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Opening of Lacy'S cytoplasmic cavity

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made with VMD

Escherichia coli are bacteria living in the intestines of mammals as part of their healthy gut flora, but also causing disease outside of the gut. The bacteria import from their environment nutriments, for example molecules of lactose, a sugar. For this purpose Escherichia coli employs in its cell membrane a protein channel, lactose permease, that translocates the sugar outside-in. This is the bacterium's "sweet tooth". To establish the unidirectional sugar transport, the bacterium utilizes an electrical potential maintained in the form of a trans-membrane proton gradient (more protons on the outer cellular than on the inner cellular side of the membrane). Protons, very small ions, that enter the channel from the outside one at a time, open the outer channel entrance. This permits access of lactose that gets bound inside the channel. Release of the proton to the cell interior closes the outer channel entrance and opens the inner channel entrance, such that the bound lactose can enter the cell. Despite extensive and elegant biochemical studies, the physical mechanism that couples unidirectional proton and sugar translocation is not yet known in detail. A crystallographic structure of lactose permease permitted now investigations into this mechanism by means of molecular dynamics simulations using NAMD. The simulations, reported in a recent publication, showed one step of the proton - sugar translocation, namely how binding and unbinding of the proton activates a spring-like bond, a so-called salt bridge, that closes and opens the inner channel exit. More information on the lactose permease project can be found here.