Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; International Max Planck Research School (IMPRS) for Advanced Methods in Process and Systems Engineering, Magdeburg, Germany.
Biochim Biophys Acta Biomembr. 2017 Aug;1859(8):1335-1349. doi: 10.1016/j.bbamem.2017.04.021. Epub 2017 Apr 25.
The small GTPase Rab5 is a key regulator of endosomal trafficking processes and a marker for the early endosome. The C-terminal hypervariable region (HVR) of Rab5 is post-translationally modified at residues Cys and Cys to accommodate two geranylgeranyl anchors (C20 carbon chain length) in order to associate Rab5 with the membrane. The structural role of the HVR regarding protein-early endosome membrane recruitment is not resolved due to its high degree of flexibility and lack of crystallographic information. Here, full-atomistic and coarse-grained molecular dynamics simulations of the truncated Rab5 HVR in three model membranes of increasing complexity (pure phospholipid bilayer, ternary membrane with cholesterol, six-component early endosome) were performed. Specific electrostatic interactions between the HVR Arg residue and the phosphate group of the inositol ring of PI(3)P were detected. This shows that PI(3)P acts as a first contact site of protein recruitment to the early endosome. The free energy change of HVR extraction from the bilayer was largest for the physiological negatively charged membrane. 5μs coarse-grained simulations revealed an active recruitment of PI(3)P to the HVR supporting the formation of Rab5- and PI(3)P enriched signaling platforms.
小分子 GTPase Rab5 是内体运输过程的关键调节因子，也是早期内体的标志物。Rab5 的 C 端超可变区（HVR）在残基 Cys 和 Cys 处发生翻译后修饰，以容纳两个 geranylgeranyl 锚（C20 碳链长度），从而将 Rab5 与膜结合。由于其高度的灵活性和缺乏晶体学信息，HVR 关于蛋白质-早期内体膜募集的结构作用尚未得到解决。在这里，对三种复杂程度不断增加的模型膜中的截断 Rab5 HVR 进行了全原子和粗粒度分子动力学模拟（纯磷脂双层、含胆固醇的三元膜、六组分早期内体）。检测到 HVR Arg 残基与 PI(3)P 的肌醇环磷酸基团之间的特定静电相互作用。这表明 PI(3)P 作为蛋白质募集到早期内体的第一接触位点。从双层中提取 HVR 的自由能变化对于生理上带负电荷的膜最大。5μs 粗粒度模拟显示 PI(3)P 被主动募集到 HVR 上，支持 Rab5 和 PI(3)P 丰富的信号平台的形成。
