Elucidating the Molecular Basis of pH Activation of an Engineered Mechanosensitive Channel

Mechanosensitive (MS) channels detect and respond to changes in the pressure profile of cellular membranes and transduce the mechanical energy into electrical and/or chemical signals. However, by re-engineering the MS channels, chemical signals such as pH change can trigger the activation of some MS channels. This paper elucidate the activation mechanism of an engineered MS channel of large conductance (MscL) at an atomic level through a combination of equilibrium, non-equilibrium, biased, and unbiased molecular dynamics (MD) simulations for the first time. Comparing the wild-type and engineered MscL activation processes at an atomic level suggests that the two systems are likely to be associated with different active states and different transition pathways. These findings indicate that (1) periplasmic loops play a key role in the activation process of MscL, (2) the loss of various hydrogen bonds and salt bridge interactions in the engineered MscL channel causes the spontaneous opening of the channel, and (3) the most significant interactions lost during the activation process are those between the transmembrane (TM) helices 1 and 2 (TM1 and TM2) in engineered MscL channel. In this research, the orientation-based biasing approach for producing and optimizing an open MscL model is a promising way to characterize unknown protein functional states and to research the activation processes in ion channels. String method with swarms of trajectories (SMwST) was used to identify the optimal transition pathway and elucidate the activation mechanism of the engineered MscL. Finally, the free energy profile of engineered MscL associated with the activation process using a novel along-the-path free energy calculation approach is constructed. This work paves the way for a computational framework for the studies aimed at designing pH-triggered channel-functionalized drug delivery liposomes.