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41708

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

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Last updated: 04 Jan 2025

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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.   .

DOI

10.21608/jpd.2017.41708

Keywords

Hepatitis C virus, p7 protein, Ab initio, proteinstructure prediction, motifs and PTMs

Authors

First Name

Mahmoud

Last Name

El Hefnawi

MiddleName

-

Affiliation

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

Email

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City

Sadat city

Orcid

-

First Name

Mohamed

Last Name

Hasan

MiddleName

-

Affiliation

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

Email

-

City

Sadat city

Orcid

-

First Name

Amal

Last Name

Mahmoud

MiddleName

-

Affiliation

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

Email

-

City

Sadat city

Orcid

-

First Name

El-Sayed

Last Name

El-Absawy

MiddleName

-

Affiliation

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

Email

-

City

Sadat city

Orcid

-

First Name

Yahia

Last Name

Khder

MiddleName

-

Affiliation

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

Email

-

City

Sadat city

Orcid

-

First Name

Alaa

Last Name

Hemeida

MiddleName

-

Affiliation

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

Email

-

City

Sadat city

Orcid

-

Volume

22

Article Issue

1

Related Issue

6555

Issue Date

2017-01-01

Receive Date

2016-10-15

Publish Date

2017-01-01

Page Start

83

Page End

102

Print ISSN

1110-2543

Online ISSN

2682-3322

Article File

JPD_Volume 22_Issue 1_Pages 83-102.pdf

PDF . 501.0kB

Link

https://jpd.journals.ekb.eg/article_41708.html

Detail API

https://jpd.journals.ekb.eg/service?article_code=41708

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6

Type

Original Article

Type Code

867

Publication Type

Journal

Publication Title

Journal of Productivity and Development

Publication Link

https://jpd.journals.ekb.eg/

MainTitle

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

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Type

Article

Created At

22 Jan 2023