Simulating the Motion Underlying the Mechanism of Thioredoxin Reductase.

ABSTRACT

Thioredoxin reductase (TrxR) is an essential antioxidant in most cells; it reduces thioredoxin (Trx) and several more substrates, utilizing NADPH. However, the enzyme's internal active site is too small to accommodate the Trx substrate. Thus, TrxR evolved a disulfide shuttle that can carry reducing equivalents from the active site to the docking site of thioredoxin on the enzyme surface. Yet, in all available atomic structures of TrxR, access to the active site by the shuttle is sterically blocked. We find with computational dynamics that thermal motion at 37 °C allows the oxidized shuttle x to transiently access the active site. Once the shuttle is reduced, it becomes polar. Again, with molecular dynamics, we show that the polar shuttle will move outward toward the solution interface, whereas the oxidized, neutral shuttle will not. This work provides physical evidence for crucial steps in the enzyme mechanism that thus far were just conjectures. The total shuttle motion, from the active site toward the surface, is over 20 Å. TrxR may thus also be termed a molecular machine.