File S1 - Molecular Dynamics Simulations Reveal the HIV-1 Vpu Transmembrane Protein to Form Stable Pentamers

Supporting Information.
Table S1, Interhelical van der Waals interaction energy. Figure S1, Orientation of Ser23 before the REX/MD simulations. (A) Tetramer (B) Pentamer (C) Hexamer. Figure S2, Pair-wise RMSD values depicting how the two models vary over the trajectory. (A) Model 1 vs Model 2 (B) Model 1 vs Model 1 (C) Model 2 vs Model 2. Figure S3, Interhelical distance and protein-lipid interactions. (A) Probability distribution of interhelical distance in the explicit membrane simulations. The distance between the centres-of-mass of all helix pairs has been calculated and then averaged. (B) Hydrogen bonds between polar residues and headgroups at different intervals for Arg30 and headgroup (left panel), and Tyr30 and headgroup (right panel). Data shown is for model 2. Figure S4, Interhelical interactions. (A) Interhelical contact maps. Residue-residue distances have been averaged over time. (B) Arg30 (orange) and Glu28 (mauve) shown in licorice representation. The phosphate group (“CPK” representation) on a nearby POPC molecule (“bonds” representation) is also shown. The orientations of Arg30 and Glu28 in the tetramer, pentamer and hexamer are also shown. Figure S5, Pore profile, (A) View along the pore axis from the C-terminal showing the Ser23 residue in “licorice” representation. (B) Side view of the pentamer model showing Ser23 (“licorice” representation) and water molecules. (C) Pore radius across the axis of the pentamer model. Figure S6, Structural features of the pentamer. (A) Kink around the Ile17 residue in the pentamer model. (B) The three residues known to interact with tetherin shown in van der Waals representation.
(PDF)

辅助信息（Supporting Information）。
表S1：螺旋间范德华相互作用能。
图S1：REX/MD模拟前Ser23的取向。(A) 四聚体；(B) 五聚体；(C) 六聚体。
图S2：描述两种模型在模拟轨迹中变化情况的成对均方根偏差（RMSD）值。(A) 模型1与模型2；(B) 模型1与模型1；(C) 模型2与模型2。
图S3：螺旋间距离与蛋白-脂质相互作用。(A) 显式膜模拟中螺旋间距离的概率分布：已计算所有螺旋对的质心间距并取平均值。(B) 不同时间间隔下，Arg30与脂质头部基团（左图）、Tyr30与脂质头部基团（右图）的极性残基与脂质头部基团间形成的氢键。所有展示的数据均来自模型2。
图S4：螺旋间相互作用。(A) 螺旋间接触图谱：残基-残基间距已随时间取平均。(B) 以棍式（licorice）表示的Arg30（橙色）与Glu28（淡紫色）；同时展示了附近POPC（1-棕榈酰-2-油酰-sn-甘油-3-磷酸胆碱）分子的磷酸基团（采用CPK样式表示）以及以化学键样式表示的POPC分子。此外还展示了四聚体、五聚体与六聚体中Arg30与Glu28的空间取向。
图S5：孔道轮廓。(A) 沿孔道轴从C端视角观察，以棍式表示的Ser23残基。(B) 五聚体模型的侧视图，展示以棍式（licorice）表示的Ser23与水分子。(C) 五聚体模型沿孔道轴的孔道半径分布。
图S6：五聚体的结构特征。(A) 五聚体模型中Ile17残基周围的弯折结构。(B) 三种已知与tetherin相互作用的残基，采用范德华样式表示。
(PDF)