Probing the ligand recognition and discrimination environment of the globin-coupled oxygen sensor protein YddV by FTIR and time-resolved step-scan FTIR spectroscopy
Probing the ligand recognition and discrimination environment of the globin-coupled oxygen sensor protein YddV by FTIR and time-resolved step-scan FTIR spectroscopy
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通过 FTIR 和时间分辨步进扫描 FTIR 光谱探测球蛋白偶联氧传感器蛋白 YddV 的配体识别和辨别环境
DOI：
10.1039/c5cp01708d
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
Eftychia Pinakoulaki
中科院分区：
文献类型：
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作者：
Andrea Pavlou;Marketa Martinkova;Toru Shimizu;Kenichi Kitanishi;Martin Stranava;Eftychia Pinakoulaki
YddV是一种新发现的能识别O2和CO的信号转导血红素蛋白，其配体结合血红素复合物的结构差异反映了O2和CO对血红素复合物催化调节的差异。进行Y43F和Y43W突变体以确定一氧化碳（CO）光解离后的位点特异性蛋白质动力学。这些突变的目的是扰乱附近的铁结合的气体配体（CO）的静电场，也让我们调查的蛋白质和血红素的远端残基之间的通信途径。红外光谱分析表明，血红素丙酸酯分子处于质子化和去质子化状态。此外，酰胺I的振动的衰减速率在时间尺度上与CO的再结合速率一致，这表明远端血红素环境中的连接动力学与（i）蛋白质骨架的松弛和（ii）血红素丙酸酯感测的环境之间存在耦合。在L65 M、L65 T和Y43 W中的快速重组速率暗示了L65和Y43在控制配体动力学中的重要作用。这些结果的影响，相对于血红素丙酸酯和带电或质子捐赠残基的远端口袋中，这是至关重要的稳定结合的气体配体的作用，进行了讨论。
YddV is a newly discovered signal transducer heme protein that recognizes O2 and CO. Structural differences in the ligand-bound heme complex in YddV reflect variations in catalytic regulation by O2 and CO. Time-resolved step-scan (TRS2) FTIR studies of the wild type and of the important in oxygen recognition and stability of the heme Fe(II)–O2 complex L65M, L65T, Y43A, Y43F and Y43W mutants were performed to determine the site-specific protein dynamics following carbon monoxide (CO) photodissociation. These mutations were designed to perturb the electrostatic field near the iron-bound gaseous ligand (CO) and also to allow us to investigate the communication pathway between the distal residues of the protein and heme. TRS2-FTIR spectra of YddV–heme–CO show that the heme propionates are in protonated and deprotonated states. Moreover, the rate of decay of the vibrations of amide I is on a time scale that coincides with the rate of rebinding of CO, which suggests that there is coupling between ligation dynamics in the distal heme environment and (i) relaxation of the protein backbone and (ii) the environment sensed by the heme propionates. The fast recombination rates in L65M, L65T and Y43W imply a significant role of L65 and Y43 in controlling the ligand dynamics. The implications of these results with respect to the role of the heme propionates and the charged or proton-donating residues in the distal pocket, which are crucial for stabilizing bound gaseous ligands, are discussed.