Coarse-grained molecular dynamics study of wettability influence on protein translocation through solid nanopores

Abstract

Protein translocation through nanopores is widely involved in molecular sensing and analyzing devices, whereby nanopore surface properties are crucial. However, fundamental understanding of how these properties affect protein motion inside nanopores remains lacking. In this work, we study the influence of nanopore surface wettability on voltage-driven protein translocation through nanopores with coarse-grained molecular dynamics simulations. The results show that the electrophoretic mobility of protein translocation increases as the contact angle of nanopore surface increases from 0°to 90°, but becomes almost constant as the contact angle is above 90°. This observation can be attributed to the variation of the friction coefficient of protein translocation through the nanopores with different nanopore contact angles. We further show that the interaction between nanopore and water, rather than that between the nanopore and protein, dominates the protein transport in nanopores. These findings provide new insights into protein translocation dynamics across nanopores and will be beneficial to the design of highefficiency nanopore devices for single molecule protein sensing.

Brownian dynamics of cylindrical capsule-like particles in a nanopore in an electrically biased solid-state membrane

“…There are many ways to approach a nanopore system via modelling, from extremely detailed atomic level models 28,29 to simpler models that yield broader statistical information on the system. 30–33 Atomic level modelling can be expensive in computational resources and time, while modelling particles using Brownian dynamics (BD) and rigid, coarse-grained structures 34 considerably reduces the computational cost and provides a good agreement with atomic level approaches.…”

Nanoscale Friction of Biomimetic Hair Surfaces

“…39,40 While most of these studies have employed all-atom force fields, 36 the large, heterogenous surfaces and macromolecules commonly encountered in biological systems are more suited to the use of coarse-grained representations. 41 Coarse-grained force fields have already been used to study, for example, the intermonolayer friction of lipid bilayer membranes 42,43 the friction of protein translocation through nanopores, 44 and the adsorption and desorption of polymers on heterogeneous substrates that are representative of the surface of the hair under shear flow. 45 In this study, we use NEMD simulations and chemical colloidal probe (CCP) AFM to study the kinetic friction between model hair surfaces.…”

Langevin dynamics simulation of protein dynamics in nanopores at microsecond timescales

“…This analytical approach provides a good starting point for estimating the effects of some of the factors on the dynamics of protein during translocation through a nanopore. Specific details can become important in many situations, for example, Liu et al 29 investigated the effect of wettability condition inside the nanopore on the CG protein translocation velocity, stronger attraction between the water molecules and the nanopore can slow down the protein dynamics significantly in hydrophilic nanopores instead of protein-nanopore interactions. Such insight could be obtained by molecular modeling, otherwise it could have been wrongly attributed to some other factor.…”

“…Most likely the drastic change in protein dynamics is originating from electroosmotic interactions. In order to account for hydrodynamics in such systems, generally explicit solvent molecules are considered atomistically [20][21][22] or CG 24,29 , or less often through hybrid model: coupling MD of the biomolecule with hydrodynamic interactions from Lattice-Boltzmann (LB) calculations 32 . Such hybrid model can still be computationally expensive, requiring numerical LB calculations over the grids at different timesteps.…”