Anton Simulations Reveal How Dangerous Bacteria Install Critical Proteins
 
Why It’s Important
 
In an era of diminishing antibiotic effectiveness, it’s no wonder that bacteria, how they live—and what molecular components they can’t live without—are an important focus for biomedical science. This “beta barrel protein” inserts other beta barrel proteins into the outer bacterial membrane, including those that import nutrients or export toxins that kill host cells. The process is a promising target for antibacterial drugs.
 
How Anton Helped
 
The researchers revealed BamA’s side exit using molecular dynamics (MD) simulations that lasted from one- to two-millionths of a second. In the world of computational biochemistry, that’s a very long time—supercomputers take months to perform simulations of the necessary length. On Anton, a special-purpose supercomputer designed to dramatically increase the speed of MD simulations, it can be accomplished in a day. The researchers reported their work in the journal Nature.
 
“Anton was critical for the work,” Gumbart says. “If limited to conventional systems, I probably would have run about 50 to 100 nanoseconds”—a tenth or less the time scale. If he’d only looked at this scale, he says, he might have thought, “Well, I don’t see anything, and that’s what it is.” Anton allowed him to push farther, to a remarkable result.

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