TSRI Scientists Lead New Age of Electron Microscopy

By Madeline McCurry-Schmidt

We were supposed to have moon colonies by 2014. We were going to be using cold fusion and robot maids. At the very least, shouldn’t we have hover boards by now?

The craziest sci-fi dreams rarely come true—that is, unless you’re in the field of electron microscopy. 

With more stable microscopes and a new generation of cameras, researchers in electron microscopy (EM) can now peer at biological molecules at near-atomic resolution to see how proteins involved in disease really interact. This leap from low-resolution to near-atomic images has shocked even those who have spent their entire careers pushing the field forward. 

“Three years ago it wasn’t possible to get to this resolution,” said Professor Ron Milligan, who joined The Scripps Research Institute (TSRI) 28 years ago. “I never thought we’d see this.” 

Yet at the recent week-long “Workshop in Advanced Topics in EM Structure Determination,” organized by TSRI faculty members and EM experts Bridget Carragher, Clint Potter and Milligan, nearly 60 posters of structures—many at near-atomic resolution—lined the hallways. These images showed viruses, bacteria and human cells with more detail than researchers had ever seen before. 

It’s a new era for EM, and researchers are using the tools they’ve developed over the last 30 years to answer some of the toughest questions in biomedical research.

A Giant Leap 

“This level of resolution was a dream”—that’s what Liz Wilson-Kubalek, senior staff scientist in Milligan’s lab, thought of atomic-resolution images back in the 1980s when she first became involved in electron microscopy structure determination. 

In EM, scientists illuminate samples using high-energy electrons. The electrons beam down through a vertical, tube-like microscope column, and electro-magnetic lenses focus the beam of electrons to form a high-resolution image. Today, although the overall process is the same as it was 30 years ago, the data collection processes and the quality of images are very different.

Milligan used to build his molecular models out of balsa wood, not lines of code on a computer. And just six years ago, Wilson-Kubalek was developing her images in a dark room. 

In 2001, Milligan and other EM experts started the Center for Integrative Molecular Biosciences at TSRI.  Professors Potter and Carragher were recruited to develop programs to automate EM image acquisition and processing techniques. This approach spread rapidly within the field and now most labs collect and process EM data using programs based on ideas developed by Carragher and Potter at TSRI. 

A critical advance came in 2014, when TSRI added two new microscopes to its microscopy suite. One of the new microscopes, the FEI Titan Krios, is coupled to a new generation of digital camera, the Gatan K2 Summit. This camera is superior for EM because it detects electrons directly instead of having to convert electrons to light. The new detectors also capture images at a very high speed, essentially capturing a movie of the specimen during imaging, rather than a single frame. The frames of the movie can be computationally aligned to solve the longstanding problem of image movement. In the best cases, the result is an image containing near-atomic resolution information that can be combined with others to calculate a detailed three-dimensional map of the biological material of interest. 

“Now that we can get to high resolution, we can do some really cool biology,” said Milligan. 

A Foundation for Fighting Disease 

At TSRI, scientists are using these new capabilities to find the structures of proteins and large complexes—molecular machines—crucial to cancer, HIV and even the Ebola virus.

One of the projects in Milligan’s lab focuses on the process of cell division. During cell division, chromosomes attach to microtubules that pull them part. Milligan, Wilson-Kubalek and Assistant Professor Gabriel Lander are using EM to find the structure of one of the molecular machines that helps attach the chromosomes to the microtubules. This basic research provides the foundation for understanding how cancer cells divide unchecked—information that helps cancer researchers develop new strategies and therapies.

Carragher and Potter take advantage of opportunities for collaboration with biologists at TSRI and across the country. Much of this work is carried out as part of the NIH supported National Resource for Automated Molecular Microscopy, of which they are co-directors. At TSRI, one of their collaborators is TSRI Professor Jack Johnson, who uses EM to study the structures of viruses to learn how they mature and become infectious. 

Johnson’s lab demonstrated the power of EM in recent imaging experiments with Nudaurelia capensis omega virus, a pathogen that infects insects. Through EM, the researchers were able to acquire detailed images of how the viral RNA is packaged and positioned for delivery. Johnson noted every animal and bacterial virus studied matures before morphing into an infectious form.

“Electron microscopy is absolutely the most wonderful method for following the maturation process,” said Johnson. “This could lead to new strategies for improving human health in the long term. And Scripps Research is just about the best-equipped place in the world for this.”

The ability to solve structures faster was also crucial this year when TSRI researchers used EM to study how an experimental Ebola treatment, ZMapp, interacted with the deadly virus. TSRI Professor Erica Ollmann Saphire and Assistant Professor Andrew Ward led the project, which confirmed the existence of a vulnerable spot in Ebola’s outer layer. They plan to use the same techniques to test future treatments.

Other TSRI scientists are also using EM to tackle many other diseases. Ward and Ian Wilson, Hansen Professor of Structural Biology, are leading studies on HIV/AIDS and influenza virus that should ultimately help in the development of vaccines. Associate Professor Francisco Asturias is studying gene regulation and its tie to cancer and inherited developmental disorders. Assistant Professor Gabriel Lander is looking into toxic protein aggregates with implications for Huntington’s, Parkinson’s and Alzheimer’s diseases. And Professor Nigel Unwin is investigating cell receptors and the workings of the nervous system.

“It’s so exciting to see that these new developments are now making it possible to solve problems that people have been struggling with for more than a decade,” said Wilson-Kubalek.

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