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Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly
Authors Standley D , van der Giezen M
Received 4 October 2011
Accepted for publication 25 October 2011
Published 12 January 2012 Volume 2012:2 Pages 1—8
Review by Single anonymous peer review
Peer reviewer comments 3
Daron M Standley1, Mark van der Giezen2
1Laboratory of Systems Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan; 2Centre for Eukaryotic Evolutionary Microbiology, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
Abstract: Alternative oxidases (AOX) of human parasites represent attractive drug targets due to their absence in humans. However, the lack of a structure has prevented structure-based drug design. Moreover, a large helical insertion proves difficult for automated structural modeling efforts. We have used a novel hybrid structural modeling approach to generate a model that is globally consistent with a previous model but based on a phylogenetically closer template and systematic sampling of known fragments in the helical insertion. Our model, in agreement with site-directed mutagenesis studies, clearly assigns E200 as the iron-ligating residue as opposed to the previously suggested E201. Crystallization of AOX from another species has recently been reported suggesting that our blind prediction can be independently validated in the near future.
Keywords: homology modeling, protein structure, blind prediction, fragment assembly, active site, parasite, mitosome, hydrogenosome, evolution
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