DURHAM – Although most research laboratories at Duke University are shuttered to prevent future transmission of the COVID-19 coronavirus, one of the few to remain open is the Shared Materials Instrumentation Facility (SMIF), which houses a Duke shared cleanroom and characterization facilities. And of the typical 550+ SMIF users, only a few are now allowed to work in the facility on COVID-19 research.
One of the key instruments in the SMIF is a multimillion-dollar cryo-electron microscope (cryo-EM for short), the Titan Krios, which is able to “see” proteins in atomic-level detail by taking hundreds of thousands of molecular images of a biological specimen and then classifying and averaging them with powerful software to create a 3D image, and ultimately, a model of the protein.
And keeping the machine creating these atomic-level images is no easy feat. In the time of coronavirus, the complex machine is being entirely supported by only two engineers—Mark Walters, director of SMIF, in which the Titan Krios resides, and Holly Leddy, a cryo-EM specialist on the SMIF staff.
In the case of the coronavirus, Duke School of Medicine scientist Priyamvada Acharya and her team are using the Krios to determine structures of the coronavirus spike protein—the part of the virus that sticks out, attaches with the host and helps the virus enter into human cells.
“We are using the information to learn, at a basic level, details of how the spike functions, and translate this knowledge for vaccine design,” said Acharya, PhD, an associate professor of surgery in the School of Medicine and director of the Division of Structural Biology at the Duke Human Vaccine Institute.
Better understanding of the structure and function of the spike will also help the team develop molecular hooks to pull out antibodies from the blood of COVID-19 patients, which could be used for vaccine development.
Acharya has been using a similar approach in her quest to develop a vaccine for HIV.
“Cryo-EM helps you rapidly figure out the fine details of intermolecular interactions, thereby giving you the tools to manipulate those interactions to make the best vaccines to trigger the immune system to make protective antibodies,” she said.
But figuring out these fine details is harder than it sounds and is made even harder by the personnel and distancing restrictions made necessary to keep everyone involved safe. For example, the Titan Krios’s sample chamber continuously consumes liquid nitrogen to keep samples at sufficiently low temperatures to work—hence the term “cryo.” And it’s a hungry beast. The machine goes through a large canister of liquid nitrogen about every five days.
“With the building being locked and with a significantly reduced staff, we have to closely coordinate to make sure the deliveries arrive when Holly or I are here to let the Airgas nitrogen delivery into the lab,” said Walters. “We also have to stagger our schedules and practice social distancing while we’re helping the researchers.”
For example, only two people are allowed at the Cryo-EM controls at a time, and those two people must maintain at least a six-foot distance from each other. This means one person will be working the controls while the other is standing back more than six feet. They also wipe down the keyboards and controls at least daily and wear gloves when touching them. Once samples are loaded into the machine and initial alignments are performed, however, just about all the other functions can be controlled remotely.
“A typical experiment using the Cryo-EM has Holly loading the samples then stepping away so that I can come in and assist the researchers with the alignments and getting the run set up,” said Walters. “Then once it’s set up, we leave and the researchers and I can run and monitor data collection remotely.”
Despite these challenges and complications, everyone agrees that keeping the machine running is worth the hassle. This operation is a great example of how the School of Medicine and the Pratt School of Engineering (where SMIF resides) support each other and work together on critical COVID-19 research.
“As we move towards the development of a safe and effective vaccine for COVID-19, it’s absolutely imperative that we understand which parts of the virus we need to use for immunization,” said Colin Duckett, vice dean for basic sciences in the School of Medicine. “The right parts will train the immune system to kill virally-infected cells without harmful side effects, but we can only figure that out if we know the active structure of the key proteins, especially the spike protein. That’s where Dr. Acharya’s group comes in. The progress that Dr. Acharya and her team have made so rapidly is nothing short of remarkable.”