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Binding of 2CA1P (nocturnal inhibitor) to the active site of RubisCO using Genetic Algorithm (GA)
Authors:Ounissi Mourad  Kameli Abdelkrim  Boudjeniba Messaoud  Kherraz Khaled  Redouane Nouredine
Affiliation:Biology department, Ecole Normale Superieure, ENS-Kouba, PB 92, Algiers, Algeria
Abstract:Ribulose-1, 5- Bisphosphate carboxylase/ oxygenase (RubisCO) catalyzes the first step in net photosynthetic assimilation andphotorespiratory carbon oxidation. The activity of this enzyme is modulated in response to changes in light intensity as suggested in anumber of early reports. Several studies found that the natural inhibitor 2CA1P is involved in the inhibition of the enzyme under reducedlight intensity in rice (Oryza sativa). Due to the lack of studies and information on the interaction between this inhibitor and the active site ofthe enzyme, we attempted to predict the interaction between the amino acids in the active site and the inhibitor using both Hyperchem7.5and GOLD software. After the docking; three possibilities having the highest fitness score were found (65.71, 64.72, 62.04), in thesepossibilities the inhibitor was bound to the enzyme, the phosphate and carboxylate groups in the same positions with a clear difference in theposition of OH. In order to confirm the accuracy of the genetic algorithm, the artificial inhibitor 2CABP was docked back in the active siteof the enzyme using the same parameters used in the case of the 2CA1P and the algorithm''s predictions were compared with theexperimentally observed binding mode. The results showed that the difference in the active sites before and after the docking was in therange of 0.93 Å which indicated that the results were very accurate. Depending on this result it was concluded that the results obtained in thecase of the 2CA1P were close to the experimental results.
Keywords:RubisCO   2CA1P   CABP   GOLD   Hyperchem 7.5   Genetic algorithm
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