3-D STRUCTURE PREDICTION AND ANALYSIS OF THE P7-TRANSACTIVATED PROTEIN1OF HEPATITIS C VIRUS
El Hefnawi, M., Hasan, M., Mahmoud, A., El-Absawy, E., Khder, Y., Hemeida, A. (2017). 3-D STRUCTURE PREDICTION AND ANALYSIS OF THE P7-TRANSACTIVATED PROTEIN1OF HEPATITIS C VIRUS. EKB Journal Management System, 22(1), 83-102. doi: 10.21608/jpd.2017.41708
Mahmoud El Hefnawi; Mohamed Hasan; Amal Mahmoud; El-Sayed El-Absawy; Yahia Khder; Alaa Hemeida. "3-D STRUCTURE PREDICTION AND ANALYSIS OF THE P7-TRANSACTIVATED PROTEIN1OF HEPATITIS C VIRUS". EKB Journal Management System, 22, 1, 2017, 83-102. doi: 10.21608/jpd.2017.41708
El Hefnawi, M., Hasan, M., Mahmoud, A., El-Absawy, E., Khder, Y., Hemeida, A. (2017). '3-D STRUCTURE PREDICTION AND ANALYSIS OF THE P7-TRANSACTIVATED PROTEIN1OF HEPATITIS C VIRUS', EKB Journal Management System, 22(1), pp. 83-102. doi: 10.21608/jpd.2017.41708
El Hefnawi, M., Hasan, M., Mahmoud, A., El-Absawy, E., Khder, Y., Hemeida, A. 3-D STRUCTURE PREDICTION AND ANALYSIS OF THE P7-TRANSACTIVATED PROTEIN1OF HEPATITIS C VIRUS. EKB Journal Management System, 2017; 22(1): 83-102. doi: 10.21608/jpd.2017.41708

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

Journal of Productivity and Development
Article 6, Volume 22, Issue 1, January 2017, Page 83-102  XML PDF (489.25 K)
Document Type: Original Article
DOI: 10.21608/jpd.2017.41708
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Authors
Mahmoud El Hefnawi* 1; Mohamed Hasan2; Amal Mahmoud2; El-Sayed El-Absawy2; Yahia Khder3; Alaa Hemeida2
1Informatics and Systems Department, Division of Engineering Research Sciences, the National Research Centre, Egypt.
2Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, Sadat City University, Egypt.
3Plant Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, Sadat City University, Egypt.
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.
 
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Keywords
Hepatitis C virus; p7 protein; Ab initio; proteinstructure prediction; motifs and PTMs
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