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Picking particles faster than one at a time

Computer scientists and biologists at the Department of Energy's Lawrence Berkeley National Laboratory have developed software that can select tens of thousands of high-quality images of biological molecules from electron microgaphs, rapidly and automatically, with accuracy approaching that of experienced human analysts.

The new algorithm, described as "particle picking by segmentation," promises to greatly increase the speed and power of methods for determining biological structures at high resolution, based on data from electron microscopy. The researchers report their results in the forthcoming issue of the Journal of Structural Biology in an article now available to subscribers online.

When what's needed is a high-resolution structure of a large and complicated biological molecule -- a ribosome, say, which combines protein and RNA, or a membrane protein that readily falls apart in water and is hard to crystallize -- biologists often turn to cryo-electron microscopy (cryo-EM) to perform single-particle reconstruction.

Understanding structure is often the key to devising antibiotics and other therapies that can interfere with unwanted biological activity -- for example, the ability of infectious bacteria to synthesize proteins can be wrecked by jamming their ribosomes, if the ribosome structure is known in detail. Single-particle reconstruction with cryo-EM holds the promise of providing many high-resolution structures which may be difficult or impossible to obtain otherwise.

Instead of trying to coax molecules to arrange themselves in a repeating crystalline structure, as is necessary for x-ray crystallography, cryo-EM uses individual molecules frozen in random orientations. Capturing two-dimensional images of the molecule from many different angles allows powerful computers to recreate the structure in three dimensions, a process molecular biologist Robert Glaeser of Berkeley Lab's Physical Biosciences and Life Sciences Division
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Source:DOE/Lawrence Berkeley National Laboratory


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