CONFINEMENT DYNAMICS OF PROTEINS AT NANOSCALE
Date14th Feb 2022
Time04:00 PM
Venue Online meeting link: https://meet.google.com/oeb-gsay-qqv
PAST EVENT
Details
Nanopore-based sensors, which provide unique ways to analyze molecules at single-molecule resolution, have gained recent centrality in relation to sequencing and fingerprinting of biomolecules. Dynamics of biomolecules such as proteins in nanoconfinement preordain the effectiveness of such sensing applications at the nanoscale. For example, the fast translational motion of analytes in a nanopore results in low detection rates and hence it is imperative to slow down the translational velocity of protein inside nanopore for the potential use of this technology. Also, rotational diffusion of biomolecules contains vital information regarding the identity of a specific molecule under the query. The effects of nanoconfinement size and external force on the nanopore translation of a sample protein were studied using coarse-grained molecular dynamics. As the nanopore radius approaches the protein hydrodynamic radius, the translational motion was observed to increase by two orders of magnitude. Coarse-grained molecular dynamics simulations also reveal a two-fold reduction in magnitude from the bulk rotational diffusion coefficient value as the confinement radius reaches double the size of the protein’s hydrodynamic radius. However, the changes in the rotational diffusion coefficient are relatively small compared to the changes in the translational diffusion coefficient. Further, the logic behind the reduction of rotational diffusion is sought with the help of local viscosity calculations. Solvent dynamics at the interstices between protein and pore surface, especially local viscosity increase of the solvent particles in the second hydration layer, were deduced to be the primary reason for the decelerated diffusion of proteins. Drag forces due to non-bonded interaction between pore and protein were found to be responsible for a hindered rotational diffusion and force-dependent translational mobility of proteins in nanoconfinement.
Speakers
Mr. Navaneeth Haridasan (AM15D015)
Department of Applied Mechanics