Zuiderweg Erik R P, Case David A, Williams Charles H
Department of Biological Chemistry, The University of Michigan Medical School, Ann Arbor, Michigan 48109, United States.
Institute for Molecules and Materials, Faculty of Science, Radboud University, Nijmegen, XZ 6525, The Netherlands.
ACS Omega. 2024 Jun 25;9(27):29682-29690. doi: 10.1021/acsomega.4c01382. eCollection 2024 Jul 9.
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.
硫氧还蛋白还原酶（TrxR）是大多数细胞中一种重要的抗氧化剂；它利用烟酰胺腺嘌呤二核苷酸磷酸（NADPH）还原硫氧还蛋白（Trx）和其他几种底物。然而，该酶的内部活性位点太小，无法容纳Trx底物。因此，TrxR进化出了一种二硫键穿梭机制，该机制可以将还原当量从活性位点传递到酶表面硫氧还蛋白的对接位点。然而，在TrxR所有可用的原子结构中，穿梭机制对活性位点的访问在空间上受到阻碍。我们通过计算动力学发现，37℃的热运动使氧化型穿梭体x能够短暂地进入活性位点。一旦穿梭体被还原，它就会变成极性的。同样，通过分子动力学，我们表明极性穿梭体将向外移动至溶液界面，而氧化型中性穿梭体则不会。这项工作为迄今为止只是推测的酶作用机制中的关键步骤提供了物理证据。穿梭体从活性位点向表面的总移动距离超过20埃。因此，TrxR也可被称为分子机器。
