Srivastava Ashutosh, Hirota Tsuyoshi, Irle Stephan, Tama Florence
Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.
PRESTO, JST, Nagoya, Japan.
Proteins. 2018 Mar;86(3):344-353. doi: 10.1002/prot.25444. Epub 2017 Dec 25.
Protein kinase, casein kinase II (CK2), is ubiquitously expressed and highly conserved protein kinase that shows constitutive activity. It phosphorylates a diverse set of proteins and plays crucial role in several cellular processes. The catalytic subunit of this enzyme (CK2α) shows remarkable flexibility as evidenced in numerous crystal structures determined till now. Here, using analysis of multiple crystal structures and long timescale molecular dynamics simulations, we explore the conformational flexibility of CK2α. The enzyme shows considerably higher flexibility in the solution as compared to that observed in crystal structure ensemble. Multiple conformations of hinge region, located near the active site, were observed during the dynamics. We further observed that among these multiple conformations, the most populated conformational state was inadequately represented in the crystal structure ensemble. The catalytic spine, was found to be less dismantled in this state as compared to the "open" hinge/αD state crystal structures. The comparison of dynamics in unbound (Apo) state and inhibitor (CX4945) bound state exhibits inhibitor induced suppression in the overall dynamics of the enzyme. This is especially true for functionally important glycine-rich loop above the active site. Together, this work gives novel insights into the dynamics of CK2α in solution and relates it to the function. This work also explains the effect of inhibitor on the dynamics of CK2α and paves way for development of better inhibitors.
蛋白激酶，酪蛋白激酶II（CK2），是一种广泛表达且高度保守的具有组成型活性的蛋白激酶。它能使多种蛋白质磷酸化，并在多个细胞过程中发挥关键作用。该酶的催化亚基（CK2α）表现出显著的灵活性，这在迄今为止确定的众多晶体结构中得到了证明。在这里，我们通过对多个晶体结构的分析和长时间尺度的分子动力学模拟，探索了CK2α的构象灵活性。与晶体结构集合中观察到的情况相比，该酶在溶液中表现出更高的灵活性。在动力学过程中，观察到活性位点附近的铰链区存在多种构象。我们进一步观察到，在这些多种构象中，晶体结构集合中最丰富的构象状态没有得到充分体现。与“开放”的铰链/αD状态晶体结构相比，发现催化脊柱在这种状态下拆解程度较小。未结合（无配体）状态和抑制剂（CX4945）结合状态下的动力学比较表明，抑制剂会抑制该酶的整体动力学。对于活性位点上方功能重要的富含甘氨酸的环来说尤其如此。总之，这项工作为CK2α在溶液中的动力学提供了新的见解，并将其与功能联系起来。这项工作还解释了抑制剂对CK2α动力学的影响，为开发更好的抑制剂铺平了道路。
