MD Simulations of Lipid A Phosphoethanol Transferase from Neisseria meningitidis (NmEptA) in pure DPPE and mixed PE/PG bilayer

MD simulations of a full-length Lipid A phosphoethanolamine transferase from <i>Neisseria meningitidis </i>(<i>Nm</i>EptA, PDB code: 5FGN). NmEptA decorates lipid A with phosphoethanolamine (PEA) by transferring the moiety from phosphoethanolamine (PE) lipids found in the bacterial membrane, resulting with the reduced negative charge of the bacterial surface and increased colistin resistance. The full publication can be found here: <br>doi: 10.1073/pnas.1612927114The uploaded files contain total of 9 independent simulations of <i>Nm</i>EptA embedded in two membrane models - pure DPPE bilayer and mixed PE/PG bilayer. A set of three simulations were carried out in DPPE bilayer ar 298 K and three at 310 K, while another set of triplicates was run in a bilayer containing 80% PE and 20% PG lipids at 298 K. A detailed description of MD setup is uploaded in a separate file and the input files used to run the simulations are also provided (.<i>mdp</i>). All the simulations were carried out using GROMACS 3.3.3 engine in conjunction with GROMOS 54a7 force field. Links to the lipid parameters used in these simulations are given below.<br>The uploaded files contain:* The starting structure of <i>Nm</i>EptA embedded in the DPPE bilayer (NmEptA_DPPE_Zn.gro) and the mixed PE/PG bilayer (NmEptA_PEPG_Zn.gro).* Set of trajectories in DPPE bilayer and the corresponding input <i>mdp</i> files at 298 K (NmEptA_DPPE_run1-3-298K.xtc/mdp) and at 310 K (NmEptA_DPPE_run1-3-310K.xtc/mdp).* Set of trajectories in PE/PG bilayer and the corresponding mdp files run at 298 K (NmEptA_PEPG_run1-3-298K.xtc/mdp).* PPoPE lipid paramteres (<i>PPoPE.itp</i>) and the equilibrated mixed PE/PG bilayer snapshot (80_PPoPE-20_DMPG.pdb).* MD simulation protocol (MD_Setup.pdf)<br><br>

本数据集涵盖脑膜炎奈瑟菌（*Neisseria meningitidis*）全长脂质A磷酸乙醇胺转移酶（NmEptA，蛋白质数据库PDB编号：5FGN）的分子动力学（MD, Molecular Dynamics）模拟数据。NmEptA可从细菌膜的磷脂酰乙醇胺（PE）脂质中转移磷酸乙醇胺（PEA）基团，并将其修饰于脂质A之上，以此降低细菌表面负电荷，同时增强其对粘菌素的耐药性。完整研究论文可通过以下DOI查阅：10.1073/pnas.1612927114。

本次上传的文件包含9组独立模拟样本，均为嵌入两类膜模型的NmEptA：一类为纯二棕榈酰磷脂酰乙醇胺（DPPE）双分子层，另一类为磷脂酰乙醇胺（PE）与磷脂酰甘油（PG）混合双分子层。其中3组模拟于纯DPPE双分子层中、298K条件下完成，另有3组于310K下完成；剩余3组重复模拟则在含80%PE与20%PG脂质的双分子层中、298K条件下运行。分子动力学模拟设置的详细说明已上传至单独文件，同时提供了模拟所用的输入文件（.mdp）。所有模拟均采用GROMACS 3.3.3引擎结合GROMOS 54a7力场完成。本次模拟所用脂质参数的获取链接如下：

上传文件详情如下：
· 嵌入DPPE双分子层的NmEptA初始结构（NmEptA_DPPE_Zn.gro），以及嵌入PE/PG混合双分子层的NmEptA初始结构（NmEptA_PEPG_Zn.gro）；
· DPPE双分子层中的轨迹文件及对应输入.mdp文件：298K下的NmEptA_DPPE_run1-3-298K.xtc/mdp，以及310K下的NmEptA_DPPE_run1-3-310K.xtc/mdp；
· PE/PG混合双分子层中的轨迹文件及对应输入.mdp文件：298K下的NmEptA_PEPG_run1-3-298K.xtc/mdp；
· PPoPE脂质参数文件（PPoPE.itp）以及平衡后的PE/PG混合双分子层快照（80_PPoPE-20_DMPG.pdb）；
· 分子动力学模拟流程文档（MD_Setup.pdf）。