Gill D S, Roush D J, Willson R C
Department of Chemical Engineering, University of Houston, TX 77204-4792.
J Biomol Struct Dyn. 1994 Apr;11(5):1003-15. doi: 10.1080/07391102.1994.10508048.
The in vitro complexes formed between cytochrome b5 and other proteins (e.g. cytochrome c) have served as a useful means to probe electrostatic contributions to macromolecular recognition. Extensive experimentation has been carried out to test the specificity and stability of these complexes, including site-directed mutagenesis based on the heterologous expression of rat cytochrome b5 in E. coli. Despite this interest, there has not been a determination of the complete structure of cytochrome b5. Here we report coordinates for the complete tertiary structure of the heme-binding domain of rat cytochrome b5 based on homology modeling. Protein Data Bank (PDB) coordinates derived from the crystal structure of the highly homologous bovine cytochrome b5 were used for main chain scaffolding. Secondary structures for the termini missing in the bovine structure were generated using homologous sequences derived from an exhaustive search of the PDB database. The model structure was solvated and further refined using energy minimization techniques. The N-terminal residues of the model appear to be in a beta sheet conformation while the carboxy terminus is in a helical conformation. The rest of the rat model is folded virtually identically to the bovine x-ray crystal structure (r.m.s. deviation 1.28 A), despite six sequence differences between the two cores. This homology-based structure should be useful for structure-function analyses of molecular recognition involving cytochrome b5.
细胞色素b5与其他蛋白质（如细胞色素c）在体外形成的复合物，已成为探究静电作用对大分子识别贡献的一种有用手段。人们已进行了大量实验来测试这些复合物的特异性和稳定性，包括基于大鼠细胞色素b5在大肠杆菌中的异源表达进行定点诱变。尽管有这些研究兴趣，但细胞色素b5的完整结构尚未确定。在此，我们报告基于同源建模得到的大鼠细胞色素b5血红素结合结构域完整三级结构的坐标。源自高度同源的牛细胞色素b5晶体结构的蛋白质数据库（PDB）坐标用于主链搭建。利用从PDB数据库详尽搜索得到的同源序列生成牛结构中缺失的末端二级结构。模型结构经溶剂化处理，并使用能量最小化技术进一步优化。模型的N端残基似乎处于β折叠构象，而羧基末端处于螺旋构象。尽管两个核心之间存在六个序列差异，但大鼠模型的其余部分折叠方式与牛的x射线晶体结构几乎相同（均方根偏差为1.28 Å）。这种基于同源性的结构对于涉及细胞色素b5的分子识别结构-功能分析应是有用的。
