Vitamin B12 (or cobalamin) is an enzymatic cofactor either produced or taken up by bacterial cells. The first stage of its uptake to E. coli cells occurs through binding of vitamin B12 to the outer-membrane receptor BtuB. BtuB interacts with the inner-membrane TonB protein which leads to unfolding of the BtuB luminal domain and release of vitamin B12 to the periplasm. Peptide nucleic acid (PNA) is a synthetic DNA analogue that hybridizes with natural nucleic acids. PNA oligomers are used to sequence-specifically block DNA or RNA in various laboratory applications. PNA is not readily taken up by cells but we have experimentally found that conjugation of vitamin B12 to a PNA oligomer helps PNA enter E. coli cells. We have thus investigated the mechanism of transport of vitamin B12 and its conjugate with PNA through the BtuB receptor. We built an asymmetric and heterogenous membrane model around the BtuB structure (PDB code 2GSK) with explicitly modeled water and ions. We combined both steered and random-acceleration all-atom molecular dynamics to simulate the transport of vitamin B12 and its conjugate with PNA. The simulations were performed with NAMD 2.11 and Amber force field parameters. Trajectories have shown that the transport of the vitamin B12—PNA conjugate through the BtuB protein is mechanically possible. We observed that the otherwise compact structure of a PNA oligomer extends inside the BtuB receptor allowing for PNA passage. Therefore, as also supported by our experimental evidence, we suggest that vitamin B12—PNA conjugates may be transported through the BtuB protein in the E. coli outer membrane.

Transport of vitamin B12-peptide nucleic acid conjugates through the BtuB outer membrane receptor of E. coli

254th National Meeting (2017)

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