Carlson M L, Regan R M, Gibson Q H
Department of Biochemistry and Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, USA.
Biochemistry. 1996 Jan 30;35(4):1125-36. doi: 10.1021/bi951767k.
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 (G8) 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 A to accommodate the presence of a mobile diatomic ligand, suggesting a mechanism for communication between the heme site and the exterior of the protein.
实验表明，肌红蛋白中的远端突变会显著影响快速相和慢速相对闪光光解后一氧化氮皮秒级双分子复合反应的贡献。早期对远端口袋突变体中配体扩散的模拟显示，配体与血红素铁之间的碰撞速率差异很大，这表明远端残基通过控制配体与铁的接触来影响复合反应[吉布森，Q. H.，里根，R.，埃尔伯，R.，奥尔森，J. S.，&卡弗，T.（1992）《生物化学杂志》267，22022 - 22034]。在这项工作中，对抹香鲸肌红蛋白以及68位（E11）和107位（G8）的突变进行了分子动力学模拟，以研究控制配体扩散和铁可及性的结构机制。对远端配体可及空间的可视化显示出一种腔的模式（其他血红蛋白和肌红蛋白也有），这些腔由于蛋白质运动而波动并相互连接。在天然结构中，铁原子的可及性对这些波动高度敏感，这可能是远端残基高度保守的一个原因。监测远端血红素位点周围螺旋的位置，以评估更集体的蛋白质运动在配体扩散中的作用。配体的迁移以及与铁的碰撞似乎与由于螺旋运动导致的远端蛋白质基质的扩张有关。远端位点周围的螺旋也会进行约0.5埃量级的相对调整，以适应可移动双原子配体的存在，这表明了血红素位点与蛋白质外部之间的一种通讯机制。
