Matamala Adelio R, Almonacid Daniel E, Figueroa Maximiliano F, Martínez-Oyanedel José, Bunster Marta C
Facultad de Ciencias Químicas, Universidad de Concepción, Casilla 160-C, Edmundo Larenas 129, Concepción, Chile.
J Comput Chem. 2007 May;28(7):1200-7. doi: 10.1002/jcc.20628.
A semiempirical methodology to model the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer (FRET) pathways in the rods of the phycobilisomes (PBSs) from Fremyella diplosiphon is presented. Using the Förster formulation of FRET and combining experimental data and PM3 calculation of the dipole moments of the aromatic portions of the chromophores, transfer constants between pairs of chromophores in the phycocyanin (PC) structure were obtained. Protein docking of two PC hexamers was used to predict the optimal distance and axial rotation angle for the staked PCs in the PBSs' rods. Using the distance obtained by the docking process, transfer constants between pairs of chromophores belonging to different PC hexamers were calculated as a function of the angle of rotation. We show that six preferential FRET pathways within the PC hexameric ring and 15 pathways between hexamers exist, with transfer constants consistent with experimental results. Protein docking predicted the quaternary structure for PCs in rods with inter-phycocyanin distance of 55.6 A and rotation angle of 20.5 degrees . The inter-phycocyanin FRET constant between chromophores at positions beta(155) is maximized at the rotation angle predicted by docking revealing the crucial role of this specific inter-phycocyanin channel in defining the complete set of FRET pathways in the system.
本文提出了一种半经验方法，用于模拟来自双岐鱼腥藻（Fremyella diplosiphon）的藻胆体（PBS）棒状结构中藻蓝蛋白内和藻蓝蛋白间的荧光共振能量转移（FRET）途径。利用FRET的Förster公式，并结合实验数据和发色团芳香部分偶极矩的PM3计算，获得了藻蓝蛋白（PC）结构中发色团对之间的转移常数。通过对两个PC六聚体进行蛋白质对接，预测了PBS棒状结构中堆叠PC的最佳距离和轴向旋转角度。利用对接过程得到的距离，计算了属于不同PC六聚体的发色团对之间的转移常数随旋转角度的变化。我们表明，PC六聚体环内存在六条优先FRET途径，六聚体之间存在15条途径，其转移常数与实验结果一致。蛋白质对接预测了棒状结构中PC的四级结构，藻蓝蛋白间距离为55.6 Å，旋转角度为20.5度。在对接预测的旋转角度下，β(155)位置发色团之间的藻蓝蛋白间FRET常数最大，揭示了这种特定藻蓝蛋白间通道在定义系统中完整FRET途径集方面的关键作用。
