Direct observation of ligand migration within human hemoglobin at work
Direct observation of ligand migration within human hemoglobin at work
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工作时直接观察人血红蛋白内的配体迁移
DOI：
10.1073/pnas.1913663117
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Park Sam-Yong
中科院分区：
文献类型：
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作者：
Shibayama Naoya;Sato-Tomita Ayana;Ohki Mio;Ichiyanagi Kouhei;Park Sam-Yong
血红蛋白是结构和功能方面最具特征的蛋白质之一，但内部配体扩散途径仍然不清楚和有争议。本研究利用高重复脉冲激光技术，在低温条件下，通过晶体学技术捕捉到了人血红蛋白紧态(T)、松弛态(R)和第二松弛态（R2）四元结构中的CO迁移过程。我们发现，在每个四元结构中，光解CO分子沿着α和β亚基的不同路径迁移，通过在内部空腔之间跳跃，并伴有大型非极性残基(如α 14trp (A12), α 105leu (G12), β 15trp （A12）和β 71phe （E15）的相关侧链运动。我们还观察到远端组氨酸[α58/β 63his (E7)]与四元结构无关的电子密度证据，尽管在α亚基中不如在β亚基中明显，这表明一些CO分子直接通过E7门逃逸。值得注意的是，在t态Fe(II)-Ni（II）杂交血红蛋白中，无论是α亚基还是β亚基都含有不能结合CO的Ni（II）血红素，光解的CO分子不仅停靠在原Fe（II）亚基的空腔上，而且即使在95 K时也能从蛋白质基质中逸出并进入相邻Ni（II）亚基的空腔，显示出血红蛋白分子的高透气性和孔隙性。我们的研究结果提供了血红蛋白中配体运动的全面图景，并强调了空腔、非极性残基和远端组氨酸在促进配体迁移中的相关性。
Hemoglobin is one of the best-characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here we captured the CO migration processes in the tense (T), relaxed (R), and second relaxed (R2) quaternary structures of human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatures. We found that in each quaternary structure, the photodissociated CO molecules migrate along distinct pathways in the α and β subunits by hopping between the internal cavities with correlated side chain motions of large nonpolar residues, such as α14Trp(A12), α105Leu(G12), β15Trp(A12), and β71Phe(E15). We also observe electron density evidence for the distal histidine [α58/β63His(E7)] swing-out motion regardless of the quaternary structure, although less evident in α subunits than in β subunits, suggesting that some CO molecules have escaped directly through the E7 gate. Remarkably, in T-state Fe(II)-Ni(II) hybrid hemoglobins in which either the α or β subunits contain Ni(II) heme that cannot bind CO, the photodissociated CO molecules not only dock at the cavities in the original Fe(II) subunit, but also escape from the protein matrix and enter the cavities in the adjacent Ni(II) subunit even at 95 K, demonstrating the high gas permeability and porosity of the hemoglobin molecule. Our results provide a comprehensive picture of ligand movements in hemoglobin and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.