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Structural and Functional Annotation and Molecular Docking Analysis of a Hypothetical Protein from Neisseria gonorrhoeae: An In-Silico Approach

Background. Worldwide, Neisseria gonorrhoeae-related sexually transmitted infections (STIs) continue to be of significant public health concern. This obligate-human pathogen has developed a number of defenses against both innate and adaptive immune responses during infection, some of which are media...

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Published in:BioMed research international 2022-09, Vol.2022, p.4302625-12
Main Authors: Mazumder, Lincon, Hasan, Md. Rakibul, Fatema, Kanij, Islam, Md. Zahirul, Tamanna, Sanjida Khanam
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creator Mazumder, Lincon
Hasan, Md. Rakibul
Fatema, Kanij
Islam, Md. Zahirul
Tamanna, Sanjida Khanam
description Background. Worldwide, Neisseria gonorrhoeae-related sexually transmitted infections (STIs) continue to be of significant public health concern. This obligate-human pathogen has developed a number of defenses against both innate and adaptive immune responses during infection, some of which are mediated by the pathogen’s proteins. Hence, the uncharacterized proteins of N. gonorrhoeae can be annotated to get insight into the unique functions of this organism related to its pathogenicity and to find a more efficient therapeutic target. Methods. In this study, a hypothetical protein (HP) of N. gonorrhoeae was chosen for analysis and an in-silico approach was used to explore various properties such as physicochemical characteristics, subcellular localization, secondary structure, 3D structures, and functional annotation of that HP. Finally, a molecular docking analysis was performed to design an epitope-based vaccine against that HP. Results. This study has identified the potential role of the chosen HP of N. gonorrhoeae in plasmid transfer, cell cycle control, cell division, and chromosome partitioning. Acidic nature, thermal stability, cytoplasmic localization of the protein, and some of its other physicochemical properties have also been identified through this study. Molecular docking analysis has demonstrated that one of the T cell epitopes of the protein has a significant binding affinity with the human leukocyte antigen HLA-B∗15 : 01. Conclusions. The in-silico characterization of this protein will help us understand molecular mechanism of action of N. gonorrhoeae and get an insight into novel therapeutic identification processes. This research will, therefore, enhance our knowledge to find new medications to tackle this potential threat to humankind.
doi_str_mv 10.1155/2022/4302625
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Rakibul ; Fatema, Kanij ; Islam, Md. Zahirul ; Tamanna, Sanjida Khanam</creator><contributor>Harrison, Paul ; Paul Harrison</contributor><creatorcontrib>Mazumder, Lincon ; Hasan, Md. Rakibul ; Fatema, Kanij ; Islam, Md. Zahirul ; Tamanna, Sanjida Khanam ; Harrison, Paul ; Paul Harrison</creatorcontrib><description>Background. Worldwide, Neisseria gonorrhoeae-related sexually transmitted infections (STIs) continue to be of significant public health concern. This obligate-human pathogen has developed a number of defenses against both innate and adaptive immune responses during infection, some of which are mediated by the pathogen’s proteins. Hence, the uncharacterized proteins of N. gonorrhoeae can be annotated to get insight into the unique functions of this organism related to its pathogenicity and to find a more efficient therapeutic target. Methods. In this study, a hypothetical protein (HP) of N. gonorrhoeae was chosen for analysis and an in-silico approach was used to explore various properties such as physicochemical characteristics, subcellular localization, secondary structure, 3D structures, and functional annotation of that HP. Finally, a molecular docking analysis was performed to design an epitope-based vaccine against that HP. Results. This study has identified the potential role of the chosen HP of N. gonorrhoeae in plasmid transfer, cell cycle control, cell division, and chromosome partitioning. Acidic nature, thermal stability, cytoplasmic localization of the protein, and some of its other physicochemical properties have also been identified through this study. Molecular docking analysis has demonstrated that one of the T cell epitopes of the protein has a significant binding affinity with the human leukocyte antigen HLA-B∗15 : 01. Conclusions. The in-silico characterization of this protein will help us understand molecular mechanism of action of N. gonorrhoeae and get an insight into novel therapeutic identification processes. This research will, therefore, enhance our knowledge to find new medications to tackle this potential threat to humankind.</description><identifier>ISSN: 2314-6133</identifier><identifier>ISSN: 2314-6141</identifier><identifier>EISSN: 2314-6141</identifier><identifier>DOI: 10.1155/2022/4302625</identifier><identifier>PMID: 36105928</identifier><language>eng</language><publisher>United States: Hindawi</publisher><subject>Amino acids ; Annotations ; Antigens ; Bacterial proteins ; Bioinformatics ; Causes of ; Cell cycle ; Cell division ; Chromosomes ; Epitopes ; Epitopes, T-Lymphocyte ; Genomes ; Gonorrhea ; Gonorrhea - drug therapy ; Histocompatibility antigen HLA ; Humans ; Identification and classification ; Immunity, Humoral ; Infections ; Leukocytes ; Localization ; Lymphocytes ; Lymphocytes T ; Methods ; Molecular docking ; Molecular Docking Simulation ; Neisseria gonorrhoeae ; Neisseria gonorrhoeae - genetics ; Pathogenicity ; Pathogens ; Phylogenetics ; Physicochemical properties ; Physiological aspects ; Protein structure ; Protein structure prediction ; Proteins ; Public health ; Secondary structure ; Sexually transmitted diseases ; STD ; Structure ; Structure-function relationships ; Therapeutic targets ; Thermal stability ; Vaccines</subject><ispartof>BioMed research international, 2022-09, Vol.2022, p.4302625-12</ispartof><rights>Copyright © 2022 Lincon Mazumder et al.