“The good thing about simulations is that you can monitor the position of every atom,” Tajkhorshid said. Their work relied on detailed crystallographic studies of the molecules provided by University of Virginia researcher Michael C. By entering detailed data about the position and characteristics of every atom in the system, the researchers ran simulations of various scenarios to test which hypotheses were most feasible. The programs, NAMD and VMD, respectively, simulate and visualize complex molecular interactions. of I.’s National Institutes of Health Resource for Macromolecular Modeling and Bioinformatics.
UNRAVEL TWO BARREL SOFTWARE
To address these limitations, Tajkhorshid and graduate student James Gumbart used two software programs developed in the U.
“And sometimes the labeling agent that they use diffuses into the beta-barrel and labels the inside: You don’t know whether what you have labeled is happening inside or outside.” “It’s very difficult to assess this experimentally because they have to look at the accessibility of certain (amino acids) before and after activation,” Tajkhorshid said. Molecular biologists have difficulty studying systems that involve complex interactions between proteins, particularly when one domain moves into and out of a structure like a beta-barrel, said biochemistry professor Emad Tajkhorshid, principal investigator on the study. Previous studies had been inconclusive, however. Researchers had hypothesized that TonB somehow draws the luminal domain out of the barrel or changes its conformation to make way for the large molecules. Another region of the protein, the luminal domain, clogs this barrel until the cell is ready to allow large molecules to pass through.Ĭrystallographic studies had shown that TonB binds to one end of the luminal domain.
UNRAVEL TWO BARREL SERIES
This TonB-dependent transporter (TBDT) contains a beta-barrel domain: a series of parallel sheets that form a tunnel through which large molecules can pass. The new study examined an outer membrane transport system that depends on an energy-generating inner membrane protein, TonB. The cells must be selective in what substances they take up, and the outer membrane contains no energy-generating machinery to power the job of hauling large molecules inside. Transporting large molecules, such as vitamin B12, citric acid or other vital nutrients across the outer membranes of Gram-negative bacteria is not a simple task. Their study, which includes a collaborator from the University of Virginia, appears online in the Biophysical Journal and was described in the May 25 edition of Science. Their findings provide a rare window on the complex interplay of proteins involved in the active transport of materials across cell membranes. Using X-ray data and advanced computer simulation and visualization software, researchers at the University of Illinois have painstakingly modeled a critical part of a mechanism by which bacteria take up large molecules. To view the results of the simulation, please go to: view moreĬredit: Image courtesy of Emad Tajkhorshid The yellow sphere represents the point on the TonB protein at which the force was applied.
researchers simulated the interaction of part of the inner membrane protein TonB (shown in red) and the luminal domain (in green and dark blue) of the outer membrane transporter.
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