Computational protocol: Cytosolic 5′-Triphosphate Ended Viral Leader Transcript of Measles Virus as Activator of the RIG I-Mediated Interferon Response

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Protocol publication

[…] Using a BLAST search of the RIG-I sequence against the pdb , we identified a structural homologue, Hef (pdb code 1WP9) . We then searched RIG-I for the Walker A, Ia, Walker B, III, IV, V, VI helicase motifs . Using the MUSCLE program , we performed a multiple sequence alignment among RIG-I, Mda-5 (accession number: Q9BYX4), Hef, PcrA (pdb code 1PJR), a DNA helicase from Bacillus stearothermophilus, and Rep (pdb code 1UAA), a DNA helicase from E. coli. The resulting alignment was then manually adjusted so as to align the conserved helicase motifs. A good correlation was observed between the RIG-I predicted secondary structure elements (as obtained by using Psipred and those observed in the crystal structure of Hef (see ), which points out the reliability of the sequence alignment. This refined sequence alignment was used as a template to build a homology-derived 3D model of the RIG-I helicase domain by using the Swiss-model server . Notably, a threading approach using 3D-PSSM led to a model that is nicely superimposable onto the homology-derived one (rmsd of 1.35 Å, data not shown). The two models share the same overall topology, despite minor structural differences within loops (data not shown). The good agreement between the two models points out the reliability of the structural prediction.We then performed a multiple structural alignment among the RIG-I model, PcrA, Rep, and the NS3 helicase from HCV (pdb code 1A1V) using the MSDFOLD server . […]

Pipeline specifications

Software tools MUSCLE, PSIPRED
Application Nucleotide sequence alignment
Organisms Measles morbillivirus, Homo sapiens
Diseases HIV Infections