Molecular dynamics study of the structural basis of dysfunction and the modulation of reactive oxygen species generation by pathogenic mutants of human dihydrolipoamide dehydrogenase

Abstract

Human dihydrolipoamide dehydrogenase (LADH, E3) is a component in the pyruvate-, alpha-ketoglutarate-and branched-chain ketoacid dehydrogenase complexes and in the glycine cleavage system. The pathogenic mutations of LADH cause severe metabolic disturbances, called E3 deficiency that often involve cardiological and neurological symptoms and premature death. Our laboratory has recently shown that some of the known pathogenic mutations augment the reactive oxygen species (ROS) generation capacity of LADH, which may contribute to the clinical presentations. A recent report concluded that elevated oxidative stress generated by the above mutants turns the lipoic acid cofactor on the E2 subunits dysfunctional. In the present contribution we generated by molecular dynamics (MD) simulation the conformation of LADH that is proposed to be compatible with ROS generation. We propose here for the first time the structural changes, which are likely to turn the physiological LADH conformation to its ROS-generating conformation. We also created nine of the pathogenic mutants of the ROS-generating conformation and again used MD simulation to detect structural changes that the mutations induced in this LADH conformation. We propose the structural changes that may lead to the modulation in ROS generation of LADH by the pathogenic mutations.

Protein Redox Modification as a Cellular Defense Mechanism against Tissue Ischemic Injury

“…It has been established that mitochondrial complexes I and III are the major two sites for mitochondrial ROS production [57, 58]. Other enzyme systems in mitochondria that can generate ROS include complex II [60], α -keto acid dehydrogenase complexes that contain dihydrolipoamide dehydrogenase [61–65]. Outside mitochondria, NADPH oxidase [66, 67], xanthine oxidase [68, 69], and cytochrome P-450 enzymes [70] can also generate ROS.…”

Pyruvate dehydrogenase complex and nicotinamide nucleotide transhydrogenase constitute an energy-consuming redox circuit

“…accelerate O 2 • − /H 2 O 2 production [5]. More recently, a number of other mitochondrial enzymes have been identified as sources of oxidant production, including succinate dehydrogenase (complex II; [6]), the electron-transferring flavoprotein/ETF:ubiquinone oxidoreductase [7, 8], glycerol-3-phosphate dehydrogenase [9], dihydroorotate dehydrogenase [9], and the matrix dehydrogenase enzyme complexes α-ketoglutarate dehydrogenase (αKGDH), branched-chain keto-dehydrogenase (BCKDH), and pyruvate dehydrogenase (PDH) [10-15]. The latter three enzyme complexes, all 2-oxoacid dehydrogenases with similar structures and catalytic mechanisms, are particularly intriguing given each occupy a pivotal position in metabolism.…”

The 2-Oxoacid Dehydrogenase Complexes in Mitochondria Can Produce Superoxide/Hydrogen Peroxide at Much Higher Rates Than Complex I

“…, branched-chain 2-oxoacid dehydrogenase (BCKDH) complex (22), and pyruvate dehydrogenase (PDH) complex (20,23). Proline dehydrogenase has also been implicated (24).…”