New player emerges in mapping protein structures

Sep 20, 2013 by Dan Krotz

( —If you keep up with biology, you've probably seen those colorful images in which the atom-by-atom structure of a protein is portrayed by a tangle of ribbons. For the past couple of decades, scientists have been hard at work deriving these structures, which provide clues as to what proteins do.

It's critical research. Proteins are workhorse compounds that sustain all living things. The next drug breakthrough, or insight into how life works at the molecular scale, could originate from one of these images.

Most protein structures are obtained via x-ray crystallography. Scientists also use to solve structures. And coming in at a distant third is a technique called single-particle cryoelectron microscopy (cryo-EM), in which a macromolecule is immobilized in a thin film of vitrified buffer and inserted into the vacuum of an .

Cryo-EM's back-of-the-pack status is changing, however, thanks in part to technology developed at Berkeley Lab.

The shift is due to advances in the camera, or detector. Traditional high-performance cameras record the image indirectly. Electrons hit a scintillator, and the resulting light is sent to a CCD chip, where it is converted to an electronic image and read-out.

But a new generation of cameras offers a more direct approach. With these cameras, electrons hit the silicon pixels directly, and the resulting events are collected by microfabricated electronics that render an image.

One such direct-conversion owes its origins to a camera developed for one of the world's most powerful electron microscopes, TEAM, which is located at Berkeley Lab's National Center for Electron Microscopy. The camera was engineered by Berkeley Lab's Peter Denes and colleagues, and began its service when TEAM started operating in 2009.

A version of the Berkeley Lab camera has since been commercialized by the Pleasanton, California-based Gatan, Inc. Its 16 million pixels capture events at 400 frames per second. Several are now in use at UC San Francisco, Caltech, and in the UC Berkeley lab of Eva Nogales, who is also a scientist in Berkeley Lab's Life Sciences Division.

This camera, along with two other commercially available direct-conversion electron cameras, are making cryo-EM a real player when it comes to mapping protein structures.

For example, scientists from the United Kingdom used the method to derive a 4.5-angstrom resolution image of the yeast ribosome, and did so using only two percent of the data than was necessary for earlier efforts that produced lower-resolution results. Previously, scientists had to merge data from as many as a couple of million single particles in order to improve the signal-to-noise ratio, and even then they were not able see ribosomal structures such as side chains. Now, only 35,000 particles are needed.

"That's a huge and sudden improvement," says Robert Glaeser, a scientist in Berkeley Lab's Life Sciences Division and a pioneer in using cryo-EM to determine the structure of proteins. Glaeser outlined the impacts of direct-conversion cameras in a recent News and Views article for Nature Methods.

In addition, as Glaeser outlines in the Nature Methods article, the new, direct-conversion camera makes it possible to record a 'stroboscopic movie' while exposing a protein to electrons. Such movies are important because the cryo-EM specimen constantly moves while an image is being recorded, probably because of stresses caused by radiation damage.

Improvements like these put many important proteins within reach for the first time. Recently, scientists from UC San Francisco used cryo-EM to solve the structure of a much smaller protein complex than previously possible with the technique: the 20S proteasome. And Nogales is using the technique to derive high-resolution structures of a microtubule, a protein that helps to maintain the structure of a cell among other functions.

There are several advantages to using cryo-EM for deriving protein structures. Unlike , a protein doesn't have to be crystallized in order to map it, which is a time consuming process. And a protein's structure can be determined in its biochemically native solution.

So, the next time you see an image of a near atomic-scale structure of a , be sure to read the caption. Don't be surprised if it's derived from single-particle cryo-EM.

Explore further: Proteins under the (high-end) microscope

Related Stories

Proteins under the (high-end) microscope

Sep 10, 2013

Two new transmission electron microscopes (TEM) will give Monash University researchers unprecedented insights into the structure and function of proteins and contribute to breakthroughs in treating conditions from cancer ...

Structure reveals how cells 'sugar-coat' proteins

Mar 11, 2008

Biologists at the U.S. Department of Energy's Brookhaven National Laboratory, Stony Brook University, and the University of Wurzburg, Germany, have deciphered the structure of a large protein complex responsible for adding ...

Recommended for you

Researchers successfully clone adult human stem cells

Apr 18, 2014

( —An international team of researchers, led by Robert Lanza, of Advanced Cell Technology, has announced that they have performed the first successful cloning of adult human skin cells into stem ...

Researchers develop new model of cellular movement

Apr 18, 2014

( —Cell movement plays an important role in a host of biological functions from embryonic development to repairing wounded tissue. It also enables cancer cells to break free from their sites of ...

For resetting circadian rhythms, neural cooperation is key

Apr 17, 2014

Fruit flies are pretty predictable when it comes to scheduling their days, with peaks of activity at dawn and dusk and rest times in between. Now, researchers reporting in the Cell Press journal Cell Reports on April 17th h ...

User comments : 0

More news stories

Researchers successfully clone adult human stem cells

( —An international team of researchers, led by Robert Lanza, of Advanced Cell Technology, has announced that they have performed the first successful cloning of adult human skin cells into stem ...

NASA's space station Robonaut finally getting legs

Robonaut, the first out-of-this-world humanoid, is finally getting its space legs. For three years, Robonaut has had to manage from the waist up. This new pair of legs means the experimental robot—now stuck ...

Ex-Apple chief plans mobile phone for India

Former Apple chief executive John Sculley, whose marketing skills helped bring the personal computer to desktops worldwide, says he plans to launch a mobile phone in India to exploit its still largely untapped ...

Filipino tests negative for Middle East virus

A Filipino nurse who tested positive for the Middle East virus has been found free of infection in a subsequent examination after he returned home, Philippine health officials said Saturday.

Egypt archaeologists find ancient writer's tomb

Egypt's minister of antiquities says a team of Spanish archaeologists has discovered two tombs in the southern part of the country, one of them belonging to a writer and containing a trove of artifacts including reed pens ...