Reports of Biochemistry and Molecular Biology
rbmb.net
Basic Sciences
http://rbmb.net
1
admin
2322-3480
2322-3480
10.61186/rbmb
en
jalali
1395
2
1
gregorian
2016
5
1
4
2
online
1
fulltext
en
In silico Prediction and Docking of Tertiary Structure of LuxI, an Inducer Synthase of Vibrio fischeri
بیوشیمی
Biochemistry
<p style="text-align: justify;"><em><strong>Background:</strong></em> LuxI is a component of the quorum sensing signaling pathway in <em>Vibrio fischeri</em> responsible for the inducer synthesis that is essential for bioluminescence.</p>
<p style="text-align: justify;"><em><strong>Methods: </strong></em>Homology modeling of LuxI was carried out using Phyre2 and refined with the GalaxyWEB server. Five models were generated and evaluated by ERRAT, ANOLEA, QMEAN6, and Procheck.</p>
<p style="text-align: justify;"><strong><em>Results: </em></strong>Five refined models were generated by the GalaxyWEB server, with Model 4 having the greatest quality based on the QMEAN6 score of 0.732. ERRAT analysis revealed an overall quality of 98.9%, while the overall quality of the initial model was 54%. The mean force potential energy, as analyzed by ANOLEA, were better compared to the initial model. Sterochemical quality estimation by Procheck showed that the refined Model 4 had a reliable structure, and was therefore submitted to the protein model database. Drug Discovery Workbench V.2 was used to screen 2700 experimental compounds from the DrugBank database to identify inhibitors that can bind to the active site between amino acids 24 and 110. Ten compounds with high negative scores were selected as the best in binding.</p>
<p style="text-align: justify;"><em><strong>Conclusion:</strong></em> The model produced, and the predicted acteyltransferase binding site, could be useful in modeling homologous sequences from other microorganisms and the design of new antimicrobials.</p>
Docking, Homology modeling, LuxI, Quorum sensing
66
75
http://rbmb.net/browse.php?a_code=A-10-1-52&slc_lang=en&sid=1
Mohammed Zaghlool Saeed
Al-Khayyat
assel4444@hotmail.com
10031947532846006124
10031947532846006124
Yes
Biology Department, College of Education for Pure Sciences, University of Mosul, Mosul, Iraq;
Ammar Ghanem Ameen
Al-Dabbagh
10031947532846006125
10031947532846006125
No
Biology Department, College of Sciences, University of Mosul, Mosul city, Iraq