</rights><rights>COPYRIGHT 2022 John Wiley &amp; Sons, Inc.</rights><rights>Copyright © 2022 Lincon Mazumder et al. This is an open access article distributed under the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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Rakibul</creatorcontrib><creatorcontrib>Fatema, Kanij</creatorcontrib><creatorcontrib>Islam, Md. Zahirul</creatorcontrib><creatorcontrib>Tamanna, Sanjida Khanam</creatorcontrib><title>Structural and Functional Annotation and Molecular Docking Analysis of a Hypothetical Protein from Neisseria gonorrhoeae: An In-Silico Approach</title><title>BioMed research international</title><addtitle>Biomed Res Int</addtitle><description>Background. Worldwide, Neisseria gonorrhoeae-related sexually transmitted infections (STIs) continue to be of significant public health concern. This obligate-human pathogen has developed a number of defenses against both innate and adaptive immune responses during infection, some of which are mediated by the pathogen’s proteins. Hence, the uncharacterized proteins of N. gonorrhoeae can be annotated to get insight into the unique functions of this organism related to its pathogenicity and to find a more efficient therapeutic target. Methods. In this study, a hypothetical protein (HP) of N. gonorrhoeae was chosen for analysis and an in-silico approach was used to explore various properties such as physicochemical characteristics, subcellular localization, secondary structure, 3D structures, and functional annotation of that HP. Finally, a molecular docking analysis was performed to design an epitope-based vaccine against that HP. Results. This study has identified the potential role of the chosen HP of N. gonorrhoeae in plasmid transfer, cell cycle control, cell division, and chromosome partitioning. Acidic nature, thermal stability, cytoplasmic localization of the protein, and some of its other physicochemical properties have also been identified through this study. Molecular docking analysis has demonstrated that one of the T cell epitopes of the protein has a significant binding affinity with the human leukocyte antigen HLA-B∗15 : 01. Conclusions. 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Rakibul</au><au>Fatema, Kanij</au><au>Islam, Md. Zahirul</au><au>Tamanna, Sanjida Khanam</au><au>Harrison, Paul</au><au>Paul Harrison</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structural and Functional Annotation and Molecular Docking Analysis of a Hypothetical Protein from Neisseria gonorrhoeae: An In-Silico Approach</atitle><jtitle>BioMed research international</jtitle><addtitle>Biomed Res Int</addtitle><date>2022-09-05</date><risdate>2022</risdate><volume>2022</volume><spage>4302625</spage><epage>12</epage><pages>4302625-12</pages><issn>2314-6133</issn><issn>2314-6141</issn><eissn>2314-6141</eissn><abstract>Background. Worldwide, Neisseria gonorrhoeae-related sexually transmitted infections (STIs) continue to be of significant public health concern. This obligate-human pathogen has developed a number of defenses against both innate and adaptive immune responses during infection, some of which are mediated by the pathogen’s proteins. Hence, the uncharacterized proteins of N. gonorrhoeae can be annotated to get insight into the unique functions of this organism related to its pathogenicity and to find a more efficient therapeutic target. Methods. In this study, a hypothetical protein (HP) of N. gonorrhoeae was chosen for analysis and an in-silico approach was used to explore various properties such as physicochemical characteristics, subcellular localization, secondary structure, 3D structures, and functional annotation of that HP. Finally, a molecular docking analysis was performed to design an epitope-based vaccine against that HP. Results. This study has identified the potential role of the chosen HP of N. gonorrhoeae in plasmid transfer, cell cycle control, cell division, and chromosome partitioning. Acidic nature, thermal stability, cytoplasmic localization of the protein, and some of its other physicochemical properties have also been identified through this study. Molecular docking analysis has demonstrated that one of the T cell epitopes of the protein has a significant binding affinity with the human leukocyte antigen HLA-B∗15 : 01. Conclusions. The in-silico characterization of this protein will help us understand molecular mechanism of action of N. gonorrhoeae and get an insight into novel therapeutic identification processes. This research will, therefore, enhance our knowledge to find new medications to tackle this potential threat to humankind.</abstract><cop>United States</cop><pub>Hindawi</pub><pmid>36105928</pmid><doi>10.1155/2022/4302625</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-5679-3244</orcidid><orcidid>https://orcid.org/0000-0001-6463-9418</orcidid><orcidid>https://orcid.org/0000-0001-8943-4443</orcidid><orcidid>https://orcid.org/0000-0002-9193-5594</orcidid><orcidid>https://orcid.org/0000-0003-4880-9311</orcidid><oa>free_for_read</oa></addata></record>
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subjects Amino acids
Annotations
Antigens
Bacterial proteins
Bioinformatics
Causes of
Cell cycle
Cell division
Chromosomes
Epitopes
Epitopes, T-Lymphocyte
Genomes
Gonorrhea
Gonorrhea - drug therapy
Histocompatibility antigen HLA
Humans
Identification and classification
Immunity, Humoral
Infections
Leukocytes
Localization
Lymphocytes
Lymphocytes T
Methods
Molecular docking
Molecular Docking Simulation
Neisseria gonorrhoeae
Neisseria gonorrhoeae - genetics
Pathogenicity
Pathogens
Phylogenetics
Physicochemical properties
Physiological aspects
Protein structure
Protein structure prediction
Proteins
Public health
Secondary structure
Sexually transmitted diseases
STD
Structure
Structure-function relationships
Therapeutic targets
Thermal stability
Vaccines
title Structural and Functional Annotation and Molecular Docking Analysis of a Hypothetical Protein from Neisseria gonorrhoeae: An In-Silico Approach
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