Computational protocol: The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain

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Protocol publication

[…] Protein tertiary structure comparisons were performed using the Dali server at http://ekhidna.biocenter.helsinki.fi/dali_server/start. PDB 4A36 was used as the query structure. Results were sorted by Z-score, a statistical method describing goodness of fit defined in Ranjith-Kumar et al. (). From these results, 22 structures representing unique proteins were selected based on a cutoff of Z ≥ 15. These structures were then used in primary and secondary structural alignments which were also performed using the Dali server. No structures fitting the above criteria were excluded. The selected window depicted in Figure contains a portion of the full secondary structure alignment encompassing residues 383–433 of hs RIG-I.RIG-I/eIF4a structural alignment was performed using Pymol. Regions to be aligned from the DExD/H-box-containing RecA-like folds of both proteins were selected to include all matching secondary structural elements within the boundaries of these domains. The alignment was performed using the built-in ‘align’ function, and the color was applied using the ‘colorbyrmsd’ script found at http://www.pymolwiki.org/index.php/ColorByRMSD. […]

Pipeline specifications

Software tools DALI, PyMOL
Application Protein structure analysis
Chemicals Tretinoin