the size of protein’s hydrodynamic radius. However, the changes in the rotational diffusion coefficient are relatively small compared to the changes in the translational diffusion coefficient. Interestingly, the rotational anisotropy also varies considerably when pore radii approach protein dimensions. Our simulations point out that the confinement effects cause the breakdown of small angular displacement theory when the pore radius is close to the protein hydrodynamic radius.