Storch E M, Daggett V
Department of Medicinal Chemistry, University of Washington, Seattle 98195-7610, USA.
Biochemistry. 1996 Sep 10;35(36):11596-604. doi: 10.1021/bi960598g.
Molecular dynamics simulations of rat and bovine apocytochrome b5 were performed to investigate the structural and dynamical consequences of heme removal. A crystal structure is available for the bovine holoprotein, while experimental studies of apocytochrome b5 have focused on the rat protein. The rat and bovine proteins are 93% homologous by sequence, and the sequence differences (six residues) appear to have no effect on the structure of the native holoprotein, as seen by the correlation of a bovine simulation with rat holocytochrome b5 experimental data (Storch & Daggett, 1995). There was a marked effect, however, on the structure and dynamics of the apo form. The bovine apocytochrome b5 simulation displayed subtle inconsistencies when compared to the experimental results on the rat apoprotein. Therefore, the rat protein was constructed from the bovine crystal structure coordinates. The MD simulation of the rat apoprotein displayed greater deviations from the crystal structure, yet it was in much closer agreement to the experimental data for the apoprotein. Additionally, the six variant residues fall in the regions where the bovine protein deviated from experiment. The two hydrophobic cores of the rat protein behaved very differently. Core 2 was well maintained, retained native-like structure, and is in good agreement with NMR data (Moore & Lecomte, 1990). Conversely, core 1, which is normally constrained by the prosthetic heme group, exhibited conformational heterogeneity, increased mobility, and some loss of secondary structure. Thus, the model of rat apocytochrome b5 complements past studies by providing structural information about core 1 that has proved difficult to obtain by experiment. The bovine simulation serves as a prediction, since little to no experimental data exist for this form of the apoprotein.
进行了大鼠和牛脱辅基细胞色素b5的分子动力学模拟，以研究血红素去除的结构和动力学后果。牛全蛋白有晶体结构，而脱辅基细胞色素b5的实验研究主要集中在大鼠蛋白上。大鼠和牛的蛋白序列同源性为93%，序列差异（六个残基）似乎对天然全蛋白的结构没有影响，这从牛模拟与大鼠全细胞色素b5实验数据的相关性中可以看出（斯托奇和达格特，1995年）。然而，对脱辅基形式的结构和动力学有显著影响。与大鼠脱辅基蛋白的实验结果相比，牛脱辅基细胞色素b5模拟显示出细微的不一致。因此，大鼠蛋白是根据牛晶体结构坐标构建的。大鼠脱辅基蛋白的分子动力学模拟与晶体结构有更大偏差，但与脱辅基蛋白的实验数据更接近。此外，六个变异残基位于牛蛋白与实验结果有偏差的区域。大鼠蛋白的两个疏水核心表现非常不同。核心2保持良好，保留了类似天然的结构，与核磁共振数据（摩尔和勒孔特，1990年）吻合良好。相反，通常受辅基血红素基团约束的核心1表现出构象异质性、流动性增加和一些二级结构的丧失。因此，大鼠脱辅基细胞色素b5模型通过提供关于核心1的结构信息补充了以往的研究，而核心1的结构信息已证明难以通过实验获得。牛模拟可作为一种预测，因为这种脱辅基蛋白形式几乎没有实验数据。
