Exploring the Conformational Transition Between the Fully Folded and Locally Unfolded Substates of the Escherichia coli thiol peroxidase

Thiol peroxidase from Escherichia coli (EcTPx) is a peroxiredoxin that catalyzes the reduction of different hydroperoxides. During the catalytic cycle of EcTPx, the peroxidatic cysteine (C-P) is oxidized to a sulfenic acid by peroxide, then the resolving cysteine (C-R) condenses with the sulfenic acid of C-P to form a disulfide bond, which is finally reduced by thioredoxin. Purified EcTPx as dithiol and disulfide behaves as a monomer under near physiological conditions. Although secondary structure rearrangements are present when comparing different redox states of the enzyme, no significant differences in unfolding free energies are observed under reducing and oxidizing conditions. A conformational change denominated fully folded (FF) to locally unfolded (LU) transition, involving a partial unfolding of alpha H2 and alpha H3, must occur to enable the formation of the disulfide bond since the catalytic cysteines are 12 angstrom apart in the FF conformation of EcTPx. To explore this process, the FF -> LU and LU -> FF transitions were studied using conventional molecular dynamics simulations and an enhanced conformational sampling technique for different oxidation and protonation states of the active site cysteine residues C-P and C-R. Our results suggest that the FF -> LU transition has a higher associated energy barrier than the refolding LU -> FF process in agreement with the relatively low experimental turnover number of EcTPx. Furthermore, in silico designed single-point mutants of alpha H3 enhanced locally unfolding events, suggesting that the native FF interactions in the active site are not evolutionarily optimized to fully speed-up the conformational transition of wild-type EcTPx.