In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding SiteReport as inadecuate




In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site - Download this document for free, or read online. Document in PDF available to download.

BioMed Research InternationalVolume 2013 2013, Article ID 172784, 14 pages

Research Article

Department of Biology, Shahed University, Tehran-Qom Express Way, Tehran 3319118651, Iran

Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran 1435944711, Iran

Received 27 April 2013; Revised 21 July 2013; Accepted 31 July 2013

Academic Editor: Paul Harrison

Copyright © 2013 Fatemeh Sefid et al. 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.

Abstract

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.





Author: Fatemeh Sefid, Iraj Rasooli, and Abolfazl Jahangiri

Source: https://www.hindawi.com/



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