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bioRxiv · 10.1101/2025.02.10.637407

Asymmetric nature of MscL opening revealed by molecular dynamics simulations

Rogacheva, O. N.·Kopec, W.
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Abstract

We employed all-atom unbiased molecular dynamics to simulate the L17A, V21A mutant of MscL. Under a tension of 30 mN/m, the closed state adopts a funnel-like conformation. Subsequently, five chains of MscL undergo sequential transitions, leading to the formation of the asymmetric states (S1, S2, etc.). After the first chain crossed the barrier, the next transition favors the neighboring clockwise chain. This study focuses on the S1 state. Within its "open" fragment, this state is similar to the expanded state of M. acetivorans MscL, and has a conductance 10 times lower than the open state. We applied committor analysis and a nonlinear regression model to construct a reaction coordinate for the transition between the closed and the S1 state as a linear combination of interatomic distances and contacts. The main contributions to the reaction coordinate are: 1) the disruption of the "cytoplasmic" contact sites between the considered chain and two adjacent chains 2) the delipidation of the lipid-binding pocket, formed by the I82, V86, and V22 residues. The result is the pulling of the considered chain via the "cytoplasmic" tension sensor. The free energy profile along the reaction coordinate was calculated using the umbrella sampling approach. The S1 state is approximately 5 kJ/mol more favorable than the closed state under tension, and the height of the free energy barrier for the transition towards the S1 state is approximately 10 kJ/mol. This barrier is in a reasonable agreement with the corresponding average transition time, estimated to be 133 {+/-} 13 ns. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/637407v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@169cc74org.highwire.dtl.DTLVardef@edf539org.highwire.dtl.DTLVardef@7e75c3org.highwire.dtl.DTLVardef@657542_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Rogacheva, O. N., Kopec, W.. 2025-02-12. Asymmetric nature of MscL opening revealed by molecular dynamics simulations. https://doi.org/10.1101/2025.02.10.637407

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