层理席藻质体蓝素与层理席藻细胞色素f相互作用的布朗动力学研究
A Brownian dynamics study of the interaction of Phormidium laminosum plastocyanin with Phormidium laminosum cytochrome f.
作者信息
Gross Elizabeth L
机构信息
Department of Biochemistry, The Ohio State University, Columbus, Ohio 34210, USA.
出版信息
Biophys J. 2004 Sep;87(3):2043-59. doi: 10.1529/biophysj.103.038497.
The interaction of Phormidium laminosum plastocyanin (PC) with P. laminosum cytochrome f (cyt f) was studied using Brownian dynamics (BD) simulations. Few complexes and a low rate of electron transfer were observed for wild-type PC. Increasing the positive electrostatic field on PC by the addition of a Zn(2+) ion in the neighborhood of D44 and D45 on PC (as found in crystal structure of plastocyanin) increased the number of complexes formed and the calculated rates of electron transfer as did PC mutations D44A, D45A, E54A, and E57A. Mutations of charged residues on Phormidium PC and Phormidium cyt f were used to map binding sites on both proteins. In both the presence and absence of the Zn(2+) ion, the following residues on PC interact with cyt f: D44, D45, K6, D79, R93, and K100 that lie in a patch just below H92 and Y88 and D10, E17, and E70 located on the upper portion of the PC molecule. In the absence of the Zn(2+) ion, K6 and K35 on the top of the PC molecule also interact with cyt f. Cyt f residues involved in binding PC, in the absence of the Zn(2+) ion, include E165, D187, and D188 that are located on the small domain of cyt f. The orientation of PC in the complexes was quite random in accordance with NMR results. In the presence of the Zn(2+) ion, K53 and E54 in the lower patch of the PC molecule also interact with cyt f and PC interacts with E86, E95, and E123 on the large domain of cyt f. Also, the orientation of PC in the complexes was much more uniform than in the absence of the Zn(2+) ion. The difference may be due to both the larger electrostatic field and the greater asymmetry of the charge distribution on PC observed in the presence of the Zn(2+) ion. Hydrophobic interactions were also observed suggesting a model of cyt f-PC interactions in which electrostatic forces bring the two molecules together but hydrophobic interactions participate in stabilizing the final electron-transfer-active dock.
利用布朗动力学（BD）模拟研究了席藻层状藻蓝蛋白（PC）与席藻细胞色素f（cyt f）的相互作用。野生型PC观察到少量复合物且电子转移速率较低。如在藻蓝蛋白晶体结构中所发现的，通过在PC上D44和D45附近添加Zn(2+)离子来增强PC上的正静电场，增加了形成的复合物数量以及计算出的电子转移速率，PC突变体D44A、D45A、E54A和E57A也有同样效果。对席藻PC和席藻cyt f上带电残基进行突变，以确定两种蛋白质上的结合位点。无论有无Zn(2+)离子，PC上以下残基与cyt f相互作用：位于H92和Y88下方一片区域的D44、D45、K6、D79、R93和K100，以及位于PC分子上部的D10、E17和E70。在没有Zn(2+)离子时，PC分子顶部的K6和K35也与cyt f相互作用。在没有Zn(2+)离子时，参与结合PC的cyt f残基包括位于cyt f小结构域的E165、D187和D188。根据核磁共振结果，复合物中PC的取向相当随机。在有Zn(2+)离子时，PC分子下部一片区域的K53和E54也与cyt f相互作用，并且PC与cyt f大结构域上的E86、E95和E123相互作用。此外，复合物中PC的取向比没有Zn(2+)离子时更加一致。这种差异可能是由于在有Zn(2+)离子时观察到PC上有更大的静电场以及电荷分布有更大的不对称性。还观察到疏水相互作用，这表明了一种cyt f - PC相互作用模型，其中静电力使两个分子靠近，但疏水相互作用参与稳定最终的电子转移活性对接。
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