Cryo-EM: It’s a Small, Small World

Scientists in the new St. Jude Cryo-EM and Tomography Center zoom in on staggeringly small structures to better understand biological systems.

 

By Keith Crabtree, PhD; Photo by Seth Dixon

Glimpse inside a protein: CryoEM allows scientists to see 3-D structures of proteins at atomic resolution.

 
 
  • A Titan Krios electron microscope with a Volta phase plate. Check.

  •  A Talos Arctica electron microscope (which, like the Krios, is equipped with K3 direct electron detector and energy filter). Check.

  • A Vitrobot and a plasma cleaner for sample preparation. Check.
 

These are only a few of the items required to assemble a world-class cryo-electron microscopy (cryo-EM) center.

St. Jude Children’s Research Hospital opened such a facility in 2018. In the Cryo-Electron Microscopy and Tomography Center, scientists can zoom in to see 3-D molecular and cellular images at atomic resolution.

How small is that?

Well, atoms measure about one ten-billionth (1/10,000,000,000) of a meter.

Now, that’s small.

Just look at the thing

In 1960, a scientist from Caltech proposed a new field of “small-scale” physics. “It is very easy to answer many of these fundamental biological questions,” said Nobel laureate Richard Feynman, PhD. “You just look at the thing.”

Feynman challenged physicists to increase the power of electron microscopes. For decades, X-ray crystallography was the main technique for imaging proteins — the building blocks of cells. Then came the cryo-EM resolution revolution. Suddenly, scientists were able to see proteins that had once been too floppy or wiggly to image.

At St. Jude, Liang Tang, PhD, director of the Cryo-EM Center, calls the hospital’s new electron microscope a “monster.”

Located in the Danny Thomas Research Center, the Titan Krios nearly fills one of two rooms dedicated to this equipment. The smaller Talos Artica is in the other room.

The Krios sits atop a platform designed to pick up and absorb ambient vibrations — voices, footsteps, even a dropped mug. White Lego-like panels filled with flowing water hang from the wall to regulate room temperature, since electrons are sensitive to temperature. With this equipment, scientists can render high-resolution pictures of many kinds of molecules, including membrane proteins.

Charalampos “Babis” Kalodimos, PhD, and Liang Tang, PhD, examine a sample.

The resolution revolution

Charalampos “Babis” Kalodimos, PhD (at left), St. Jude Structural Biology chair, and Liang Tang, PhD, director of the Cryo-EM Center, examine a sample that will be analyzed using the Talos Arctica electron microscope, situated behind them. With this equipment, scientists can zoom in to see 3-D molecular and cellular images at atomic resolution.

World-class resource

It’s crucial that scientists be able to scrutinize the structures of biomolecules, especially membrane proteins, which are targeted by many drugs.

“Membrane proteins are typically difficult to capture with X-ray crystallography,” says Stephen White, DPhil, dean of the St. Jude Graduate School of Biomedical Sciences and former Structural Biology chair. “But with cryo-EM, you can access membrane proteins really well.”

In cryo-EM, a tiny bit of a protein sample is frozen by plunging it into liquid ethane. Then an electron gun shoots electrons through the protein molecules at a high speed while a detector captures them. A computer algorithm sorts the resulting images, and a software program — averaging hundreds of thousands of molecules — creates a 3-D composite image in ultra-high resolution.

By knowing the 3-D structure of a protein — for example, one that carries a disease-causing mutation — scientists will be able to better understand how the protein works.

Liang Tang, PhD

 
 

A complete toolset

“Cryo-EM is probably the most powerful tool you can have in structural biology,” says Charalampos “Babis” Kalodimos, PhD, St. Jude Structural Biology chair.

Nevertheless, in order to build the world’s premier structural biology program, Kalodimos and his colleagues require additional tools to study the structure and dynamics of large molecules.

“We’re investing heavily in complementary techniques,” Kalodimos says, “because you need to have the complete toolset.”

The St. Jude toolset includes not only cryo-EM but also nuclear magnetic resonance spectroscopy, X-ray crystallography, single-molecule imaging and mass spectrometry.

In 2019, St. Jude will install one of the world’s most powerful magnets for the study of biomolecules.

“This integrated approach,” Kalodimos says, “gives us confidence that we will be able to tackle any biological system, no matter how challenging.”

Using cryo-EM to advance cures  

Some pathways to developing new medicines and preventing catastrophic diseases are already known.

“By knowing the 3-D structure of a protein — for example, one that carries a disease-causing mutation — scientists will be able to better understand how the protein works,” Tang says. “This may enable scientists to find ways to manipulate its function and interfere with the occurrence or progression of the disease.”

With a complete toolbox, St. Jude scientists are equipped to “just look at the thing,” to increase their understanding of miniscule biological systems and to design new medicines and therapies.

From Promise, Winter, 2019

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