Binding of 2CA1P (nocturnal inhibitor) to the active site of RubisCO using Genetic Algorithm (GA)

Abstract

Ribulose-1, 5- Bisphosphate carboxylase/ oxygenase (RubisCO) catalyzes the first step in net photosynthetic assimilation and photorespiratory carbon oxidation. The activity of this enzyme is modulated in response to changes in light intensity as suggested in a number of early reports. Several studies found that the natural inhibitor 2CA1P is involved in the inhibition of the enzyme under reduced light intensity in rice (Oryza sativa). Due to the lack of studies and information on the interaction between this inhibitor and the active site of the enzyme, we attempted to predict the interaction between the amino acids in the active site and the inhibitor using both Hyperchem7.5 and GOLD software. After the docking; three possibilities having the highest fitness score were found (65.71, 64.72, 62.04), in these possibilities the inhibitor was bound to the enzyme, the phosphate and carboxylate groups in the same positions with a clear difference in the position of OH. In order to confirm the accuracy of the genetic algorithm, the artificial inhibitor 2CABP was docked back in the active site of the enzyme using the same parameters used in the case of the 2CA1P and the algorithm's predictions were compared with the experimentally observed binding mode. The results showed that the difference in the active sites before and after the docking was in the range of 0.93 Å which indicated that the results were very accurate. Depending on this result it was concluded that the results obtained in the case of the 2CA1P were close to the experimental results.

Selection of orlistat as a potential inhibitor for lipase from Candida species

“…(2) A mechanism for placing the ligand in the binding site; GOLD uses a unique method to do this, which is based on fitting point. (3) A search algorithm to explore possible binding modes; GOLD uses a genetic algorithm (GA) [ 17 – 18 ]. This method allows a partial flexibility of protein and full flexibility of ligand [ 19 ] for each of the 10 independent GA runs.…”