Centre of New Technologies, University of Warsaw, Warsaw, Poland.
Department of Drug Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, Warsaw, Poland.
PLoS Comput Biol. 2020 Jul 1;16(7):e1008024. doi: 10.1371/journal.pcbi.1008024. eCollection 2020 Jul.
Vitamin B12 (or cobalamin) is an enzymatic cofactor essential both for mammals and bacteria. However, cobalamin can be synthesized only by few microorganisms so most bacteria need to take it up from the environment through the TonB-dependent transport system. The first stage of cobalamin import to E. coli cells occurs through the outer-membrane receptor called BtuB. Vitamin B12 binds with high affinity to the extracellular side of the BtuB protein. BtuB forms a β-barrel with inner luminal domain and extracellular loops. To mechanically allow for cobalamin passage, the luminal domain needs to partially unfold with the help of the inner-membrane TonB protein. However, the mechanism of cobalamin permeation is unknown. Using all-atom molecular dynamics, we simulated the transport of cobalamin through the BtuB receptor embedded in an asymmetric and heterogeneous E. coli outer-membrane. To enhance conformational sampling of the BtuB loops, we developed the Gaussian force-simulated annealing method (GF-SA) and coupled it with umbrella sampling. We found that cobalamin needs to rotate in order to permeate through BtuB. We showed that the mobility of BtuB extracellular loops is crucial for cobalamin binding and transport and resembles an induced-fit mechanism. Loop mobility depends not only on the position of cobalamin but also on the extension of luminal domain. We provided atomistic details of cobalamin transport through the BtuB receptor showing the essential role of the mobility of BtuB extracellular loops. A similar TonB-dependent transport system is used also by many other compounds, such as haem and siderophores, and importantly, can be hijacked by natural antibiotics. Our work could have implications for future delivery of antibiotics to bacteria using this transport system.
维生素 B12（或钴胺素）是一种酶辅因子，对哺乳动物和细菌都必不可少。然而，只有少数微生物才能合成钴胺素，因此大多数细菌需要通过 TonB 依赖的转运系统从环境中摄取它。钴胺素进入大肠杆菌细胞的第一阶段是通过称为 BtuB 的外膜受体进行的。维生素 B12 与 BtuB 蛋白的细胞外侧结合具有高亲和力。BtuB 形成一个具有内腔域和细胞外环的β-桶。为了机械地允许钴胺素通过，内腔域需要在内膜 TonB 蛋白的帮助下部分展开。然而，钴胺素渗透的机制尚不清楚。使用全原子分子动力学，我们模拟了嵌入不对称和异质大肠杆菌外膜中的 BtuB 受体中的钴胺素转运。为了增强 BtuB 环的构象采样，我们开发了高斯力模拟退火方法（GF-SA）并将其与伞状采样相结合。我们发现钴胺素需要旋转才能通过 BtuB。我们表明，BtuB 细胞外环的流动性对于钴胺素结合和转运至关重要，类似于诱导契合机制。环的流动性不仅取决于钴胺素的位置，还取决于内腔域的延伸。我们提供了钴胺素通过 BtuB 受体转运的原子细节，表明了 BtuB 细胞外环流动性的重要作用。类似的 TonB 依赖转运系统也被许多其他化合物（如血红素和铁载体）使用，重要的是，它可以被天然抗生素劫持。我们的工作可能对未来使用该转运系统将抗生素递送到细菌产生影响。
