Energetics of Ion Permeation Process through Mechanosensitive Channels of Large Conductance by Adaptive Biasing Force Method

In this study, the permeation process of oppositely charged ions through mechanosensitive channels oflarge conductance is investigated using the steered molecular dynamics (SMD) simulation along with adaptive biasingforce technique. Since some of the mentioned amino acids exist in the interior pore of the other membrane proteins,studying the mechanism of interaction of these basic components with different substrates and their role in the gatingprocess of the utmost importance. The barriers of energy and their location required for the ion to permeate through thedifferent sidechains of the channel are studied by the potential of mean force. Furthermore, it was demonstrated that theselective function of Val21 sidechain on oppositely charged ions arises from the completely different electrostaticinteraction of the sidechain with the ions.

Keywords:

Ion Permeation , Membrane Protein , Adaptive Biasing Force , Molecular Dynamics Simulation