Department of Chemistry, University of Basel, Basel, Switzerland.
J Am Chem Soc. 2010 Mar 10;132(9):2968-82. doi: 10.1021/ja9078144.
NO dioxygenation, i.e., the oxidation of nitric oxide to nitrate by oxygen-bound truncated hemoglobin (trHbN) is studied using reactive molecular dynamics simulations. This reaction is an important step in a sequence of events in the overall NO detoxification reaction involving trHbN. The simulations ( approximately 160 ns in total) reveal that the reaction favors a pathway including (i) NO binding to oxy-trHbN, followed by (ii) rearrangement of peroxynitrite-trHbN to nitrato-trHbN, and finally (iii) nitrate dissociation from nitrato-trHbN. Overall, the reactions occur within tens of picoseconds and the crossing seam of the reactant and product are found to be broad. The more conventional pathway, where the peroxynitrite-trHbN complex undergoes peroxide cleavage to form free NO(2) and oxo-ferryl trHbN, is found to be too slow due to a considerable barrier involved in peroxide bond dissociation. The energetics of this step is consistent with earlier electronic structure calculations and make this pathway less likely. The role of Tyr33 and Gln58 in the NO dioxygenation has been investigated by studying the reaction in mutants of trHbN. The mutation study suggests that residues Tyr33 and Gln58 preorient the reactive ligands through a highly dynamical H-bonding network which facilitates the reaction. In particular, the Y33A mutation leads to a significant retardation in NO dioxygenation, in agreement with experiments which reveal a strong influence of the protein environment on the reaction rate.
本文使用反应分子动力学模拟研究了无氧气化作用，即氧结合截断血红蛋白（trHbN）将一氧化氮氧化为硝酸盐的反应。该反应是涉及 trHbN 的整体 NO 解毒反应序列中的重要步骤。模拟（总计约 160 ns）表明，该反应有利于包括（i）NO 与氧-trHbN 结合，随后（ii）过氧亚硝酸盐-trHbN 重排为硝酰基-trHbN，最后（iii）硝酰基-trHbN 从硝酸盐中解离的途径。总体而言，反应发生在数十皮秒内，并且反应物和产物的交叉缝被发现很宽。由于过氧化物键解离涉及相当大的势垒，因此发现过氧亚硝酸盐-trHbN 复合物经历过氧化物裂解以形成游离的 NO(2)和氧代铁基 trHbN 的更传统途径过于缓慢。这一步的能量学与早期的电子结构计算一致，使得这种途径不太可能。通过研究 trHbN 的突变体，研究了 Tyr33 和 Gln58 在 NO 双氧化中的作用。突变研究表明，残基 Tyr33 和 Gln58 通过高度动态的氢键网络预先定向反应配体，从而促进了反应。特别是，Y33A 突变导致 NO 双氧化明显延迟，这与实验结果一致，实验结果表明蛋白质环境对反应速率有强烈影响。
