Background: The p7-transactivated protein1 of Hepatitis C virus is a small integral
membrane protein of 127 amino acids, which is crucial for assembly and release of
infectious virions. Ab initio or comparative modelling, is an essential tool to solve the
problem of protein structure prediction and to comprehend the physicochemical fundamental
of how proteins fold in nature.
Results: Only one domain (1-127) of p7-transactivated protein1 has been predicted using
the systematic in silico approach, ThreaDom. I-TASSER was ranked as the best server for
full-length 3-D protein structural predictions of p7-transactivated protein1 where the
benchmarked scoring system such as C-score, TM-score, RMSD and Z-score are used to
obtain quantitative assessments of the I-TASSER models. Scanning protein motif databases,
along with secondary and surface accessibility predictions integrated with post
translational modification sites (PTMs) prediction revealed functional and protein binding
motifs. Three protein binding motifs (two Asp/Glutamnse, CTNNB1- bd_N) with high
sequence conservation and two PTMs prediction: Camp_phospho_site and Myristyl site
were predicted using BLOCKS and PROSITE scan. These motifs and PTMs were related
to the function of p7-transactivated protein1 protein in inducing ion channel/pore and release
of infectious virions. Using SCOP, only one hit matched protein sequence at 71-120
was classified as small proteins and FYVE/PHD zinc finger superfamily.
Conclusion: Integrating this information about the p7-transactivated protein1 with SCOP
and CATH annotations of the templates facilitates the assignment of structure–function/
evolution relationships to the known and the newly determined protein structures.