Computational protocol: The First Extracellular Domain Plays an Important Role in Unitary Channel Conductance of Cx50 Gap Junction Channels

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Protocol publication

[…] The sequence of mouse Cx50 was aligned with that of Cx26 for homology structure models. High sequence identity is observed in these two proteins (overall 49% and on the structurally resolved domains 57%). The Cx26 crystal structure (2ZW3) [] was used as a template for the Cx50 structure. When a Cx50 residue replacement in the structure caused an abnormal inter-atomic contact, this was adjusted by hand initially in COOT and then revised by CNS energy refinement. After the energy refinement, structural validity of the model was inspected manually as described earlier [,]. Adaptive Poisson-Boltzmann Solver (APBS) [] and PDB2PQR server (http://nbcr-222.ucsd.edu/pdb2pqr_1.8/) were used to calculate the electrostatic potentials of all atoms in the protein and their influence in the pore centre. The APBS parameters were set as described previously []. PyMOL program was used for the diameter measurements and the structure presentations []. To obtain the electrostatic potentials in the centre of the channel, the centre of the pore in the homology model was first aligned with the x-axis using PoreWalker [] and then rotated 90° to align with the z-axis. Electrostatic potentials were re-calculated using APBS as implemented in PyMOL v1.7.4.1, and the values for the grid points along the z-axis were extracted from the DX file using OpenDX with “potential.net”, a modified version of the sample program “PlotLine.net” (bundled with OpenDX 4.4.4). “Potential.net” is a text file provided in the Supporting Information () and can be used once it is edited to provide the path to the DX file. […]

Pipeline specifications

Software tools PDB2PQR, PyMOL, PoreWalker
Application Protein structure analysis