A new approach to possible substrate binding mechanisms for nitrile hydratase |
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Authors: | Taştan Bishop A Ozlem Sewell Trevor |
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Affiliation: | Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa. ozlem@tuks.co.za |
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Abstract: | We combined normal mode analysis (NMA) with cavity calculations as a method to get more insight into static crystal structures. We used nitrile hydratase (NHase) as a case study, and the crystal structure of a complex of Pseudonocardia thermophila NHase (1UGP) with n-butyric acid was chosen as a reference structure. The reference structure was compared with the other available NHase crystal structures. Cavity calculations of the static structures showed the entrances to the active site and also a possible function of the N-terminal in the substrate selection of the Co-type NHase. When NMA was combined with cavity calculations, a closing-opening passage was observed. Analysis of low frequency modes combined with cavity calculations led us to propose "breathing" and "flip-flop" mechanisms which might be a key part of the substrate binding mechanism. |
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Keywords: | NHase Substrate binding mechanism Breathing Flip-flop Normal mode Cavity |
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