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ABSTRACT: Vibrio cholerae uses quorum sensing communication system to interact with other bacteria and for gauzing environmental parameters. This organism dwells equally well in both human host and aquatic environments. Quorum sensing regulates multitude of activities and is one of the lucrative targets presently pursued for drug design in bacteria to encounter virulence. Histidine phosphotransfer protein LuxU and response regulator LuxO of V. cholerae are known to play important roles in biofilms and virulence machinery. In the present study, we used computational methods to model LuxU and LuxO and simulated the interactions of LuxO and LuxU. Since no structural details of the proteins were available, we employed homology modeling to construct the three-dimensional structures and then performed molecular dynamics simulations to study dynamic behavior of the LuxO and LuxU from V. cholerae. The modeled proteins were validated and subjected to molecular docking analyses. This allowed us to predict the binding modes of the proteins to elucidate probable sites of interference.
Journal of biomolecular structure & dynamics 06/2012; 30(5):574-84. · 4.99 Impact Factor
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Arabian Journal of Chemistry 01/2012; · 1.37 Impact Factor
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Journal of biomolecular structure & dynamics 01/2012; · 4.99 Impact Factor
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ABSTRACT: The diatom Didymosphenia geminata is a single-celled alga found in lakes, streams, and rivers. Nuisance
blooms of D geminata affect the diversity, abundance, and productivity of other aquatic organisms. Because
D geminata can be transported by humans on waders and other gear, accurate spatial prediction of habitat
suitability is urgently needed for early detection and rapid response, as well as for evaluation of monitoring
and control programs. We compared four modeling methods to predict D geminata’s habitat distribution;
two methods use presence–absence data (logistic regression and classification and regression tree [CART]),
and two involve presence data (maximum entropy model [Maxent] and genetic algorithm for rule-set production
[GARP]). Using these methods, we evaluated spatially explicit, bioclimatic and environmental variables
as predictors of diatom distribution. The Maxent model provided the most accurate predictions, followed
by logistic regression, CART, and GARP. The most suitable habitats were predicted to occur in the
western US, in relatively cool sites, and at high elevations with a high base-flow index. The results provide
insights into the factors that affect the distribution of D geminata and a spatial basis for the prediction of
nuisance blooms.
Frontiers in Ecology and the Environment 01/2009; 7(8):415-420. · 9.11 Impact Factor
