Cryo-EM tool on DiaGrid offers an easier way to image virus structures in 3-D

Anybody who’s had a cold knows the problem with viruses, but the problem goes beyond a stuffy nose and bad cough. Viruses also underlie maladies — from Ebola and Zika to hepatitis and influenza — deadly for millions of people around the world.

A high-resolution, three-dimensional map of virus molecular structure can provide insights on viral infections and help in developing more effective prevention and treatment strategies. Purdue biology Professor Wen Jiang creates such maps using computer imaging techniques in combination with electron cryo-microscopy. The latter bombards a virus sample with electrons, generating 2-D information about virus particles from a variety of orientations, which is then assembled into a 3-D map of the structure at near atomic resolution.

Now, anybody using the technique, or students learning to use it, can do so through DiaGrid by employing a web-based Single Particle Cryo-EM 3-D Reconstruction tool that Jiang and DiaGrid staff developed. The DiaGrid Cryo-EM tool is basically identical to the technology Jiang uses in his research, and that Purdue researchers used to map the structure of Zika virus for the first time in 2016. It incorporates image processing and 3-D reconstruction methods developed by Jiang’s lab and the open source EMAN/EMAN2 software.

But where Jiang and his colleagues do their computational work on Purdue’s research supercomputers, the “science as a service” Cryo-EM tool runs in a web browser and taps the processing muscle of campus and national supercomputers behind DiaGrid.

“It’s a complete solution,” Jiang says. “You don’t need to worry about downloading, installing, compiling or any other headache. You need real serious computing cycles to back up the software and DiaGrid provides that as well.”

Purdue faculty and students can use DiaGrid by signing in with their Purdue user names and passwords. Non-Purdue users just need to create an account on DiaGrid to start using it.

In one test case, Jiang and the DiaGrid team worked with Direct Electron, a maker of cutting-edge cameras for electron cryo-microscopy, and a large virus dataset of nearly 29,000 virus particle images from UCLA to successfully image a virus structure in 3-D at a resolution of 2.93 angstroms.

Viral infections remain a major threat to human health, so anything that might contribute to improved methods of treating them, or forestalling them altogether, could be significant. Jiang’s technique also can offer a window into the structure of the molecular machines permeating our bodies, such as DNA molecules and the myriad proteins that fulfill key biological roles.

Beyond biology, the ability to map a structure at the level where Jiang is working could be useful in understanding and manipulating tiny structures involved in nanotechnology.

 

Dr. Wen Jiang
Professor of Biological Sciences
Purdue University