School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel.
Viruses. 2022 Jun 10;14(6):1264. doi: 10.3390/v14061264.
Gene V protein (gVp) of the bacteriophages of the Ff family is a non-specific single-stranded DNA (ssDNA) binding protein. gVp binds to viral DNA during phage replication inside host cells, thereby blocking further replication and signaling the assembly of new phage particles. gVp is a dimer in solution and in crystal form. A structural model of the complex between gVp and ssDNA was obtained via docking the free gVp to structures of short ssDNA segments and via the detection of residues involved in DNA binding in solution. Using solid-state NMR, we characterized structural features of the gVp in complex with full-length viral ssDNA. We show that gVp binds ssDNA with an average distance of 5.5 Å between the amino acid residues of the protein and the phosphate backbone of the DNA. Torsion angle predictions and chemical shift perturbations indicate that there were considerable structural changes throughout the protein upon complexation with ssDNA, with the most significant variations occurring at the ssDNA binding loop and the C-terminus. Our data suggests that the structure of gVp in complex with ssDNA differs significantly from the structure of gVp in the free form, presumably to allow for cooperative binding of dimers to form the filamentous phage particle.
噬菌体 Ff 科的基因 V 蛋白（gVp）是一种非特异性的单链 DNA（ssDNA）结合蛋白。gVp 在宿主细胞内噬菌体复制过程中与病毒 DNA 结合，从而阻止进一步复制并发出组装新噬菌体颗粒的信号。gVp 在溶液中和晶体形式中都是二聚体。通过将游离 gVp 对接至短 ssDNA 片段的结构，并通过检测溶液中参与 DNA 结合的残基，获得了 gVp 与 ssDNA 之间复合物的结构模型。使用固态 NMR，我们对 gVp 与全长病毒 ssDNA 复合物的结构特征进行了表征。我们表明，gVp 与 ssDNA 的结合平均距离为 5.5 Å，介于蛋白质的氨基酸残基和 DNA 的磷酸骨架之间。扭转角预测和化学位移扰动表明，在与 ssDNA 复合后，整个蛋白质发生了相当大的结构变化，其中 ssDNA 结合环和 C 末端的变化最为显著。我们的数据表明，gVp 与 ssDNA 形成复合物的结构与游离形式的 gVp 结构有很大的不同，这可能允许二聚体协同结合形成丝状噬菌体颗粒。
