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Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å - MaRDI portal

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Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å

From MaRDI portal



DOI10.5281/zenodo.3951861Zenodo3951861MaRDI QIDQ6709804

Dataset published at Zenodo repository.

Author name not available (Why is that?)

Publication date: 28 August 2020

Copyright license: No records found.



Description

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 calc-density.tcl. In VMD TK-Console: mol new system.psf mol addfile system.dcd waitfor all source /path/to/scripts/LipNetwork.tcl align source /path/to/scripts/calc-density.tcl dmpcdensity outname [output] outname_ltailden.dx Convert from .dx to .mrc using UCSF-ChimeraVolume_Viewerplugin. [output] outname_ltailden.mrc Using Relion: $ relion_image_handler --i outname_ltailden.mrc --o outname_ltailden_D6-Sym.mrc --sym D6 [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 andfull trajectory files (2ps/frame), please contact Dr. Steve Reichow (reichow@pdx.edu).






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