3-D STRUCTURE PREDICTION AND ANALYSIS OF THE P7-TRANSACTIVATED PROTEIN1OF HEPATITIS C VIRUS

El Hefnawi, Mahmoud; Hasan, Mohamed; Mahmoud, Amal; El-Absawy, El-Sayed; Khder, Yahia; Hemeida, Alaa

doi:10.21608/jpd.2017.41708

3-D STRUCTURE PREDICTION AND ANALYSIS OF THE P7-TRANSACTIVATED PROTEIN1OF HEPATITIS C VIRUS

Document Type : Original Article

Authors

¹ Informatics and Systems Department, Division of Engineering Research Sciences, the National Research Centre, Egypt.

² Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, Sadat City University, Egypt.

³ Plant Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, Sadat City University, Egypt.

10.21608/jpd.2017.41708

Abstract

The p7-transactivated protein 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 and comparative modelling, is an essential tool to solve the problem of protein structure prediction and to comprehend the physicochemical fundemental of how proteins fold in nature. Only one domain (1-127) of p7 had been predicted using the systematic in silico approach, Threa Dom. I-TASSERwas ranked as the best server for full-length 3-Dprotein structural predictions of p7 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 protein in inducing ion channel/pore and release of infectious virions. Using SCOP, only one hit matched protein sequence at 71-120 andwas classified as small proteins and FYVE/PHD zinc finger super family.
Integrating this information about the p7protein with SCOP and CATH annotations of the templates facilitate the assignment of structure–function/ evolution relationships to known and newly determined protein structures.

.

Keywords