Simulating Membrane Transport
For a bacterium to admit certain large nutrients, a steady tug from inside might do the trick, according to computer simulations recently published in Biophysical Journal.
Bacterial membranes are loaded with a vast number of specialized transporters. For some of these to function, an energized inner membrane protein must transmit its energy to an outer membrane protein so that nutrients can enter the cell. The question is: How does that work? Does the inner protein shuttle across the membrane, unplug a pore, or simply yank open a gap?
“I don’t know of any other model in which you energize a protein and then send it out to take energy to the outer membrane,” says Emad Tajkhorshid, PhD, assistant professor of biochemistry, pharmacology and biophysics at the University of Illinois, Champaign, a co-author on the paper along with his student James Gumbart. “We are trying to improve the picture of this mechanism by doing this simulation,” he says.
Bacteria can seem obsessed with finding and absorbing nutrients from the environment. Indeed, they dedicate more than 50 percent of their genetic material and 50 percent of their energy to membrane transport. For large nutrient molecules, such as vitamin B12, bacteria rely on TonB dependent transporters such as BtuB. These barrel-shaped molecules reside in the outer membrane with their tails (known as the plug domain) tucked in and plugging the barrel. TonB itself is anchored to the inner membrane with its tail end mating up with BtuB’s plug domain, according to X-ray crystallographic results published last year in Science.
Based on experimental evidence, researchers know that when TonB is energized, nutrients can pass through the TonB dependent transporter. Scientists have proposed several possible mechanisms: TonB acting as a shuttle; or TonB forcibly pulling open the plugged barrel either by unfolding the luminal domain or by unplugging it entirely. Last year, with the new structural information about the TonB/BtuB complex, Tajkhorshid and his colleagues decided to simulate the “pulling” theory in order to determine where the force would be felt first.
“It was possible that if you pull on TonB it might just come off,” says Tajkhorshid. But that didn’t happen. The connection between TonB and BtuB held, while the luminal domain of BtuB unfolded. After pulling for 100 angstroms, this produced an opening wide enough for vitamin B12 to pass through. The team also tested the “unplugging” theory, but found that it took ten times as much force to remove the entire luminal domain. “Unfolding is much easier to induce than coming off as one piece,” says Tajkhorshid.
But, he says, there are still plenty of unknowns. They didn’t try to simulate the shuttle theory because it would require too much computing power to do so. And, “in our simulation, we had to pull for 100 angstroms to observe enough opening to let the substrate permeate the transporter. But it’s obvious to me that there is no way you can have 100 angstroms of pulling from something on the inner membrane. There must be other things going on.”
Susan Buchanan, PhD, an investigator in the Laboratory of Molecular Biology at National Institute of Diabetes and Digestive and Kidney Disease, agrees that a linear movement of 100 angstroms is unlikely. But, she says, “The simplest thing to do in simulations is to apply a linear force as he did. In vivo, it could be a combination of some sort of rigid body movement, conformational changes, and rotation. But those things are hard to simulate.” What’s important, she says, is that this work provides a model that people can look at further. “With the recently solved crystal structure,” she says, “it’s important to do simulations at this point because no one’s been able to do this in vivo yet.”