Computational protocol: Reduced APOBEC3H Variant Anti-Viral Activities Are Associated with Altered RNA Binding Activities

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Protocol publication

[…] Homology modeling of A3H-HapII was carried out using both the program Modeller and the modeling server I-TASSER , which has been ranked as the best server in the recent CASP7 and CASP8 modeling contests . Both Modeller and I-TASSER produced very similar models, suggesting convincing modeling results. Prior to modeling in Modeller, multiple sequence alignment was carried out for APOBEC2, the amino-terminal domain of A3G (A3G-NTD), carboxyl-terminal domain of A3G (A3G-CTD), and A3H-HapII by using the program MUSCLE . The availability of crystal structures of two homologous APOBECs, APOBEC2 and A3G CTD , , helped to validate and manually improve the alignment. The aligned sequences of A3G-NTD/A3H-HapII, APOBEC2, and A3G-CTD were input into Modeller for homology modeling using the two crystal structures as multiple templates, which improved the quality of the modeling. The high degree of homology among the proteins and the similarity of the resulting models impart confidence in the homology modeling, especially for the regions in which the conserved motif RLYYFW and A3H-HapII residues 15N, 105, 121, and 178 are located. […]

Pipeline specifications

Software tools MODELLER, I-TASSER, MUSCLE
Applications Protein structure analysis, Nucleotide sequence alignment
Organisms Human immunodeficiency virus 1, Homo sapiens
Diseases HIV Infections
Chemicals Amino Acids, Cytidine