By refining an emerging imaging technique and harnessing a powerful computer network, researchers have glimpsed the three-dimensional structure of a virus in unprecedented detail. The images, which capture the virus in a near-native state, have fine enough resolution that the backbones of individual proteins can be traced–a feat never before accomplished for a whole, intact organism.
“This particular achievement is basically a showcase of how this technique has progressed to a level that is near atomic resolution, and that allows us to image a real living infectious virus in a near-native environment,” says Wen Jiang, assistant professor of biological sciences at Purdue University, who led the study. The results appeared in the February 28 issue of the journal Nature.
The technique, called single-particle electron cryomicroscopy, involves flash-freezing whole viruses in a watery solution, a method that preserves their natural structure. The freezing process is so fast that the resulting ice is amorphous rather than crystalline, meaning that there are no ice crystals to damage the viral particles. The frozen sample is then bombarded with a beam of electrons from an electron microscope.
The resulting images allowed the researchers to distinguish between structures as close together as 4.5 angstroms. At just under half a nanometer, that distance is tiny enough to reveal near-atomic-level details. Earlier images of the same virus, also generated by Jiang’s group, yielded a resolution of about 9.5 angstroms–fine enough to illuminate some large-scale features of individual proteins, but not fine enough to trace those proteins’ backbones.
In other types of imaging, the structures to be imaged–whether they’re whole viruses or elaborate protein assemblies–must be arranged so that all the individual particles are oriented in exactly the same direction. That process requires advanced crystallization techniques to which many structures, including the virus used in this study, are not amenable.
The virus, called epsilon 15, belongs to a family of viruses that infect bacteria and have double-stranded DNA genomes and tails. “When you have a tail sticking out, it makes crystallization pretty hard,” says Jiang.
Single-particle electron cryomicroscopy eliminates the crystallization step entirely. The many particles to be imaged are arrayed and imaged in random orientations, and then a single composite three-dimensional model is assembled from tens of thousands of those images. In fact, the more orientations are captured, the better the model will be.
“It gives you the opportunity to solve structures that cannot be crystallized,” says Matsudaira.
The single-particle approach also improves image quality by protecting the relatively frail viruses from significant degradation by the microscope’s electron beam. Since the final model is constructed from images of a large number of viral particles, no single particle must be bombarded long enough to accumulate major damage.
Assembling the many images into a composite requires an enormous amount of computing power. Jiang and his group harnessed Purdue’s Condor pool, a resource that uses idle CPU cycles from computers across the campus. In total, the project took about one million CPU hours, spread over about 100 days.