Abstract
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.
Highlights
The outer membrane of Gram-negative bacteria permits downhill diffusion of small hydrophilic molecules into the periplasmic space
We performed analogous steered molecular dynamics (SMD) simulations, and, we did not observe any substantial motion of vitamin B12 towards the periplasmic space (S1 Fig)
Cbl was held by the extracellular loops and did not follow the luminal domain upon its unfolding
Summary
The outer membrane of Gram-negative bacteria permits downhill diffusion of small hydrophilic molecules into the periplasmic space. Bulky molecules (over *600 Da) or compounds present in the extracellular medium in scarce amounts, such as organometallic species, cannot permeate through porins, and their transport requires different routes. Since these compounds are fundamental for bacterial growth and viability, and largely determine the virulence of pathogens, bacteria developed specific and selective receptor-dependent active transport systems for these molecules. This kind of system has been best characterized for vitamin B12, called cobalamin (Cbl). Most bacteria including Enterobacteriaceae, Bacillus subtilis and group A Streptococci need to take up vitamin B12 from the environment
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
