AccScience Publishing / GPD / Volume 1 / Issue 1 / DOI: 10.36922/gpd.v1i1.65
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ORIGINAL RESEARCH ARTICLE

Structural, functional, phylogenetic, and molecular dynamic simulation study of PEST-containing nuclear protein: An e-science view

Nazeer Hussain Khan1,2 Muhammad Shahid3 Wenkang Wang4 Saadullah Khatak1,2 Ebenezeri Erasto Ngowi1,5 Salma S. Mahmoud1,6 Hao-Jie Chen1 Lei Qian1 Yangzhe Qin1 Tao Li1 Muhammad Zubair7 Shazrul Fazry3 Dong-Dong Wu1,8* Chun Yang Zhang9,10* Xin-Ying Ji1,11*
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1 Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China
2 School of Life Sciences, Henan University, Kaifeng, Henan, China
3 Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
4 Department of Breast Surgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, China
5 Department of Biological Sciences, Faculty of Science, Dar es Salaam University College of Education, Dar es Salaam, Tanzania
6 Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
7 Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Pattoki Campus, Pakistan
8 School of Stomatology, Henan University, Kaifeng, Henan, China
9 Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
10 Department of General Thoracic Surgery, Hami Central Hospital, Hami, Xinjiang, P.R. China
11 Kaifeng Key Laboratory of Infection and Biological Safety, Henan University College of Medicine, Kaifeng, Henan, China
Submitted: 12 April 2022 | Accepted: 19 May 2022 | Published: 3 June 2022
© 2022 by the Authors. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
Abstract

PEST-containing nuclear protein (PCNP) is a short-lived novel nuclear protein. It has been well evaluated that PCNP mediates the progression of several cancers, but the exact mechanisms are still under investigation. In this study, we provided an e-science view of PCNP protein from the aspects of protein structure, interactions, and bioinformatics-based analysis related to evolutionary features as well as proteomic profile. The phylogenetic relationship results reveal that PCNP is closely related to Pan troglodytes and the Bovidae family, while being distantly related to the Muridae family. The analysis of the physicochemical properties of PCNP demonstrated that it is a thermolabile protein which is slightly acidic and hydrophilic in nature. Further, coexpression and protein-protein interaction analyses were carried out, which demonstrated that the PCNP gene was remarkably expressed with MORF4LI and RSL24D1 genes and has close interactions with TRAM1, PSMC6, SRP9, PRKRIR, UHRF2, and BMI1 proteins. Gene ontology and pathway enrichment analyses showed that PCNP has a high tendency to work in cell cycle regulation. Moreover, among the four 3D structure generating tools, I-TASSER-generated structure had the highest quality factor score. The validation analysis revealed that the I-TASSER-generated structure exhibited the best quality factor score with maximum amino acids in the favored region. In addition, molecular dynamic simulation analysis approved the stable structure of the PCNP. This is the first study that highlights the usefulness of the understanding of the structural and functional analysis of the PCNP, which lays the groundwork for further experimental studies to validate the outcome.

Keywords
3D structure
Molecular dynamic simulation
PEST-containing nuclear protein
Phylogeny
Physiochemical properties
Protein interactions
Funding
National Natural Science Foundation of China
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Conflict of interest
All the authors declare no conflict of interest.
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Gene & Protein in Disease, Electronic ISSN: 2811-003X Published by AccScience Publishing