Mechanosensitive Membrane Channels in Action

Abstract

The tension-driven gating process of MscL from Mycobacterium tuberculosis, Tb-MscL, has been addressed at near-atomic detail using coarse-grained molecular dynamics simulations. To perform the simulations, a novel coarse-grained peptide model based on a thermodynamic parameterization of the amino-acid side chains has been applied. Both the wild-type Tb-MscL and its gain-of-function mutant V21D embedded in a solvated lipid bilayer have been studied. To mimic hypoosmotic shock conditions, simulations were performed at increasing levels of membrane tension approaching the rupture threshold of the lipid bilayer. Both the wild-type and the mutant channel are found to undergo significant conformational changes in accordance with an irislike expansion mechanism, reaching a conducting state on a microsecond timescale. The most pronounced expansion of the pore has been observed for the V21D mutant, which is consistent with the experimentally shown gain-of-function phenotype of the V21D mutant.

Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry

“…Simulations of MscL gating were performed using the Martini coarse-grain (CG) model (45)(46)(47) and the GROMACS 4.X simulation package (48) following a similar protocol as described previously (14,15). In short, the topology of MscL was derived from the crystal structure of the closed state Tb-MscL (PDB ID code 2OAR) (1, 40) using CG Martini 2.0.…”

“…These models agree upon (i) the hydrophobic pore constriction of the channel and (ii) the channel opens by an iris-like rotation-i.e., a tilting and outward movement of transmembrane helices that make the channel wider and shorter (5). This mechanism is supported by patchclamp (10), disulfide cross-linking (11), FRET spectroscopy (12), and site-directed spin labeling EPR experiments (6, 7), as well as computational studies (13)(14)(15). So far, direct experimental results have only been observed for short-range local structural changes, and no measure of the overall global structural changes during channel gating have been reported.…”

“…To correlate the observed increase in rotationally averaged collision cross-sections of charge-activated MscL in its very early open states as determined by IM-MS with tension-induced MscL gating, we performed coarse-grained molecular dynamics simulations. Using the closed-state crystal structure of MscL from M. tuberculosis (1, 40), a coarse-grained model (14,15) was generated and embedded in a 1,2-dioleoyl-snglycero-3-phosphocholine (DOPC) bilayer. By applying high tension (65 dyn/cm) on the membrane, we were able to simulate initial channel opening.…”

The gating mechanism of the bacterial mechanosensitive channel MscL revealed by molecular dynamics simulations

“…This opening process, which resembles the opening of an iris in a conventional optical camera, is consistent with earlier simulation results. 21,24,45 bilayer, RMSDs of the Cα atoms of the MscL protein were calculated during the equilibration process. Figure 3 shows the time profile of RMSDs with respect to the Cα atoms during calculation relative to the initial structure.…”

Bacterial Mechanosensitive Channels: Models for Studying Mechanosensory Transduction

“…A number of more recent studies have, therefore, used coarse-grained MD simulations to extend simulations into the microsecond range (40,90,164) and combined coarse-grained simulations with experimental restraints to model the open pore of MscL and investigate the structural changes induced by membrane thinning. In addition to the above MD simulations, the gating of MscL has also been investigated using different modeling techniques such as normal mode analysis (150) and finite element methods (145,146).…”