Paper Citing NAMD - Abstract
Lee, Wook; Engels, Bernd
Clarification on the Decarboxylation Mechanism in KasA Based on the Protonation State of Key Residues in the Acyl-Enzyme State
JOURNAL OF PHYSICAL CHEMISTRY B, 117:8095-8104, JUL 11 2013
The beta-ketoacyl ACP synthase I (KasA) is a promising drug target because it is essential for the survival of Mycobacterium tuberculosis, a causative agent Of tuberculosis. It catalyzes a condensation reaction that comprises three steps. The resulting elongated acyl chains are subsequently needed for the cell wall construction. While the mechanism of the first step (acylation of Cys171 in the active site) is straightforward already, the second step (decarboxylation of malonyl substrate) has been controversial due to the difficulty in determining the correct protonation, states of the involved residues (His311, His345, Lys340, Glu354). Available experimental data suggest three possible mechanisms which differ considerably. They are not consistent with each other because these studies could not be performed for KasA at the beginning, of decarboxylation step (acyl-enzyme state of ICasA). Instead, different mutant's had to be used which are expected to resemble this situation. In this first computational study; about this topic we use the free energy, perturbation (FEP) method to compute the relevant pK(a) values in the acyl-enzyme state of KasA and use molecular dynamics (MD) simulations to rationalize the results. Subsequent density functional theory (DFT)- based quantum mechanical/molecular mechanical (QM/MM) MD simulations and umbrella samplings have been used to disentangle the close relationships between the protonation states of the involved., residues. By these simulations, we can address the preferred protonation states and roles of the residues involved in decarboxylation reaction,thereby suggesting,the possible mechanism for the decarboxylation step.
