Cordier F, Caffrey M, Brutscher B, Cusanovich M A, Marion D, Blackledge M
Institut de Biologie Structurale - Jean-Pierre Ebel C.N.R.S.-C.E.A., 41, Avenue des Martyrs, Grenoble Cedex, 38027, France.
J Mol Biol. 1998 Aug 14;281(2):341-61. doi: 10.1006/jmbi.1998.1950.
The solution structure, backbone dynamics and rotational diffusion of the Rhodobacter capsulatus cytochrome c2 have been determined using heteronuclear NMR spectroscopy. In all, 1204 NOE-derived distances were used in the structure calculation to give a final ensemble with 0.59(+/-0.08) A rms deviation for the backbone atoms (C, Calpha and N) with respect to the mean coordinates. There is no major difference between the solution structure and the previously solved X-ray crystal structure (1.07(+/-0.07) A rms difference for the backbone atoms), although certain significant local structural differences have been identified. This protein contains five helical regions and a histidine-heme binding domain, connected by a series of structured loops. The orientation of the helices provides an excellent sampling of angular space and thus allows a precise characterization of the anisotropic diffusion tensor. Analysis of the hydrodynamics of the protein has been performed by interpretation of the 15N relaxation data using isotropic, axially asymmetric and fully anisotropic diffusion tensors. The protein can be shown to exhibit significant anisotropic reorientation with a diffusion tensor with principal axes values of 1.405(+/-0.031)x10(7) s-1, 1.566(+/-0.051)x10(7) s-1 and 1.829(+/-0.054)x10(7) s-1. Hydrodynamic calculations performed on the solution structure predict values of 1.399x10(7) s-1, 1.500x10(7) s-1 and 1.863x10(7) s-1 when a solvent shell of 3.5 A is included in the calculation. The optimal orientation of the diffusion tensor has been incorporated into a hybrid Lipari-Szabo type local motion-anisotropic rotational diffusion model to characterize the local mobility in the molecule. The mobility parameters thus extracted show a quantitative improvement with respect to the model-free analysis assuming isotropic reorientation; helical regions exhibit similar dynamic properties and fewer residues require more complex models of internal motion. While the molecule is essentially rigid, a tripeptide loop region (residues 101 to 103) exhibits flexibility in the range of 20 to 30 ps, which appears to be correlated with the order in the NMR solution structure.
利用异核核磁共振光谱法测定了荚膜红细菌细胞色素c2的溶液结构、主链动力学和旋转扩散。在结构计算中总共使用了1204个由核Overhauser效应（NOE）得出的距离，以使最终集合中主链原子（C、Cα和N）相对于平均坐标的均方根偏差为0.59（±0.08）Å。溶液结构与先前解析的X射线晶体结构之间没有重大差异（主链原子的均方根差异为1.07（±0.07）Å），尽管已发现某些显著的局部结构差异。该蛋白质包含五个螺旋区域和一个组氨酸 - 血红素结合结构域，由一系列结构化环连接。螺旋的取向提供了对角空间的出色采样，从而允许对各向异性扩散张量进行精确表征。通过使用各向同性、轴向不对称和完全各向异性扩散张量对15N弛豫数据进行解释，对该蛋白质的流体动力学进行了分析。该蛋白质可以显示出具有显著的各向异性重取向，其扩散张量的主轴值为1.405（±0.031）×10^7 s^-1、1.566（±0.051）×10^7 s^-1和1.829（±0.054）×10^7 s^-1。对溶液结构进行的流体动力学计算预测，当在计算中包含3.5 Å的溶剂壳时，其值为1.399×10^7 s^-1、1.500×10^7 s^-1和1.863×10^7 s^-1。扩散张量的最佳取向已被纳入混合的Lipari - Szabo型局部运动 - 各向异性旋转扩散模型中，以表征分子中的局部流动性。由此提取的流动性参数相对于假设各向同性重取向的无模型分析显示出定量的改进；螺旋区域表现出相似的动力学性质，并且需要更复杂内部运动模型的残基更少。虽然该分子基本上是刚性的，但一个三肽环区域（残基101至103）表现出20至30皮秒范围内的灵活性，这似乎与NMR溶液结构中的有序性相关。
