Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å
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These are the molecular dynamics (MD) data that are analyzed, in Flores et al. 2020. Each trajectory file (.dcd) has an associated structure file (.psf), which can be analyzed in VMD. Each gap junction system, Cx46 & Cx50, were simulated with either KCl or NaCl in the intracellular space: Cx46_KCl/NaCl, Cx50_KCl/NaCl. All four systems were equilibrated for 30ns and then followed up with 2 separate 100ns production runs. For MD lipid-densities the Cx50_KCl system was used as the representative dataset. Lipid densities from all other systems can be calculated with the provided TCL script <em>calc-density.tcl</em>. <strong>In VMD TK-Console:</strong> > mol new <system>.psf<br> > mol addfile <system>.dcd waitfor all<br> > source /path/to/scripts/LipNetwork.tcl<br> > align<br> > source /path/to/scripts/calc-density.tcl<br> > dmpcdensity <outname><br> [output] outname_ltailden.dx<br> <br> Convert from .dx to .mrc using <em>UCSF-Chimera Volume_Viewer</em> plugin.<br> [output] outname_ltailden.mrc<br> <br> <strong>Using Relion:</strong><br> <br> $ relion_image_handler --i outname_ltailden.mrc --o outname_ltailden_D6-Sym.mrc --sym D6<br> [output] outname_ltailden_D6-Sym.mrc All trajectory files (.dcd) are 100ns longs (1,000 frames x 100ps/frame). For questions regarding MD-data analysis and full trajectory files (2ps/frame), please contact Dr. Steve Reichow (reichow@pdx.edu).
本数据集为Flores等人2020年研究中所分析的分子动力学（Molecular Dynamics, MD）数据。每条轨迹文件（.dcd）均配有对应的结构文件（.psf），可通过VMD软件进行分析。本次研究涵盖两类间隙连接系统：连接蛋白46（Cx46）与连接蛋白50（Cx50），分别在胞内液中添加氯化钾（KCl）或氯化钠（NaCl）进行模拟，对应体系命名为Cx46_KCl/NaCl、Cx50_KCl/NaCl。所有四个体系均先经过30纳秒（ns）的平衡模拟，随后开展两段独立的100纳秒生产模拟。针对MD脂质密度分析，本数据集选取Cx50_KCl体系作为代表数据集。其余所有体系的脂质密度均可通过提供的TCL脚本<em>calc-density.tcl</em>进行计算。<strong>在VMD TK控制台中：</strong><br> > mol new <system>.psf<br> > mol addfile <system>.dcd waitfor all<br> > source /path/to/scripts/LipNetwork.tcl<br> > align<br> > source /path/to/scripts/calc-density.tcl<br> > dmpcdensity <outname><br> [输出结果] outname_ltailden.dx<br> <br> 可通过<em>UCSF-Chimera Volume_Viewer</em>插件将.dx格式文件转换为.mrc格式。<br> [输出结果] outname_ltailden.mrc<br> <br> <strong>使用Relion软件时：</strong><br> <br> $ relion_image_handler --i outname_ltailden.mrc --o outname_ltailden_D6-Sym.mrc --sym D6<br> [输出结果] outname_ltailden_D6-Sym.mrc<br> <br> 所有轨迹文件（.dcd）时长均为100纳秒，包含1000帧图像，每帧间隔为100皮秒（ps）。若需咨询MD数据分析相关问题或获取全帧间隔为2皮秒/帧的完整轨迹文件，请联系Steve Reichow博士（邮箱：reichow@pdx.edu）。
