ANALYSIS OF 3D STRUCTURE OF THE PROTEIN OF HAEMOPHILUS INFLUENZAE BY HOMOLOGY MODELLING HELPS IN PREDICTING BINDING SITES FOR SUBSTRATE, LEADS TO DESIGN ANTIBIOTIC
DOI:
https://doi.org/10.55519/JAMC-02-12594%20Keywords:
Homology modeling, Modeller , Haemophilus influenza,Prosa.Abstract
Background: Haemophilus influenza persists as a well-known root of ill health in children throughout the entire world. Before the introduction of the vaccine, Haemophilus influenza remained a well-known and eminent source of septic arthritis, pneumonia, and epiglottitis. Haemophilus influenza, Neisseria meningitides, and staphylococcus pneumonia spreads through respiratory droplets and cause diseases such as meningitis, pneumonia, and other secondary infections related to respiratory diseases. Objective was to analyze the 3D structure of the protein of Haemophilus influenzae by homology modelling to design antibiotics. Methods: For the effective study of protein, computational tools were used to investigate protein structure and function, Comprehensive microbial resource (CMR) for comparative modelling, Interproscan, BLAST for sequence similarity searching, MODELLER 9.10 for homology modeling, Procheck and Protein Structure Analysis (ProSA) software for assessing model quality and structural validation. Results: The model showed that it consists of three alpha helices (red) and one beta-sheet. Ramachandran Plot statistics show that 97.4% of the debris is in the favoured region, 0% in the additional allowed region, 2.65% in the generally allowed part, and 0% in the disallowed part. Stability and energy were checked through ProSa. Z score was highly negative which showed that the model is highly stable. The greater the negative value, the more will be the stability of the model. Conclusion: Cell division protein H11025 was selected. The structure was modelled which has provided all the required information to design antibiotics to control the harmful effects regarding that protein.References
References
Hameduh T,Haddad Y,Adam V,Heger Z.Homology modeling in the time of collective and artificial intelligence.Computational and structural biotechnology journal.2020 Jan1;18:3494-506.
Jaiteh M,Rodrignes,Espigaries I,Selent J,CarlssonJ.Performance of virtual screening against GPCR homology models:Impact of template selection and treatment of binding site plasticity.PLOS computational biology.2020 Mar 13;16(3):e 1007680.
Dong S,Sun J,Mao Z,Wang L, Lu YL, Li J.A guideline for homology modeling of the proteins from newly discovered beta coronavirus;2019 novel coronavirus(2019-nCOv ).Journal of medical virology.2020 Sept;92(9):1542-8.
Bitencourt-Ferriera G,de Azevedo WF.Homology modeling of protein targets with modeler.Docking screen for drug discovery.2019;231-49.
Muhammad MT,Aki-Yalcin E.Homology Modeling in drug discovery;Overview,current applications and future perspectives.Chemical biology and drug design.2019 Jan;93(1):12-20.
Franca TC.Homology modeling : an important tool for the drug discovery.Journal of Biomolecular Structure and Dynamics.2015 Aug 3;33(8):1780-93.
Wen S, Feng D,Chen D,Yang L,Xu Z. Molecular epidemiology and evolution of Haemophilus influenzae.Infection,genetics and evolution.2020 Jun 1;80:104205.
Jalalvand F, Su YC,Morgelin M,Brant M,Hallgren O,Westergren-Thorsson G,Singh B,Riesbeck K.Haemophilus influenza protein F mediates binding to laminin and human pulmonary epithelial cells.” The journal of infectious diseases.2013 Mar 1;207(5) 803-13.
Desta IT,Kotelnikov S,Jones G,Ghani U,Abyzov M,Kholodov Y,Standley DM, Sabitova M,Beglov D,Vajda S,Kozakov D.Mapping of antibody epitope based on docking and homology modeling.Proteins: Structure,Function and Bioinformatics.2023 Feb;91(2): 171-82.
Hung JH,Weng Z.Sequence alignment and homology search with BLAST and Clustal W.Cold Spring Harbor Protocols.2016 Nov 1;2016(11):pdb-rot093088.
Meler A,Soding J. Automatic prediction of protein 3D. Structures by probabilistic multi-template homology modeling.PLoS Comput Biol.2015 Oct 23;(10):e1004343.
Labib MM,Amin MK,Alzohairy AM,Elashtokhy MMA,Samir O,Saleh I ,Arif IA,Osman GH,Hassanein SE.In silico targeting,inhibition and analysis of polyketide synthase enzyme in Aspergillus ssp.Saudi J Biol Sci.2020 Dec;27(12):3187-3198.
FiegM.Local protein structure refinement via molecular dynamics simulations with locPREFMD.Journal of chemical information and modeling.2016 July 25;56(7):1304-12.
Park H,Ovchinnikov S,Kim DE,DiMaio F,Baker D.Protein homology model refinement by large –scale energy optimization.Proceedings of the National Academy of Sciences.2018 Mar 20;115(12):3054-9.
Yu Z,Kang L,Zhao Wu S,Ding L,Zheng F,Liu J,Li J. Identification of novel umami peptides from myosin via homology modeling and molecular docking.Food chemistry.2021 May 15;344:128728.
Downloads
Published
Issue
Section
License
Copyright (c) 2024 Rehana Rasool, Maria Shafiq, Samina swati, Anila Farid, Sofia Shoukat, Madeeha Jadoon
This work is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International License.
Journal of Ayub Medical College, Abbottabad is an OPEN ACCESS JOURNAL which means that all content is FREELY available without charge to all users whether registered with the journal or not. The work published by J Ayub Med Coll Abbottabad is licensed and distributed under the creative commons License CC BY ND Attribution-NoDerivs. Material printed in this journal is OPEN to access, and are FREE for use in academic and research work with proper citation. J Ayub Med Coll Abbottabad accepts only original material for publication with the understanding that except for abstracts, no part of the data has been published or will be submitted for publication elsewhere before appearing in J Ayub Med Coll Abbottabad. The Editorial Board of J Ayub Med Coll Abbottabad makes every effort to ensure the accuracy and authenticity of material printed in J Ayub Med Coll Abbottabad. However, conclusions and statements expressed are views of the authors and do not reflect the opinion/policy of J Ayub Med Coll Abbottabad or the Editorial Board.
USERS are allowed to read, download, copy, distribute, print, search, or link to the full texts of the articles, or use them for any other lawful purpose, without asking prior permission from the publisher or the author. This is in accordance with the BOAI definition of open access.
AUTHORS retain the rights of free downloading/unlimited e-print of full text and sharing/disseminating the article without any restriction, by any means including twitter, scholarly collaboration networks such as ResearchGate, Academia.eu, and social media sites such as Twitter, LinkedIn, Google Scholar and any other professional or academic networking site.