Gibson Q H, Regan R, Elber R, Olson J S, Carver T E
Department of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853.
J Biol Chem. 1992 Nov 5;267(31):22022-34.
Time courses for intramolecular NO and O2 recombination to native and three position 29 mutants of sperm whale myoglobins were measured after laser photolysis on picosecond and nanosecond time scales. The rates for the first phase of NO recombination were 1.8, 2.5, 29, and > or = 100 ns-1 for Ala29, Val29, Leu29 (native), and Phe29 myoglobin, respectively, at room temperature. This order is not correlated with the overall association rate constants for NO binding which were all in the range 20-50 x 10(6) M-1 s-1 and is the opposite of that observed for the rate constants for the overall thermal dissociation of NO which were 5.0, 2.8, 0.98, and 0.21 x 10(-4) s-1 for Ala29, Val29, Leu29 (native), and Phe29 myoglobin, respectively, at 20 degrees C. This inverse correlation suggests that photo- and thermally dissociated ligand molecules experience similar kinetic and equilibrium barriers to rebinding. The larger side chains of Leu29 and Phe29 inhibit rapid movement of the ligand away from the iron atom facilitating geminate recombination. The smaller side chains of Val29 and Ala29 increase the space available to the ligand, decreasing the rate of geminate recombination and enhancing complete dissociation. Diffusion of NO in the distal pocket of myoglobin was simulated using a variant of the molecular dynamics program CHARMM that includes the locally enhanced sampling protocol (Elber, R., and Karplus, M. (1991) J. Am. Chem. Soc. 112, 9161-9175; Roitberg, A., and Elber, R. (1991) J. Chem. Phys. 95, 9277-9287) and the x-ray structures of Carver et al. (Carver, T. E., Brantley, R. E., Jr., Singleton, E. W., Arduini, R. M., Quillin, M. L., Phillips, G. N., Jr., and Olson, J. S. (1992) J. Biol. Chem. 267, 14443-14450). Both accelerated (5,000 K) and room temperature ligands were used, and comparisons were made between simulations with a complete hydration shell surrounding the protein and those with only eight water molecules near the distal histidine. Photodissociated ligands initially move away from the heme plane, past Leu29, and toward Leu32, Phe33, Ile107, and Ile111. These theoretical results confirm that a complete description of picosecond ligand recombination must include the dynamics of ligand movement in the distal portion of the heme pocket.
在皮秒和纳秒时间尺度上进行激光光解后，测定了抹香鲸肌红蛋白天然型及其29位三个突变体分子内一氧化氮（NO）与氧气重组的时间进程。在室温下，Ala29、Val29、Leu29（天然型）和Phe29肌红蛋白的NO重组第一阶段速率分别为1.8、2.5、29和≥100 ns⁻¹。该顺序与NO结合的整体缔合速率常数无关，其均在20 - 50×10⁶ M⁻¹ s⁻¹范围内，且与20℃时Ala29、Val29、Leu29（天然型）和Phe29肌红蛋白的NO整体热解离速率常数顺序相反，后者分别为5.0、2.8、0.98和0.21×10⁻⁴ s⁻¹。这种反相关表明光解离和热解离的配体分子在重新结合时经历相似的动力学和平衡障碍。Leu29和Phe29较大的侧链抑制了配体从铁原子快速移开，促进了双分子复合。Val29和Ala29较小的侧链增加了配体可利用的空间，降低了双分子复合速率并增强了完全解离。使用分子动力学程序CHARMM的一个变体模拟了NO在肌红蛋白远端口袋中的扩散，该变体包括局部增强采样协议（Elber, R., and Karplus, M. (1991) J. Am. Chem. Soc. 112, 9161 - 9175; Roitberg, A., and Elber, R. (1991) J. Chem. Phys. 95, 9277 - 9287）以及Carver等人的X射线结构（Carver, T. E., Brantley, R. E., Jr., Singleton, E. W., Arduini, R. M., Quillin, M. L., Phillips, G. N., Jr., and Olson, J. S. (1992) J. Biol. Chem. 267, 14443 - 14450）。使用了加速（5000 K）和室温配体，并对蛋白质周围有完整水合壳的模拟与远端组氨酸附近只有八个水分子的模拟进行了比较。光解离的配体最初从血红素平面移开，经过Leu29，并朝着Leu32、Phe33、Ile107和Ile111移动。这些理论结果证实，对皮秒级配体重组的完整描述必须包括配体在血红素口袋远端部分移动的动力学。
