耐药结瘤细胞分裂(RND)超家族的次级转运蛋白介导革兰氏阴性细菌如铜绿假单胞菌的多药耐药性。在这些RND转运蛋白中,MexB,MexF,还有Mexy,具有部分重叠的特异性,与致病性有关。只有前者的结构已经通过实验解决,再加上缺乏关于全套转运蛋白功能动态的数据,限制了对定义其独特和共同特征的分子决定因素的系统研究。在以前的工作中(Ramaswamy等人。,前面。Microbiol.,2018,9,1144),我们在原子水平上比较了MexB和MexY的两个主要推定识别位点(命名为访问和深结合袋)。在这项工作中,我们通过对这些转运蛋白和病理相关转运蛋白MexF进行扩展分子动力学(MD)模拟来扩展比较。我们采用了更真实的铜绿假单胞菌内部磷脂膜模型和更准确的力场。为了阐明结构/动力学-活性关系,我们进行了物理化学分析,并绘制了几种有机探针在所有转运蛋白上的结合倾向。我们的数据揭示了存在,同样在MexF,在相当于在MexB中检测到的进入和深结合袋的位置处的几个多功能位点。此外,我们首次报道了与外周(早期)识别底物相关的五个通道中的两个通道的多药结合能力。总的来说,我们的发现有助于定义一个共同的“识别拓扑”表征墨西哥运输者,可用于优化抗微生物化合物的运输和抑制倾向。
The secondary transporters of the resistance-nodulation-cell division (RND) superfamily mediate multidrug resistance in Gram-negative bacteria like Pseudomonas aeruginosa. Among these RND transporters, MexB, MexF, and MexY, with partly overlapping specificities, have been implicated in pathogenicity. Only the structure of the former has been resolved experimentally, which together with the lack of data about the functional dynamics of the full set of transporters, limited a systematic investigation of the molecular determinants defining their peculiar and shared features. In a previous work (Ramaswamy et al., Front. Microbiol., 2018, 9, 1144), we compared at an atomistic level the two main putative recognition sites (named access and deep binding pockets) of MexB and MexY. In this work, we expand the comparison by performing extended molecular dynamics (MD) simulations of these transporters and the pathologically relevant transporter MexF. We employed a more realistic model of the inner phospholipid membrane of P. aeruginosa and more accurate force-fields. To elucidate structure/dynamics-activity relationships we performed physico-chemical analyses and mapped the binding propensities of several organic probes on all transporters. Our data revealed the presence, also in MexF, of a few multifunctional sites at locations equivalent to the access and deep binding pockets detected in MexB. Furthermore, we report for the first time about the multidrug binding abilities of two out of five gates of the channels deputed to peripheral (early) recognition of substrates. Overall, our findings help to define a common \"recognition topology\" characterizing Mex transporters, which can be exploited to optimize transport and inhibition propensities of antimicrobial compounds.