A conserved membrane-integral pyrophosphatase anionic membrane fingerprint identified by multi-scale molecular dynamics simulations
A conserved membrane-integral pyrophosphatase anionic membrane fingerprint identified by multi-scale molecular dynamics simulations
复制标题
通过多尺度分子动力学模拟鉴定出保守的膜积分焦磷酸酶阴离子膜指纹
DOI：
10.1016/j.bpj.2021.11.1189
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发表时间：
2022
影响因子：
3.4
通讯作者：
Holmes A
中科院分区：
文献类型：
--
作者：
Holmes A
膜整合焦磷酸酶（mPPases）是负责无机焦磷酸盐的分解和跨膜转运阳离子的临床相关酶。最近的机制的发展导致的假设，蛋白质的环境可能是重要的功能和亚基间的通信。在这项研究中，分子动力学模拟在粗粒度和原子级分辨率的mPPase从海栖热袍菌（Tm-PPase）与不同的脂质双层组件组装和模拟。分析首次表明，Tm-PPases形成特定的阴离子脂质相互作用在4个不同的网站，在界面和远端区域的蛋白质。为了评估这些相互作用是否在其他mPPase中是保守的，在类似于该蛋白功能的天然双层的液泡膜中模拟来自绿豆的mPPase（Vr-PPase）。在该系统中与阴离子脂质的相互作用与Tm-PPase所观察到的相互作用相似，具有相同的4个结合位点，并且1-棕榈酰-2-油酰磷脂酸（POPA）优于其他棕榈酰-油酰磷脂。除了POPA偏好外，Vr-PPase与磷脂酰肌醇二磷酸（PIP 2）脂质高度相互作用。由于蛋白质-脂质相互作用可以稳定蛋白质并促进结构表征，因此使用来自纤细梭菌的同源建模的mPPase（Cp-PPase）来检查mPPase-脂质相互作用的预测质量。的蛋白质的静电配置文件相匹配的Tm-PPase和Vr-PPase，和脂质相互作用的网站被保留，表明这些相互作用的预测质量。的相互作用主要是与赖氨酸和精氨酸残基上的螺旋1，2，3和4的远端网站和9，10，13和14的界面网站。这些螺旋参与蛋白质稳定性和亚基间通讯，这表明这些脂质相互作用可能在mPPase机制中发挥关键作用，并使未来的结构和功能研究成为可能。
Membrane-integral pyrophosphatases (mPPases) are clinically relevant enzymes responsible for the breakdown of inorganic pyrophosphate and translocating a cation across the membrane. Recent mechanistic developments led to the hypothesis that the protein environment may be important for function and intersubunit communication. In this study, molecular dynamics simulations at the coarse-grained and atomistic resolution of the mPPase from Thermotoga maritima (Tm-PPase) with varying lipid bilayer components were assembled and simulated. Analysis demonstrated for the first time that Tm-PPases form specific anionic lipid interactions at 4 distinct sites, at the interfacial and distal regions of the protein. To assess whether these interactions were conserved in other mPPases, the mPPase from Vigna radiata (Vr-PPase) was simulated in a tonoplast membrane that resembles the native bilayer in which this protein functions. The interactions with anionic lipids in this system were similar to those seen with Tm-PPase, with the same 4 binding sites and preference for 1-palmitoyl-2-oleoyl phosphatidic acid (POPA) over other palmitoyl-oleoyl phospholipids. In addition to the POPA preference, Vr-PPase interacted highly with phosphatidylinositol bisphosphate (PIP 2) lipids. As protein-lipid interactions can stabilise proteins and facilitatestructural characterisation, the predictive quality of the mPPase-lipid interactions was examined using the homology-modelled mPPase from Clostridium leptum (Cp-PPase). The electrostatic profile of the protein matched those of Tm-PPase and Vr-PPase, and the lipid interaction sites were retained, indicating a predictive quality to these interactions. The interactions were primarily with lysine and arginine residues on helices 1, 2, 3 and 4 for the distal site and 9, 10, 13 and 14 for the interfacial site. These are helices implicated in protein stability and intersubunit communication, which indicate that these lipid interactions may play a crucial role in the mPPase mechanism and enable future structural and functional studies.