Decisive structural elements in water and ion permeation through mechanosensitive channels of large conductance: insights from molecular dynamics simulation

Abstract

In this paper, a series of equilibrium molecular dynamics simulations (EMD), steered molecular dynamics (SMD), and computational electrophysiology methods are carried out to explore water and ion permeation through mechanosensitive channels of large conductance (MscL). This research aims to identify the pore-lining side chains of the channel in different conformations of MscL homologs by analyzing the pore size. The distribution of permeating water dipole angles through the pore domains enclosed by VAL21 and GLU104 demonstrated that water molecules are oriented toward the charged oxygen headgroups of GLU104 from their hydrogen atoms to retain this interaction in a stabilized fashion. Although, this behavior was not perceived for VAL21. Numerical assessments of the secondary structure clarified that, during the ion permeation, in addition to the secondary structure alterations, the structure of Tb-MscL would also undergo significant conformational changes. It was elucidated that VAL21, GLU104, and water molecules accomplish a fundamental task in ion permeation. The mentioned residues hinder ion permeation so that the pulling SMD force is increased remarkably when the ions permeate through the domains enclosed by VAL21 and GLU102. The hydration level and potassium diffusivity in the hydrophobic gate of the transmembrane domain were promoted by applying the external electric field. Furthermore, the implementation of an external electric field altered the distribution pattern for potassium ions in the system while intensifying the accumulation of Cl⁻ in the vicinity of ARG11 and ARG98.