Brandner Astrid, De Vecchis Dario, Baaden Marc, Cohen Mickael M, Taly Antoine
Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France.
Data Brief. 2019 Aug 31;26:104460. doi: 10.1016/j.dib.2019.104460. eCollection 2019 Oct.
In this work we present a novel set of possible auto-oligomerisation states of yeast protein Fzo1 in the context of membrane docking. The dataset reports atomistic models and trajectories derived from a molecular dynamics study of the yeast mitofusin Fzo1, residues 101-855. The initial modelling was followed by coarse-grained molecular dynamics simulation to evaluate the stability and the dynamics of each structural model in a solvated membrane environment. Simulations were run for 1 μs and collected with GROMACS v5.0.4 using the martini v2.1 force field. For each structural model, the dataset comprises the production phase under semi-isotropic condition at 1 bar, 310 K and 150 mn NaCl. The integration step is 20 fs and coordinates have been saved every 1 ns. Each trajectory is associated with a ready-available visualization state for the VMD software. These structural detailed informations are a ready-available platform to plan integrative studies on the mitofusin Fzo1 and will aid the community to further elucidate the mitochondrial tethering process during membrane fusion. This dataset is based on the publication "Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking." (Brandner and De Vecchis et al., 2019)".
在这项工作中，我们展示了酵母蛋白Fzo1在膜对接背景下一组全新的可能的自寡聚化状态。该数据集报告了源自酵母线粒体融合蛋白Fzo1（残基101 - 855）分子动力学研究的原子模型和轨迹。初始建模之后进行了粗粒度分子动力学模拟，以评估每个结构模型在溶剂化膜环境中的稳定性和动力学。模拟运行1微秒，并使用martini v2.1力场通过GROMACS v5.0.4收集数据。对于每个结构模型，数据集包括在1巴、310 K和150毫摩尔氯化钠的半各向同性条件下的生产阶段。积分步长为20飞秒，坐标每1纳秒保存一次。每个轨迹都与VMD软件的一个随时可用的可视化状态相关联。这些结构详细信息是一个随时可用的平台，用于规划关于线粒体融合蛋白Fzo1的综合研究，并将帮助该领域进一步阐明膜融合过程中的线粒体 tethering 过程。该数据集基于论文“基于物理的酵母线粒体融合蛋白Fzo1在膜对接背景下分子尺度的寡聚模型”（Brandner和De Vecchis等人，2019年）。
