AlphaFold2-generated conformations overlap well with crystal structures of the open and closed state of GLIC.
<p>(A, B) Overlay of experimentally determined crystal structures in (A) the closed state (PDB ID 4NPQ) and (B) the open state (PDB ID 4HFI) with the corresponding prediction (visualized using VMD [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013187#pcbi....
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2025
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| Summary: | <p>(A, B) Overlay of experimentally determined crystal structures in (A) the closed state (PDB ID 4NPQ) and (B) the open state (PDB ID 4HFI) with the corresponding prediction (visualized using VMD [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013187#pcbi.1013187.ref042" target="_blank">42</a>]). The structures were aligned to minimize the RMSD of all C atoms in both the predicted and corresponding crystal structures. The pore hydration profiles for the predicted structures (calculated using HOLE [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1013187#pcbi.1013187.ref043" target="_blank">43</a>]) are also shown, with cyan and orange signifying wide (radius > 2.3 Å) and narrow (radius < 2.3 Å) parts of the pore, respectively. (C) Distance between the centers of mass of the pore and that of the upper part of the pore lining M2 helix (M2 spread) for AF-generated conformations ranging from closed-like (in red) to open-like (in blue). (D) The corresponding values for the predictions and the crystal structures as well as the density of states for all AF-generated conformations with an average pLDDT score above 75. (E, F) Upper spread of the extracellular domain (ECD), depicted as in panels C and D, respectively.</p> |
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