Molecular characterisation of the acyltransferase-acyl carrier protein interface in a fungal highly reducing polyketide synthase - MD simulations

This dataset contains Amber trajectories of 3 repeats of 250 ns classical MD and 1 repeat of accelerated MD simulations of a holo-SimG ACP in complex with malonyl-SimG AT associated with publication "Molecular characterisation of the acyltransferase-acyl carrier protein interface in a fungal highly reducing polyketide synthase" by Mia E. Foran, Y. T. Candace Ho, Józef R. Lewandowski and Matthew Jenner. For details of the simulation see the publication. Files: stripped-topology.prmtop - topology file in Amber format. Water and ions are stripped from this topology file. cMD1-run1-trajectory.nc - trajectory for 250 ns classical MD in Amber NetCDF format; run1 cMD1-run2-trajectory.nc - trajectory for 250 ns classical MD in Amber NetCDF format; run2 cMD1-run3-trajectory.nc - trajectory for 250 ns classical MD in Amber NetCDF format; run3 aMD1-stripped-trajectory.nc - trajectory for 200 ns accelarated MD in Amber NetCDF format malonyl-SimG-AT-holo-SimG-ACP-Figure4.pdb - model of the SimG AT-SimG ACP complex. The coordinates were extracted from the example frame from cMD used for generation of Figure 4 in the manuscript. The residue numbering is as in the manuscript with AT (chain B) corresponding to residues 525-969 and ACP (chain A) corresponding to residues 2456-2560. All trajectories were stripped of ions and water to reduce size of the files.本数据集包含结合了丙二酰-SimG酰基转移酶（malonyl-SimG AT）的全酶形式SimG酰基载体蛋白（holo-SimG ACP）的分子动力学模拟轨迹，其中包含3组重复的250纳秒经典分子动力学（classical MD, cMD）轨迹，以及1组加速分子动力学（accelerated MD, aMD）模拟轨迹，相关研究论文为Mia E. Foran、Y. T. Candace Ho、Józef R. Lewandowski与Matthew Jenner发表的《真菌高度还原型聚酮合酶中酰基转移酶-酰基载体蛋白界面的分子表征》（Molecular characterisation of the acyltransferase-acyl carrier protein interface in a fungal highly reducing polyketide synthase）。模拟细节请参阅该发表论文。 文件列表如下： stripped-topology.prmtop：Amber格式拓扑文件，已移除其中的水分子与离子。 cMD1-run1-trajectory.nc：Amber NetCDF格式的250 ns经典分子动力学轨迹（第1次重复实验） cMD1-run2-trajectory.nc：Amber NetCDF格式的250 ns经典分子动力学轨迹（第2次重复实验） cMD1-run3-trajectory.nc：Amber NetCDF格式的250 ns经典分子动力学轨迹（第3次重复实验） aMD1-stripped-trajectory.nc：Amber NetCDF格式的200 ns加速分子动力学轨迹 malonyl-SimG-AT-holo-SimG-ACP-Figure4.pdb：SimG AT-SimG ACP复合物模型，其坐标提取自论文中图4所用的经典分子动力学轨迹的代表性帧，残基编号与论文一致：酰基转移酶AT（B链）对应残基525-969，酰基载体蛋白ACP（A链）对应残基2456-2560。 所有轨迹均已移除离子与水分子以减小文件体积。