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In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site

Acinetobacter baumannii is a deadly nosocomial pathogen. Iron is an essential element for the pathogen. Under iron-restricted conditions, the bacterium expresses iron-regulated outer membrane proteins (IROMPs). Baumannii acinetobactin utilization (BauA) is the most important member of IROMPs in A. b...

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Autores principales: Sefid, Fatemeh, Rasooli, Iraj, Jahangiri, Abolfazl
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3780550/
https://www.ncbi.nlm.nih.gov/pubmed/24106696
http://dx.doi.org/10.1155/2013/172784
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author Sefid, Fatemeh
Rasooli, Iraj
Jahangiri, Abolfazl
author_facet Sefid, Fatemeh
Rasooli, Iraj
Jahangiri, Abolfazl
author_sort Sefid, Fatemeh
collection PubMed
description Acinetobacter baumannii is a deadly nosocomial pathogen. Iron is an essential element for the pathogen. Under iron-restricted conditions, the bacterium expresses iron-regulated outer membrane proteins (IROMPs). Baumannii acinetobactin utilization (BauA) is the most important member of IROMPs in A. baumannii. Determination of its tertiary structure could help deduction of its functions and its interactions with ligands. The present study unveils BauA 3D structure via in silico approaches. Apart from ab initio, other rational methods such as homology modeling and threading were invoked to achieve the purpose. For homology modeling, BLAST was run on the sequence in order to find the best template. The template was then served to model the 3D structure. All the models built were evaluated qualitatively. The best model predicted by LOMETS was selected for analyses. Refinement of 3D structure as well as determination of its clefts and ligand binding sites was carried out on the structure. In contrast to the typical trimeric arrangement found in porins, BauA is monomeric. The barrel is formed by 22 antiparallel transmembrane β-strands. There are short periplasmic turns and longer surface-located loops. An N-terminal domain referred to either as the cork, the plug, or the hatch domain occludes the β-barrel.
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spelling pubmed-37805502013-10-08 In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site Sefid, Fatemeh Rasooli, Iraj Jahangiri, Abolfazl Biomed Res Int Research Article Acinetobacter baumannii is a deadly nosocomial pathogen. Iron is an essential element for the pathogen. Under iron-restricted conditions, the bacterium expresses iron-regulated outer membrane proteins (IROMPs). Baumannii acinetobactin utilization (BauA) is the most important member of IROMPs in A. baumannii. Determination of its tertiary structure could help deduction of its functions and its interactions with ligands. The present study unveils BauA 3D structure via in silico approaches. Apart from ab initio, other rational methods such as homology modeling and threading were invoked to achieve the purpose. For homology modeling, BLAST was run on the sequence in order to find the best template. The template was then served to model the 3D structure. All the models built were evaluated qualitatively. The best model predicted by LOMETS was selected for analyses. Refinement of 3D structure as well as determination of its clefts and ligand binding sites was carried out on the structure. In contrast to the typical trimeric arrangement found in porins, BauA is monomeric. The barrel is formed by 22 antiparallel transmembrane β-strands. There are short periplasmic turns and longer surface-located loops. An N-terminal domain referred to either as the cork, the plug, or the hatch domain occludes the β-barrel. Hindawi Publishing Corporation 2013 2013-09-05 /pmc/articles/PMC3780550/ /pubmed/24106696 http://dx.doi.org/10.1155/2013/172784 Text en Copyright © 2013 Fatemeh Sefid et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Sefid, Fatemeh
Rasooli, Iraj
Jahangiri, Abolfazl
In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site
title In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site
title_full In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site
title_fullStr In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site
title_full_unstemmed In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site
title_short In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site
title_sort in silico determination and validation of baumannii acinetobactin utilization a structure and ligand binding site
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3780550/
https://www.ncbi.nlm.nih.gov/pubmed/24106696
http://dx.doi.org/10.1155/2013/172784
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