( es had been inconclusive however. Mole...)Simulations unravel outer membrane transport mechanism

es had been inconclusive, however. 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. “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. “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.”
U. of I. 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. The yellow sphere represents the point on the TonB protein at which the force was applied. To view the results of the simulation, please go to: http://www.life.uiuc.edu/emad/TonB-BtuB/btub-2.5Ans.mpg
Credit: Image courtesy of Emad Tajkhorshid

To address these limitations, Tajkhorshid and graduate student James Gumbart used two software programs developed in the U. of I.’s National Institutes of Health Resource for Macromolecular Modeling and Bioinformatics. The programs, NAMD and VMD, respectively, simulate and visualize complex molecular interactions. 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. Their work relied on detailed crystallographic studies of the molecules provided by University of Virginia researcher Michael C. Wiener.

“The good thing about simulations is that you can monitor the position of every atom,” Tajkhorshid said.

The task was enormous, however.

“The fundamental motion
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Source:University of Illinois at Urbana-Champaign

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