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首页> 外文期刊>Biochemistry >DISTAL CAVITY FLUCTUATIONS IN MYOGLOBIN - PROTEIN MOTION AND LIGAND DIFFUSION
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DISTAL CAVITY FLUCTUATIONS IN MYOGLOBIN - PROTEIN MOTION AND LIGAND DIFFUSION

机译：肌球蛋白的远腔波动-蛋白质运动和配体扩散。

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Experimentally, distal mutations in myoglobin substantially affect the contribution of fast and slow phases to picosecond geminate recombination of NO following flash photolysis. Earlier simulations of ligand diffusion among distal pocket mutants showed greatly differing rates of collisions between the ligands and the heme iron, suggesting that distal residues affect recombination by controlling ligand access to the iron [Gibson, Q. H., Regan, R., Elber, R., Olson, J. S., & Carver, T. (1992) J. Biol. Chem. 267, 22022-22034). In this work, molecular dynamics simulations of sperm whale myoglobin and mutations at positions 68 (E11) and 107 (GX) have been examined to investigate the structural mechanism that controls ligand diffusion and iron accessibility. Visualization of the distal ligand-accessible spaces shows a pattern of cavities (common to other hemoglobins and myoglobins) that fluctuate and interconnect due to protein motions. Access to the iron atom is highly sensitive to these fluctuations in the native structure, perhaps a reason for the strong conservation of distal residues. The positions of the helices surrounding the distal heme site were monitored to assess the involvement of more collective protein motions in ligand diffusion. Ligand migrations and collisions with the iron appear related to expansion of the distal protein matrix due to helix movements. The helices surrounding the distal site also make relative adjustments on the order of 0.5 Angstrom to accommodate the presence of a mobile diatomic ligand, suggesting a mechanism for communication between the heme site and the exterior of the protein.
机译：实验上，肌红蛋白的远侧突变实质上影响了快相和慢相对瞬态光解后皮秒皮秒NO重组的贡献。远端口袋突变体之间配体扩散的早期模拟显示，配体与血红素铁之间的碰撞率差异很大，这表明远端残基通过控制配体接近铁而影响重组[Gibson，QH，Regan，R.，Elber，R. ，Olson，JS，＆Carver，T。（1992）J.Biol.Chem.Soc。，1992。化学267，22022-22034）。在这项工作中，已经检查了抹香鲸肌红蛋白及其位置68（E11）和107（GX）处的突变的分子动力学模拟，以研究控制配体扩散和铁可及性的结构机理。远端配体可及空间的可视化显示了由于蛋白质运动而波动和相互连接的空腔（与其他血红蛋白和肌球蛋白常见）的模式。接近铁原子对天然结构中的这些波动高度敏感，这可能是远端残基强烈保留的原因。监测围绕远端血红素位点的螺旋的位置，以评估配体扩散中更多集体蛋白运动的参与。由于螺旋运动，配体的迁移和与铁的碰撞与远端蛋白质基质的膨胀有关。围绕远端位点的螺旋也进行了约0.5埃的相对调节，以适应可移动的双原子配体的存在，这暗示了血红素位点与蛋白质外部之间连通的机制。

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