Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations

Despite its importance
in the nucleoside (and nucleoside prodrug)
metabolism, the structure of the active conformation of human thymidine
kinase 1 (hTK1) remains elusive. We perform microsecond molecular
dynamics simulations of the inactive enzyme form bound to a bisubstrate
inhibitor that was shown experimentally to activate another TK1-like
kinase, Thermotoga maritima TK (TmTK). Our results are in excellent agreement with the experimental
findings for the TmTK closed-to-open state transition.
We show that the inhibitor induces an increase of the enzyme radius
of gyration due to the expansion on one of the dimer interfaces; the
structural changes observed, including the active site pocket volume
increase and the decrease in the monomer–monomer buried surface
area and of the number of hydrogen bonds (as compared to the inactive
enzyme control simulation), indicate that the catalytically competent
(open) conformation of hTK1 can be assumed in the presence of an activating
ligand.

人类胸苷激酶1（human thymidine kinase 1，hTK1）在核苷（及核苷前药）代谢中发挥着关键作用，但其活性构象的结构仍未得到解析。本研究针对结合双底物抑制剂的非活性酶形式开展了微秒级分子动力学模拟；该抑制剂经实验证实可激活另一类TK1样激酶——海栖热袍菌胸苷激酶（Thermotoga maritima TK，TmTK）。本研究结果与海栖热袍菌胸苷激酶闭合至开放构象转变的实验发现高度吻合。研究表明，该抑制剂通过诱导二聚体界面之一的扩张，使酶的回转半径增大；与非活性酶对照模拟相比，观测到的结构变化包括活性位点口袋体积增大、单体间掩埋表面积减少以及氢键数量下降，这些结果提示，在激活配体存在的条件下，人类胸苷激酶1可形成具有催化活性的开放构象。