Ma J G, Laberge M, Song X Z, Jentzen W, Jia S L, Zhang J, Vanderkooi J M, Shelnutt J A
Materials Theory and Computation Department, Sandia National Laboratories, Albuquerque, New Mexico 87185-1349, USA.
Biochemistry. 1998 Apr 14;37(15):5118-28. doi: 10.1021/bi972375b.
The influence of the protein on the nonplanarity of the macrocycle for nickel(II)-reconstituted cytochrome c (NiCyt-c) has been investigated with pH-dependent resonance Raman and UV-visible absorption spectroscopy and molecular mechanics calculations. The spectra reveal that NiCyt-c near neutral pH has axially coordinated Ni, but below pH 3 and above pH 12, four-coordinate species predominate. The shape of the structure-sensitive Raman line nu10 of NiCyt-c is asymmetric and broad and it changes with pH. This broad line can be decomposed well into at least two sublines, a low-frequency line that results from a nonplanar conformer and a high-frequency line that arises from a nearly planar conformer. Upon lowering the pH from 3.0 to 1.0, the amount of the nonplanar conformer decreases relative to that of the planar conformer. The decreased nonplanarity can be accounted for in terms of the disruption of a hydrogen-bonding network in the peptide backbone upon lowering the pH. Molecular mechanics (MM) calculations on iron(III) and nickel(II) microperoxidase 5 (MP-5) as well as some model heme derivatives have been carried out in order to locate the part of the protein that causes the heme distortion observed in the X-ray crystal structures of cytochromes c. The energy-optimized structures of MP-5 and the model compounds were analyzed using the normal-coordinate structural decomposition method to specify and quantify the out-of-plane macrocyclic distortions. MM calculations for MP-5 show that two hydrogen bonds formed between the amide groups in the peptide backbone are important in maintaining the ruffled deformation of the macrocycle. All evidence presented supports the hypothesis that the nonplanar distortion of the porphyrin of cytochromes c is largely maintained by a relatively small protein segment including the cysteines, the amino acids between the cysteines, and the adjacent histidine ligand. Hydrogen bonding within the backbone of this segment is important in maintaining the conformation of the peptide that induces the porphyrin distortion.
通过pH依赖的共振拉曼光谱和紫外可见吸收光谱以及分子力学计算，研究了蛋白质对镍（II）重构细胞色素c（NiCyt-c）大环非平面性的影响。光谱显示，接近中性pH值的NiCyt-c具有轴向配位的镍，但在pH值低于3和高于12时，四配位物种占主导。NiCyt-c的结构敏感拉曼线ν10的形状不对称且较宽，并且随pH值变化。这条宽线可以很好地分解为至少两条子线，一条低频线由非平面构象异构体产生，一条高频线由近乎平面的构象异构体产生。将pH值从3.0降至1.0时，非平面构象异构体的量相对于平面构象异构体减少。非平面性降低可归因于pH值降低时肽主链中氢键网络的破坏。对铁（III）和镍（II）微过氧化物酶5（MP-5）以及一些模型血红素衍生物进行了分子力学（MM）计算，以确定在细胞色素c的X射线晶体结构中导致血红素扭曲的蛋白质部分。使用正规坐标结构分解方法分析了MP-5和模型化合物的能量优化结构，以指定和量化平面外大环畸变。MP-5的MM计算表明，肽主链中的酰胺基团之间形成的两个氢键对于维持大环的褶皱变形很重要。所提供的所有证据都支持这样的假设，即细胞色素c卟啉的非平面畸变在很大程度上由一个相对较小的蛋白质片段维持，该片段包括半胱氨酸、半胱氨酸之间的氨基酸以及相邻的组氨酸配体。该片段主链内的氢键对于维持诱导卟啉畸变的肽的构象很重要。
