Guan Y, Zhang H, Wang A H
Biophysics Division, University of Illinois at Urbana-Champaign 61801, USA.
Protein Sci. 1995 Feb;4(2):187-97. doi: 10.1002/pro.5560040206.
The crystal structure of the gene V protein (GVP) from the Ff filamentous phages (M13, fl, fd) has been solved for the wild-type and two mutant (Y41F and Y41H) proteins at high resolution. The Y41H mutant crystal structure revealed crystal packing interactions, which suggested a plausible scheme for constructing the polymeric protein shell of the GVP-single-stranded DNA (ssDNA) complex (Guan Y, et al., 1994, Biochemistry 33:7768-7778). The electrostatic potentials of the isolated and the cooperatively formed protein shell have been calculated using the program GRASP and they revealed a highly asymmetric pattern of the electrostatic charge distribution. The inner surface of the putative DNA-binding channel is positively charged, whereas the opposite outer surface is nearly neutral. The electrostatic calculation further demonstrated that the formation of the helical protein shell enhanced the asymmetry of the electrostatic distribution. A model of the GVP-ssDNA complex with the n = 4 DNA-binding mode could be built with only minor conformational perturbation to the GVP protein shell. The model is consistent with existing biochemical and biophysical data and provides clues to the properties of GVP, including the high cooperatively of the protein binding to ssDNA. The two antiparallel ssDNA strands form a helical ribbon with the sugar-phosphate backbones at the middle and the bases pointing away from each other. The bases are stacked and the Phe 73 residue is intercalated between two bases. The optimum binding to a tetranucleotide unit requires the participation of four GVP dimers, which may explain the cooperativity of the GVP binding to DNA.
已通过高分辨率解析了来自Ff丝状噬菌体（M13、fl、fd）的基因V蛋白（GVP）野生型及两种突变体（Y41F和Y41H）蛋白的晶体结构。Y41H突变体的晶体结构揭示了晶体堆积相互作用，这为构建GVP-单链DNA（ssDNA）复合物的聚合蛋白外壳提出了一个合理方案（Guan Y等人，1994年，《生物化学》33:7768 - 7778）。使用GRASP程序计算了分离的和协同形成的蛋白外壳的静电势，结果显示静电电荷分布呈现高度不对称模式。推测的DNA结合通道的内表面带正电，而相对的外表面几乎呈中性。静电计算进一步表明，螺旋蛋白外壳的形成增强了静电分布的不对称性。可以构建一个具有n = 4 DNA结合模式的GVP-ssDNA复合物模型，且对GVP蛋白外壳只需进行微小的构象扰动。该模型与现有的生化和生物物理数据一致，并为GVP的特性提供了线索，包括蛋白与ssDNA结合的高度协同性。两条反平行的ssDNA链形成一条螺旋带，磷酸核糖骨架位于中间，碱基彼此远离。碱基堆积，苯丙氨酸73残基插入两个碱基之间。与四核苷酸单元的最佳结合需要四个GVP二聚体的参与，这可能解释了GVP与DNA结合的协同性。
