Structural and dynamic properties of the homodimeric hemoglobin from Scapharca inaequivalvis Thr-72-->Ile mutant: molecular dynamics simulation, low temperature visible absorption spectroscopy, and resonance Raman spectroscopy studies.
Structural and dynamic properties of the homodimeric hemoglobin from Scapharca inaequivalvis Thr-72-->Ile mutant: molecular dynamics simulation, low temperature visible absorption spectroscopy, and resonance Raman spectroscopy studies.
复制标题
来自 Scapharca inaequivalvis Thr-72-->Ile 突变体的同二聚血红蛋白的结构和动态特性：分子动力学模拟、低温可见吸收光谱和共振拉曼光谱研究。
DOI：
10.1016/s0006-3495(98)77693-3
复制
发表时间：
1998
影响因子：
3.4
通讯作者：
Ascoli,F
中科院分区：
文献类型：
--
作者：
Falconi,M;Desideri,A;Cupane,A;Leone,M;Ciccotti,G;Peterson,ES;Friedman,JM;Gambacurta,A;Ascoli,F
用分子动力学模拟、低温可见光吸收光谱和共振拉曼光谱对Scapharca等同二聚体血红蛋白突变体进行了分子动力学模拟，其中亚基界面的苏氨酸72被异亮氨酸取代。分子动力学模拟表明，在Thr-72→Ile突变体中，几个已被证明在配体结合中起作用的残基在方向和距离上波动，与天然血红蛋白CO衍生物的X射线结构中观察到的相似，尽管总体结构保持在T态。可见吸收光谱数据表明，在脱氧形式中，突变体的Soret带比天然蛋白中的Soret带不对称，这意味着更平坦的血红素结构；此外，这些数据表明，突变蛋白在连接和未连接状态下都有类似的血红素-溶剂相互作用，与天然蛋白中观察到的不同。脱氧突变体蛋白的构象敏感带III相对于天然蛋白移动了100 cm−1，约为两种蛋白低温光产物中观察到的能量的一半，表明血红素环境的极性较低或疏水性较强。共振拉曼光谱数据显示，相对于天然蛋白，脱氧突变体的铁近端组氨酸伸展模式略有偏移，这可以解释为Phe-97的苯环堆积的变化，也可以从模拟中观察到，或者是血红素口袋中的水分丢失。根据后一种解释，通过分子动力学模拟计算的动态进入亚基间界面的水分子的数量在突变体中低于天然蛋白质中。与天然蛋白质相比，一氧化碳突变体衍生物的10 ns光产物具有更高的铁近端组氨酸伸展频率。这表明在突变体中发生了亚纳秒的松弛，这与R结构的稳定一致。综上所述，分子动力学和光谱数据表明，Thr-72→Ile突变体显示出较高的氧亲和力，主要是由于二聚体界面上的局部扰动传播到血红素区域，扰乱了血红素环境的极性和丙酸相互作用。这些变化与突变体中T状态的不稳定和R状态相对于天然蛋白的稳定是一致的。
Molecular dynamics simulations, low temperature visible absorption spectroscopy, and resonance Raman spectroscopy have been performed on a mutant of theScapharca inaequivalvishomodimeric hemoglobin, where residue threonine 72, at the subunit interface, has been substituted by isoleucine. Molecular dynamics simulation indicates that in the Thr-72→Ile mutant several residues that have been shown to play a role in ligand binding fluctuate around orientations and distances similar to those observed in the x-ray structure of the CO derivative of the native hemoglobin, although the overall structure remains in the T state. Visible absorption spectroscopy data indicate that in the deoxy form the Soret band is less asymmetric in the mutant than in the native protein, suggesting a more planar heme structure; moreover, these data suggest a similar heme-solvent interaction in both the liganded and unliganded states of the mutant protein, at variance with that observed in the native protein. The "conformation sensitive" band III of the deoxy mutant protein is shifted to lower energy by >100cm−1with respect to the native one, about one-half of that observed in the low temperature photoproducts of both proteins, indicating a less polar or more hydrophobic heme environment. Resonance Raman spectroscopy data show a slight shift of the iron-proximal histidine stretching mode of the deoxy mutant toward lower frequency with respect to the native protein, which can be interpreted in terms of either a change in packing of the phenyl ring of Phe-97, as also observed from the simulation, or a loss of water in the heme pocket. In line with this latter interpretation, the number of water molecules that dynamically enters the intersubunit interface, as calculated by the molecular dynamics simulation, is lower in the mutant than in the native protein. The 10-ns photoproduct for the carbonmonoxy mutant derivative has a higher iron-proximal histidine stretching frequency than does the native protein. This suggests a subnanosecond relaxation that is slowed in the mutant, consistent with a stabilization of the R structure. Taken together, the molecular dynamics and the spectroscopic data indicate that the higher oxygen affinity displayed by the Thr-72→Ile mutant is mainly due to a local perturbation in the dimer interface that propagates to the heme region, perturbing the polarity of the heme environment and propionate interactions. These changes are consistent with a destabilization of the T state and a stabilization of the R state in the mutant relative to the native protein.