André Christophe, Martiel Isabelle, Wolff Philippe, Landolfo Marie, Lorber Bernard, Silva da Veiga Cyrielle, Dejaegere Annick, Dumas Philippe, Guichard Gilles, Oliéric Vincent, Wagner Jérôme, Burnouf Dominique Y
Institut Européen de Chimie et Biologie , Université de Bordeaux-CNRS UMR 5248, CBMN , 2, rue Robert Escarpit , 33607 Pessac , France.
Swiss Light Source (SLS) , Paul-Scherrer-Institute (PSI) , 5232 Villigen , Switzerland.
ACS Infect Dis. 2019 Jun 14;5(6):1022-1034. doi: 10.1021/acsinfecdis.9b00089. Epub 2019 Apr 5.
Bacterial sliding clamps control the access of DNA polymerases to the replication fork and are appealing targets for antibacterial drug development. It is therefore essential to decipher the polymerase-clamp binding mode across various bacterial species. Here, two residues of the E. coli clamp binding pocket, S and M, and their cognate residues in M. tuberculosis and B. subtilis clamps, were mutated. The effects of these mutations on the interaction of a model peptide with these variant clamps were evaluated by thermodynamic, molecular dynamics, X-rays crystallography, and biochemical analyses. M and corresponding residues in Gram positive clamps occupy a strategic position where a mobile residue is essential for an efficient peptide interaction. S has a more subtle function that modulates the pocket folding dynamics, while the equivalent residue in B. subtilis is essential for polymerase activity and might therefore be a Gram positive-specific molecular marker. Finally, the peptide binds through an induced-fit process to Gram negative and positive pockets, but the complex stability varies according to a pocket-specific network of interactions.
细菌滑动夹控制DNA聚合酶接近复制叉，是抗菌药物开发的有吸引力的靶点。因此，解读不同细菌物种中聚合酶与夹子的结合模式至关重要。在此，大肠杆菌夹子结合口袋的两个残基S和M，以及它们在结核分枝杆菌和枯草芽孢杆菌夹子中的同源残基被突变。通过热力学、分子动力学、X射线晶体学和生化分析评估了这些突变对模型肽与这些变体夹子相互作用的影响。革兰氏阳性夹子中的M和相应残基占据一个关键位置，一个可移动残基对于有效的肽相互作用至关重要。S具有更微妙的功能，可调节口袋折叠动力学，而枯草芽孢杆菌中的等效残基对聚合酶活性至关重要，因此可能是革兰氏阳性特异性分子标记。最后，该肽通过诱导契合过程与革兰氏阴性和阳性口袋结合，但复合物稳定性根据口袋特异性相互作用网络而有所不同。
