Process Biochemistry, Vol.50, No.9, 1363-1371, 2015
Molecular dynamics simulation integrating study for Cr3+-binding to arginine kinase
We simulated the 3D structure of arginine kinase from Exopalaemon carinicauda (ECAK) on the basis of homology modeling. Computational molecular dynamics simulations between ECAK and Cr3+ were conducted to elucidate the functional role of Cr3+ on ECAK structure and catalysis. As a result, the binding mechanism of Cr3+ to ECAK along with binding sites and structural changes were predicted. To confirm the simulation results, kinetic studies of Cr3+-mediated aggregation of ECAK were subsequently conducted. We found that Cr3+ significantly induced ECAK aggregation with a multi-phase kinetic process at a high dose of Cr3+. The spectrofluorimetric results showed that Cr3+-induced tertiary structural changes in ECAK caused extensive exposure of hydrophobic surfaces, which could be a triggering factor for inducing ECAK aggregation. Our study provides new information concerning the effect of Cr3+ on ECAK's enzymatic function and unfolding, including aggregation, which might be toxic or act as a negative regulator. (C) 2015 Elsevier Ltd. All rights reserved.