Study On The Influence Of Nanopore Surface Charateristics On Protein Translocation Based On Coarse-Grained MD Simulation

The protein translocation through nanopores exists widely in molecular sensing and analyzing devices,in which the surface characteristics of nanopores plays an important role.As the most important factor for the protein translocation dynamics,the surface characteristics have a significant influence on the analytical process and detection quality of nanopore.Therefore,the study of the nanopore surface characteristics influence on protein translocation is valuable to both scientific research and application.In this work,the influences of solid nanopore surface wettability and charges on protein translocation through the nanopore were systematically studied based on coarse-grained molecular dynamics simulation.The results and conclusions are obtained as follows:1.Influence of the nanopore surface wettability on protein through the nanopore Based on molecular dynamics simulation of protein translocation driven by external voltage,the effect of nanopore wettability on protein transport is studied.The friction of protein translocation in nanopore is obtained by Steer Molecular Dynamics simulation.The systemic study revealed that the wettability of the nanopore surface has an important influence on the transport of protein.The electrophoretic mobility of protein translocation increases as the contact angle of nanopore surface increases from 0° to 90° and the dynamics of protein remains almost the same as the contact angle is above 90°.2.Influence mechanism of the nanopore surface wettability on protein through the nanopore The effect of nanopore-water/nanoporeprotein interaction on the electrophoretic mobility of protein translocation is studied based on coarse-grained molecular dynamics simulation.With steer molecular dynamics(SMD),the friction force and friction coefficient of protein under different interactions are analyzed.It shows that protein adhesion to nanopore wall has no obvious effect on protein translocation through the nanopore,while the nanopore-water interaction has a significant effect on the electrophoretic mobility and friction coefficient.The increase of the nanopore-water interaction strengthens the influence on movement of water molecules near the nanopore wall and enlarges the difference in the movements of water molecules near nanopore wall and near protein,which leads to an increase of friction coefficient of protein translocation.It demonstrates that nanopore-water interaction plays a dominant role in the process of protein translocation,which can provide a theoretical guidance for the design of nanopores materials.3.Influence of the nanopore surface charge on protein through the nanopore The molecular dynamics simulation of voltage-driven protein through the nanopore with different surface charges is performed and the ion distribution is studied.The steer molecular dynamics simulation is applied to further investigate the mechanism of the nanopore charge influence.It demonstrates that the change of the charging condition of the nanopore wall surface leads to the different electroosmotic effects,thus affecting the protein entry behavior.As a higher voltage and a charged nanopore is applied,the protein unfolding can be observed.For the nanopore with positive charge,the combined effect of electric driving force and friction force leads to a protein unfolding outside the nanopore;For the nanopore with negative charge,the combined effect of the electric driving force,friction force and the electrostatic force accounts for the protein unfolding in the nanopore.