Coarse-Grained Molecular Dynamics Simulations of SARS-CoV-2 E Protein embedded in homogeneous mono-unsaturated model membranes

Coarse-grained MD simulations of the SARS-CoV-2 E protein (PDB ID: 5X29) embedded in homogeneous mono-unsaturated model membranes of varying equilibrium thickness. Lipids with 3, 4, 5, or 6 beads per acyl chain were used (Martini lipids DYPC, DOPC, DGPC, and a custom lipid). All simulations were performed using GROMACS 2016 and the Martini 2.2 force field. The Berendsen thermostat was set to 313 K and a semi-isotropic Berendsen barostat was set to 1 bar in both directions. The compressibility modulus in both dimensions was 3 × 10−5 bar−1 with time constant 3 ps. Electrostatics and van der Waals (vdW) were shifted with a cutoff r-value of 1.2 nm. All systems underwent 100,000 steps of steepest-descent energy minimization prior to MD simulation with a timestep of 0.025 ps. Protein backbone beads were restrained with an elastic network which bonded all backbone bead pairs within 1.4 nm of one another with force constants of 5,000 kJ mol−1 nm−1. Five replicas of each system were simulated in the NPT ensemble for 10 μs. We discarded the first half of each trajectory prior to analysis. To determine the bulk leaflet thickness t0, we performed separate 2 μs NPT simulations of membranes composed of each lipid species listed above, but without a protein embedded. We discarded the first half of each trajectory prior to analysis. Analysis performed using nougat. Figures and figure generation script included.本数据集包含嵌入不同平衡厚度均质单不饱和模型膜的严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）包膜E蛋白（PDB（Protein Data Bank）编号：5X29）的粗粒度分子动力学（Coarse-grained Molecular Dynamics, MD）模拟数据。所用脂质的酰基链分别包含3、4、5或6个粗粒度珠子，涵盖Martini脂质（Martini lipids）DYPC、DOPC、DGPC以及一种定制脂质。 所有模拟均采用GROMACS 2016软件与Martini 2.2力场（Martini 2.2 force field）完成。控温采用Berendsen恒温器（Berendsen thermostat），设置温度为313 K；半各向同性Berendsen恒压器（Berendsen barostat）在两个维度上均设置为1 bar。二维体系的压缩模量为3×10⁻⁵ bar⁻¹，时间常数为3 ps。静电相互作用与范德华（van der Waals, vdW）相互作用均采用1.2 nm的截断半径进行平移修正。所有模拟体系在开展分子动力学模拟前，均先执行100000步最速下降法能量最小化，模拟时间步长为0.025 ps。 蛋白主链珠子通过弹性网络进行约束：将间距在1.4 nm以内的所有主链珠子对进行连接，力常数设置为5000 kJ·mol⁻¹·nm⁻¹。每个体系均设置5个重复模拟，在NPT系综（NPT ensemble）下开展时长为10 μs的模拟。分析前舍弃每条轨迹的前半部分数据。为测定体相膜双层厚度t₀，我们针对上述所有脂质种类（不含嵌入蛋白）单独开展了时长2 μs的NPT系综膜模拟，分析前同样舍弃每条轨迹的前半部分数据。 数据分析使用Nougat工具完成，数据集附带所有图片及图片生成脚本。