The influence of oxygen on radiation-induced structural and functional changes in glyceraldehyde-3-phosphate dehydrogenase and lactate dehydrogenase

Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli

Recent work has begun to investigate the role of protein damage in cell death because of ionizing radiation (IR) exposure, but none have been performed on a proteome-wide basis, nor have they utilized MS (MS) to determine chemical identity of the amino acid side chain alteration. Here, we use Escherichia coli to perform the first MS analysis of IR-treated intact cells on a proteome scale. From quintuplicate IR-treated (1000 Gy) and untreated replicates, we successfully quantified 13,262 peptides mapping to 1938 unique proteins. Statistically significant, but low in magnitude (<2-fold), IR-induced changes in peptide abundance were observed in 12% of all peptides detected, although oxidative alterations were rare. Hydroxylation (+15.99 Da) was the most prevalent covalent adduct detected. In parallel with these studies on E. coli, identical experiments with the IR-resistant bacterium, Deinococcus radiodurans, revealed orders of magnitude less effect of IR on the proteome. In E. coli, the most significant target of IR by a wide margin was glyceraldehyde 3'-phosphate dehydrogenase (GAPDH), in which the thiol side chain of the catalytic Cys residue was oxidized to sulfonic acid. The same modification was detected in IR-treated human breast carcinoma cells. Sensitivity of GAPDH to reactive oxygen species (ROS) has been described previously in microbes and here, we present GAPDH as an immediate, primary target of IR-induced oxidation across all domains of life.

Substrate Channeling via a Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase

Substrate channeling studies have frequently failed to provide conclusive results due to poor understanding of this subtle phenomenon. We analyzed the mechanism of NADH-channeling from D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to L-lactate Dehydrogenase (LDH) using enzymes from different cells. Enzyme kinetics studies showed that LDH activity with free NADH and GAPDH-NADH complex always take place in parallel. The channeling is observed only in assays that mimic cytosolic conditions where free NADH concentration is negligible and the GAPDH-NADH complex is dominant. Molecular dynamics and protein-protein interaction studies showed that LDH and GAPDH can form a leaky channeling complex only at the limiting NADH concentrations. Surface calculations showed that positive electric field between the NAD(H) binding sites on LDH and GAPDH tetramers can merge in the LDH-GAPDH complex. NAD(H)-channeling within the LDH-GAPDH complex can be an extension of NAD(H)-channeling within each tetramer. In the case of a transient LDH-(GAPDH-NADH) complex, the relative contribution from the channeled and the diffusive paths depends on the overlap between the off-rates for the LDH-(GAPDH-NADH) complex and the GAPDH-NADH complex. Molecular evolution or metabolic engineering protocols can exploit substrate channeling for metabolic flux control by fine-tuning substrate-binding affinity for the key enzymes in the competing reaction paths.

Comparison of protective properties of resveratrol and melatonin in the radiation inactivation and destruction of glyceraldehyde-3-phosphate dehydrogenase and lactate dehydrogenase

Purpose: This work investigates the effect of resveratrol and melatonin on structural and functional changes of two enzymes, lactate dehydrogenase (LDH) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), exposed to radiation-induced reactive oxygen species.Materials and methods: Solutions of dehydrogenases with or without antioxidants (resveratrol or melatonin) were irradiated with X-rays under the atmosphere of air and at room temperature (21 ± 2 °C). In order to determine the protective effect of melatonin and resveratrol in radiation-induced damage to GAPDH and LDH spectroscopy and HPLC methods were used. Furthermore, plausible binding sites of melatonin or resveratrol to the GAPDH or LDH molecule were analysed.Results and conclusions: Resveratrol shows better protective properties in the inactivation of GAPDH when compared to melatonin. LDH does not contain ‒SH groups in its active site, and is not inactivated by water radiolysis products other than hydroxyl radicals or the secondary radicals of the studied low-molecular-weight compounds. Resveratrol and melatonin protected the structure of LDH to a greater extent than GAPDH. This difference can be attributed to the fact that LDH potentially binds more resveratrol or melatonin molecules (27 binding sites for resveratrol and 40 for melatonin) than GAPDH (10 binding sites for resveratrol and 18 for melatonin).