Facultad de Ciencias Químicas, Universidad de Salamanca, Plaza de los Caídos 1-5, Salamanca, E37004, Spain.
Org Biomol Chem. 2012 Mar 7;10(9):1905-13. doi: 10.1039/c2ob06717j. Epub 2012 Jan 25.
We recently reported crystallographic evidence that the hydrogen bonds which can stabilize oxygen-centered negative charge within enzyme oxyanion holes are rarely found in the place they should be expected on the basis of the analysis of small-molecule crystal structures. We investigated this phenomenon using calculations on simplified active site models. A recent paper suggested that several aspects of the analysis required further exploration. In this paper we: (i) review the results of our crystallographic study; (ii) report molecular dynamics studies which investigate the effect of protein movement; (iii) report ONIOM calculations which trace the reaction coordinate for an oxyanion hole reaction in the presence of a complete enzyme active site. These results show that the limitations of gas phase calculations on simplified models do not invalidate our comparison of competing active site geometries. These new results reaffirm the conclusion that oxyanion holes are not usually stabilized by planar arrangements of H-bonds, and that this sub-optimal transition state stabilization leads to better overall catalysis.
我们最近报道了晶体学证据，表明在酶氧阴离子穴中稳定氧中心负电荷的氢键很少出现在根据小分子晶体结构分析应该出现的位置。我们使用简化的活性位点模型的计算研究了这一现象。最近的一篇论文认为，分析的几个方面需要进一步探讨。在本文中，我们：（i）回顾我们晶体学研究的结果；（ii）报告研究蛋白质运动影响的分子动力学研究；（iii）报告在完整酶活性位点存在下追踪氧阴离子穴反应反应坐标的 ONIOM 计算。这些结果表明，简化模型的气相计算的局限性并没有使我们对竞争活性位点几何形状的比较无效。这些新结果再次证实了这样的结论，即氧阴离子穴通常不是通过氢键的平面排列来稳定的，这种次优过渡态稳定化导致更好的整体催化。
