Rogacheva Olga N, Kopec Wojciech
Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany.
Department of Chemistry, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.
J Chem Inf Model. 2025 Jun 23;65(12):6129-6143. doi: 10.1021/acs.jcim.5c00307. Epub 2025 Jun 5.
The bacterial mechanosensitive channel, MscL, opens in response to elevated membrane tension during osmotic shock. Some mutations, like L17A and V21A, can reduce the activation tension threshold, thus offering an approach to study the mechanism of MscL gating. We employed all-atom molecular dynamics to simulate the L17A, V21A double mutant of MscL under a tension of 30 mN/m. Under these conditions, the closed state initially adopts a funnel-like conformation. Subsequently, five chains of MscL undergo sequential transitions into asymmetric states (S1, S2, etc.). Within its "open" fragment, the S1 state is similar to the expanded state of 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, and (3) pulling the two neighboring chains apart via the tension sensors. 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. The height of the free energy barrier for the transition toward the S1 state is approximately 10 kJ/mol, which is in reasonable agreement with the corresponding average transition time, estimated to be 133 ± 13 ns. The results and approach can be employed to elucidate the wild-type protein gating mechanism.
细菌机械敏感通道MscL在渗透休克期间响应膜张力升高而打开。一些突变，如L17A和V21A，可以降低激活张力阈值，从而为研究MscL门控机制提供了一种方法。我们采用全原子分子动力学模拟了在30 mN/m张力下MscL的L17A、V21A双突变体。在这些条件下，关闭状态最初采用漏斗状构象。随后，MscL的五条链依次转变为不对称状态（S1、S2等）。在其“开放”片段内，S1状态类似于MscL的扩展状态，其电导率比开放状态低10倍。我们应用反应坐标分析和非线性回归模型构建了关闭状态和S1状态之间转变的反应坐标，作为原子间距离和接触的线性组合。对反应坐标的主要贡献包括：（1）所考虑链与两条相邻链之间“细胞质”接触位点的破坏；（2）由I82、V86和V22残基形成的脂质结合口袋的去脂化；（3）通过张力传感器将两条相邻链拉开。使用伞形抽样方法计算了沿反应坐标的自由能分布。在张力作用下，S1状态比关闭状态大约有利5 kJ/mol。向S1状态转变的自由能垒高度约为10 kJ/mol，这与估计为133±13 ns的相应平均转变时间合理一致。这些结果和方法可用于阐明野生型蛋白的门控机制。
