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

Nazeer Hussain Khan^1,2, Muhammad Shahid³, Wenkang Wang⁴, Saadullah Khatak^1,2, Ebenezeri Erasto Ngowi^1,5, Salma S. Mahmoud^1,6, Hao-Jie Chen¹, Lei Qian¹, Yangzhe Qin¹, Tao Li¹, Muhammad Zubair⁷, Shazrul Fazry³, Dong-Dong Wu^1,8*, Chun Yang Zhang^9,10*, Xin-Ying Ji^1,11*

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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

GPD 2022, 1(1), 65 https://doi.org/10.36922/gpd.v1i1.65

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/ )

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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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