Article
Stochastic boundary molecular dynamics simulation of L-ribose in the active site of Actinoplanes missouriensis xylose isomerase and its Val135Asn mutant with improved reaction rate.
Biochimica et biophysica acta - 20 May 2005
Santa Harri, Kammonen Juha, Lehtonen Olli, Karimäki Johanna, Pastinen Ossi, Leisola Matti, Turunen Ossi
Abstract excerpt
We used molecular dynamics simulations to study how a non-natural substrate, L-ribose, interacts with the active site of Actinoplanes missouriensis xylose isomerase. The simulations showed that L-ribose does not stay liganded in the active site in the same way as D-xylose, in which the oxygens O2 and O4 are liganded to the metal M1. The oxygen O4 of L-ribose moved away from the metal M1 to an upside down...
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