Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session I

11-POS Board 11 Homology Modelling of DapE from S.enterica: Insight into Inhibition and Cooperativity Ayse Aykut 1 , Marc Creus 2 , Torsten Schwede 1 . 1 University of Basel, Basel, Switzerland, 2 University of Basel, Basel, Switzerland. There is an urgent need to discover and develop novel antibiotics to fill the repertoire of drugs available to fight infection. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) is an essential enzyme of the anabolic pathway toward lysine in many bacteria and thus a promising target for antibiotic drug-design. The understanding of the exact enzymatic mechanism of this enzyme may thus facilitate the development of novel effective antimicrobial drugs. L-captopril has been shown to exhibit promising inhibitory activity in vitro against DapE however does not target DapE effectively in vivo. We have built homology models for S.enterica DapE in their dimeric apo and holo forms based on different template states, and docked L-captopril into both apo- and holo-model. The apo-model with ligand provides a plausible qualitative explanation for the metal-dependent selectivity of L-captopril inhibition: L- captopril targets only the Zn2+-metallo-isoform of the enzyme, whereas the Mn2+-enzyme, which is also a physiologically-relevant isoform in bacteria, is not inhibited. Here we show that DapE of the pathogen Salmonella enterica exhibits positive kinetic cooperativity, which is associated to a domain-movement in the enzyme dimer to form an ionic interaction between a conserved arginine of the dimerisation domain and a carboxylate of the substrate or substrate analog-inhibitor. Such cooperativity leads to the counterproductive effect of effective activation of enzyme activity by suboptimal dosage of competitive inhibitors occurring within a range of substrate concentration that is expected to be physiologically relevant. The holo model of DapE shows large domain movements that appear during catalysis, which are considered to give rise to the positive cooperativity in DapE. Understanding the mechanisms of inhibition and cooperativity from a structural perspective is an important step towards the discovery of new inhibitory lead compounds with improved properties.

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