New method for interpreting cryo-EM maps makes it easier to determine protein structures

phys.org | 4/26/2018 | Staff
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A new algorithm makes interpreting the results of cryo-electron microscopy maps easier and more accurate, helping researchers to determine protein structures and potentially create drugs that block their functions.

Cryo-electron microscopy, or cryo-EM, uses electron beams to obtain 3-D images of biomolecular structures. The use of this technique has skyrocketed in recent years due to technolgical advancements, but as cryo-EM gains steam in the field, additional tools are needed to interpret the images it outputs.

Product - Cryo-EM - Map - Density - Atoms

The final product of cryo-EM is a map of the density of atoms in biological molecules, including proteins and nucleotides. To get the level of detail they really need, researchers must identify atom or amino acid residue positions in a map, which requires specialized computer analysis. Programs that do this exist, but they aren't always accuracate or easy to use, said Daisuke Kihara, a professor of biological sciences and computer science at Purdue University.

Kihara and a postdoctoral researcher in his lab, Genki Terashi, have created a fully automated algorithm for interpreting maps of proteins at lower than ideal resolution – around 4 to 5 ångström (Å, a unit of length to express size of atoms and molecules). Many similar tools were developed for more detailed images or X-ray crystallography, which don't work as well for lower resolution cryo-EM images.

Kihara - Program - MAINMAST - Density - Points

Kihara's program, MAINMAST, identifies local density points in a given EM map and connects them into a tree structure – like connecting the dots. The algorithm tries different parameters for defining density points and branches in a tree.

"With this method, you don't need to tune the parameters from 1 to 1.2 to 1.5, or need any expert knowledge about how to do this. Typically, when people use this kind of software, that's critical," Kihara said. "This algorithm has the different parameters already inside, so users don't have to do...
(Excerpt) Read more at: phys.org
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