The permeation of potassium ions through the lipid scrambling path of the membrane protein nhTMEM16.
The permeation of potassium ions through the lipid scrambling path of the membrane protein nhTMEM16.
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DOI：
10.3389/fmolb.2022.903972
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发表时间：
2022
影响因子：
5
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TMEM16家族的跨膜蛋白包括钙激活的磷脂加扰酶，它也可以作为非选择性离子通道发挥作用。广泛的结构和功能研究已经证实，TMEM16 PLS膜上暴露的亲水性沟槽可以作为脂类的一条转运途径。然而，目前仍不清楚TMEM16 PLS是如何传导离子的。“蛋白质分隔的孔”模型认为离子通过凹槽区域的狭窄开口进行转移，而凹槽区域不够宽以允许脂质运动，而“蛋白质脂肪孔”模型设想离子和脂质通过凹槽的开放构象进行转移。通过长原子分子动力学(MD)模拟，研究了nhTMEM16分子在开槽状态下钾离子(K+)迁移的动态路径，并用伞形取样方法计算了离子在槽中运动的自由能分布。自由能分布确定了沿K+渗透路径的特定相互作用的影响。同样的计算也被用来研究nhTMEM16 L302a突变体中离子通过接近脂质渗透的凹槽的渗透，该凹槽显示出稳定的构象，不允许脂质扰乱。我们的结果确定了使K+渗透的结构和能量参数，并表明在模拟过程中观察到的nhTMEM16凹槽中脂类的存在在不同程度上影响K+渗透的效率。
The TMEM16 family of transmembrane proteins includes Ca2+-activated phospholipid scramblases (PLS) that can also function as non-selective ion channels. Extensive structural and functional studies have established that a membrane-exposed hydrophilic groove in TMEM16 PLS can serve as a translocation pathway for lipids. However, it is still unclear how the TMEM16 PLS conduct ions. A “protein-delimited pore” model suggests that ions are translocated through a narrow opening of the groove region, which is not sufficiently wide to allow lipid movement, whereas a “proteolipidic pore” model envisions ions and lipids translocating through an open conformation of the groove. We investigated the dynamic path of potassium ion (K+) translocation that occurs when an open groove state of nhTMEM16 is obtained from long atomistic molecular dynamics (MD) simulations, and calculated the free energy profile of the ion movement through the groove with umbrella sampling methodology. The free energy profile identifies effects of specific interactions along the K+ permeation path. The same calculations were performed to investigate ion permeation through a groove closed to lipid permeation in the nhTMEM16 L302A mutant which exhibits a stable conformation of the groove that does not permit lipid scrambling. Our results identify structural and energy parameters that enable K+ permeation, and suggest that the presence of lipids in the nhTMEM16 groove observed in the simulations during scrambling or in/out diffusion, affect the efficiency of K+ permeation to various extents.