Beyond the resolution revolution
In piano, practicing scales lays the foundation for generating great music. At UT Southwestern Medical Center, thinking across scales exerts a similar effect for science.
When Cell Biology Chair Dr. Sandra Schmid and Biophysics Chair Dr. Michael Rosen began UT Southwestern’s journey to build the University’s $22.5 million cryo-electron microscope (cryo-EM) facility in 2013, the resolution achieved with the technology still fell short of the atomic-level resolution of X-ray crystallography. With these atomic details unseen, the molecular models were more blurry than the “gold standard” structures obtained by X-ray crystallography. Hence, cryo-EM had the nickname “blob-ology.”
Not to be dissuaded, the two department Chairs shared a long-range vision. They were certain of the potential importance of cryo-EM and assumed that the technical issues – which at that point presented a roadblock to achieving high-resolution – would soon be, well, resolved.
“We were ahead of the curve. When we started the project, cryo-EM was achieving resolution that was short of the atomic level available from X-ray crystallography. By the time we finished, true atomic resolution had become attainable with cryo-EM,” Dr. Schmid recalls.
“Cryo-EM is a big University investment, and I think it’s beginning to pay wonderful dividends.”
Drs. Rosen and Schmid envisioned a multidisciplinary research program that reflected native protein structures in their cellular context. Cells work over two major scales: size and time. Cell organization occurs on size scales spanning from an entire cell down to individual atoms, a 100,000-fold range. Similarly, cellular processes occur over time scales that span from hours for circadian responses down to milliseconds for movements of individual molecules, a range greater than 1 millionfold.
“Importantly, our collaboration resulted from us thinking across scales, and thus unlike most cryo-EM facilities that emerged purely from a structural biology perspective, we focused from the beginning on complex machinery and structure in a cellular context,” says Dr. Schmid, a Professor of Cell Biology who holds the Cecil H. Green Distinguished Chair in Cellular and Molecular Biology.
Finding the right people
Next came recruiting the right people, the first of whom was Dr. Daniela Nicastro, Associate Professor of Cell Biology and Biophysics and a Cancer Prevention and Research Institute of Texas (CPRIT) Scholar, who arrived at UT Southwestern in 2015 from Brandeis University following training at the Max Planck Institute for Biochemistry in Munich, Germany, and at the University of Colorado, Boulder.
“She was the perfect first recruit, as she is rare in her ability to bring extensive knowledge and experience in cryo-EM tomography and single-particle cryo-EM – in its application as well as in methods and instrument development. A trifecta!” Dr. Schmid says.
Cryo-EM has two main branches. In single-particle cryo-EM, one isolated protein or protein complex is 3-D reconstructed. Cryo-EM tomography is usually employed to image complex mixtures of proteins.
A specialist in cryo-EM tomography, Dr. Nicastro is credited with important contributions both technically and biologically to advance cryo-EM methods. She accomplished that via a multilength scale approach that ranged from studying intact tissues to small molecular motors such as dynein, which she describes as the largest and most elusive cytoskeletal motor.
She played a key role in building UT Southwestern’s new cryo-EM facility, which opened in 2016, and is working to expand access to cryo-EM across campus.
“Dany is very generous with her time and is community-minded. She has worked hard to build a cryo-EM facility and program that would benefit everyone at UT Southwestern,” says Dr. Rosen, a Professor of Biophysics with an appointment in the Cecil H. and Ida Green Comprehensive Center for Molecular, Computational, and Systems Biology, and a Howard Hughes Medical Institute (HHMI) Investigator.
The facility’s second recruit, Dr. Xiaochen Bai, is an Assistant Professor of Biophysics and Cell Biology, a CPRIT Scholar, and a Virginia Murchison Linthicum Scholar in Medical Research. He came to UT Southwestern from the MRC Laboratory of Molecular Biology, Cambridge, United Kingdom. There, Dr. Bai worked in a laboratory down the hall from that of 2017 Nobel Prize in Chemistry co-winner Dr. Richard Henderson, recognized for his work to develop the technology that made high-resolution cryo-EM a reality.
All of the cryo-EM facility’s progress became possible due to the willingness of UT Southwestern’s leadership – Dr. Daniel K. Podolsky, President; Dr. J. Gregory Fitz, Professor of Internal Medicine; Dr. David Russell, Vice Provost and Dean of Research; and Arnim E. Dontes, Executive Vice President for Business Affairs – to share the vision of developing a word-renowned cryo-EM program.
Funding for the project came from many sources, including the President’s Office, departmental funds, a private donor, Dr. Rosen’s successful HHMI grant that purchased one of the microscopes, the UT System’s Science and Technology Acquisition and Retention program, Dr. Nicastro’s CPRIT recruitment grant, and, most recently, her CPRIT core grant to expand access to cryo-EM across campus.
“The costs were much larger than our initial estimates and the administration came through,” Dr. Schmid says.
Finally, came the implementation of the plan.
For more than a year, Drs. Nicastro and Schmid held weekly meetings with design engineers, architects, construction company representatives, special equipment vendors, and the company that made the electron microscopes. The early meetings were to design and build the state-of-the-art facility; the later ones focused on installation of the instruments, taking into account the many details necessary to get the specifications just right to enable the achievement of atomic resolution.
“Cryo-EM is a big University investment, and I think it’s beginning to pay wonderful dividends,” says Dr. Rosen.
As evidence, Dr. Rosen, who holds the Mar Nell and F. Andrew Bell Distinguished Chair in Biochemistry, pointed to back-to-back cryo-EM structural studies recently published by UT Southwestern scientists in Nature. Those studies grew out of the collaboration between Dr. Bai and Dr. Youxing Jiang, a Professor of Physiology and Biophysics and a W.W. Caruth, Jr. Scholar in Biomedical Research. Other structures solved during the facility’s first year are currently under review in top journals.
“It’s a testament to the University for bringing together the resources on that kind of scale,” Dr. Rosen says.
Dr. Fitz holds the Nadine and Tom Craddick Distinguished Chair in Medical Science.
Dr. Podolsky holds the Philip O’Bryan Montgomery, Jr., M.D. Distinguished Presidential Chair in Academic Administration and the Doris and Bryan Wildenthal Distinguished Chair in Medical Science.
Dr. Russell holds the Eugene McDermott Distinguished Chair in Molecular Genetics.