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Computational microscope peers into the working ribosome
Date:11/23/2009

CHAMPAIGN, Ill. Two new studies reveal in unprecedented detail how the ribosome interacts with other molecules to assemble new proteins and guide them toward their destination in biological cells. The studies used molecular dynamics flexible fitting (MDFF) to examine the interaction of the ribosome with two prominent molecular partners.

The first study, in Proceedings of the National Academy of Sciences, concerns the intimate signaling between the ribosome and an elongation factor (EF-Tu) that is essential to the successful assembly of a growing protein. The second, in the journal Structure, focuses on a membrane protein called SecY that sometimes latches onto the ribosome and guides a newly forming protein toward its final destination.

MDFF combines data from two reliable but limited sources of atomic-level information: X-ray crystallography, which can give a high-resolution picture of a single type of molecule, but only in a static, crystal structure; and cryo-electron microscopy (cryo-EM), which can image the dynamic, real-life interaction of two or more molecules in the cell, but at low resolution.

The problem with X-ray crystallography is that the molecules, in this case ribosomes, are artificially removed from the environment of the cell and "packed together like sardines," said University of Illinois physics professor Klaus Schulten, an author on both papers and principal investigator on the study in Structure. This gives researchers a very detailed image of the components of the ribosome, but offers no clues about its behavior when it encounters other molecules.

Cryo-EM offers a wealth of information about the ribosome in its natural habitat in the cell, but the picture is much less crisp. Like a blurry photograph of a football player maneuvering down the field, cryo-EM gives a general outline, a three-dimensional snapshot of the molecule or molecules of interest at a given point in time, Schulten said
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Contact: Diana Yates
diya@illinois.edu
217-333-5802
University of Illinois at Urbana-Champaign
Source:Eurekalert  

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