Kondrashov Dmitry A, Montfort William R
Graduate Program in Applied Mathematics and Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA.
J Phys Chem B. 2007 Aug 9;111(31):9244-52. doi: 10.1021/jp071136n. Epub 2007 Jul 10.
Nitrophorin 4 (NP4) is a heme protein that reversibly binds nitric oxide (NO), with release rates modulated by pH change. High-resolution structures of NP4 revealed that pH changes and NO binding induce a large conformational rearrangement in two loops that serve to protect the heme-bound NO molecule from solvent. We used extended (110 ns) molecular dynamics simulations of NP4 at pH 5 and pH 7, modeled by selective deprotonation of acidic groups. Conformational and dynamic changes were observed, consistent with those found in the crystal. Further, major solvent movement and NO escape were observed at pH 7, while the ligand remained in the heme binding pocket at pH 5. As a control, we also performed molecular dynamics (MD) simulations of sperm whale myoglobin, where NO migration into the interior cavities of the protein was observed, consistent with previous reports. We constructed a kinetic model of ligand escape to quantitatively relate the microscopic rate constants to the observed rates, and tested the predictions against the experimental data. The results suggest that release rates of diatomic molecules from heme proteins can be varied by several orders of magnitude through modest adjustments in geminate rebinding and gating behavior.
嗜酸性粒细胞过氧化物酶4（NP4）是一种血红素蛋白，它可逆地结合一氧化氮（NO），其释放速率受pH变化调节。NP4的高分辨率结构表明，pH变化和NO结合会在两个环中引起大规模的构象重排，这两个环用于保护血红素结合的NO分子免受溶剂影响。我们通过对酸性基团进行选择性去质子化模拟，对pH 5和pH 7条件下的NP4进行了长达110纳秒的扩展分子动力学模拟。观察到了构象和动力学变化，与晶体中发现的一致。此外，在pH 7时观察到主要的溶剂移动和NO逸出，而在pH 5时配体仍保留在血红素结合口袋中。作为对照，我们还对抹香鲸肌红蛋白进行了分子动力学（MD）模拟，观察到NO迁移到蛋白质的内部空腔中，这与之前的报道一致。我们构建了一个配体逸出的动力学模型，以定量地将微观速率常数与观察到的速率联系起来，并根据实验数据检验预测结果。结果表明，通过适度调整双分子复合再结合和门控行为，血红素蛋白中双原子分子的释放速率可以变化几个数量级。
