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Rutgers Scientists discuss importance of 2017 Chemistry Nobel Prize winner

When the 2017 Nobel Prize in Chemistry was awarded to the developers of cryo-electron microscopy (Cryo-EM), scientists at the Rutgers Center for Integrative Proteomics Research were not surprised. The technique has aided Rutgers scientists — and the University as a whole — in many ways.

The Chemistry Nobel was awarded on Oct. 4 to Jacques Dubochet, Joachim Frank and Richard Henderson “for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution.”

Getting a proper look at biomolecules such as proteins is the first step toward understanding how they work. Electron microscopy (EM) involves firing a beam of electrons at a sample and observing how the beam is disrupted, allowing scientists to back-project what the sample looks like, down to individual atoms.

Biomolecules are fragile and water-logged, two things that make their analysis tricky. Single particle Cryo-EM gets around this by freezing the proteins in glassy ice and compensating for a gentler beam of electrons by taking more images from multiple angles.

Rutgers has a strong international reputation when it comes to studying proteins, in part thanks to its position as host of the Protein Data Bank (PDB) – an international, public repository for protein structures.

As Catherine Lawson, an associate research professor in Proteomics explains, Rutgers also hosts a special database for Cryo-EM images called the Electron Microscopy Data Bank (EMDB). The PDB holds models of proteins, the EMDB holds the raw data used to create these models, called “maps."

The first electron microscopy structure was archived in the PDB in 1992 before Rutgers won the contract to manage the Data Bank. The EMDB was founded four years later as a way to better understand the models in the PDB. Not long after that, Rutgers took charge of the EMDB too.

There are now over 13,000 structures in the PDB and 5,200 maps in the EMDB. In 2016 there were over 1,000 maps submitted to the EMDB, and the rate is increasing.

Rutgers is well-connected to the newest Chemistry Nobel Laureates. Lawson points out that Richard Henderson is a Data Bank board member, and Joachim Frank works at Columbia University, making him a “local.”

Lawson helps manage the EMDB and describes her mission to “work on creating the infrastructure for collecting information about Cryo-EM experiments, to collect meaningful data and to try to make it easy for scientists.”

Brian Hudson, a research associate in proteomics and biocurator of the databanks performs quality control on new submissions. The maps do not need to be perfect, he says, but they should be standardized and informative so everyone understands how they were created.

“There are EM maps that are blobs, and there are EM maps that are detailed level of resolution. They can both be perfectly useful in their own particular ways. But you want this blob to be the best possible blob it can be,” Hudson said.

In the proteomics basement, Rutgers scientists generate their own Cryo-EM images using state-of-the-art facilities first launched in 2015. Jason Kaelber, assistant research professor in proteomics and Cryo-EM facility director, estimates that there are fewer than a hundred 200 kV electron microscopes in the world, and Rutgers has one of them.

"This is the very latest generation of instruments,” Kaelber said. “At Rutgers the instruments we have are capable of achieving the resolution you need to be useful for designing new drugs.”

Some of the best expertise at Rutgers is in imaging whole cells and parts of cells, which is exciting in terms of the fundamental understanding of cell biology, he explained.

One of those experts is Wei Dai, assistant professor in the Department of Cell Biology and Neuroscience.

In her research, Dai wants to “take a screenshot of the protein complex without purification, when they are in action in biological processes. I’m interested in several biology stories, for example host-phage interaction, protein aggregation in degenerative diseases or anti-drug resistance.”

To achieve these screenshots Dai and her team rely on a variant of Cryo-EM called cryotomography. “If you say 'single particle' you’re interested in a shared structural feature of the population. In tomography you want to look at a unique feature of individuals,” Dai said.

The difference between tomography and single particle is how the different orientations are retrieved in order to construct a 3D image, Hudson said.

“With a tomogram you have something sitting on the stage in the microscope and you just tilt the sample back and forth so that you get different views of it to reconstruct a 3D image,” he said

With single particle, the particle is embedded in vitreous ice (which is more like a glass) and there are these particles all in different orientations so when a beam is shined through it, one can observe these particles in a whole bunch of different orientations, he said.

One could use those, classify them and average them out to reconstruct a 3D image, Hudson said.

As Kaelber points out, the hard part of Cryo-EM is fitting your microscope settings to the sample. “You can get enough data to get an atomic resolution structure in a couple of days. But you usually don’t, because there’s a lot of optimization that goes into it.”

Dai said that it could take three or more years before her group members obtain publishable data from their Cryo-EM experiments.

According to Kaelber, Rutgers is eyeing a new 300 kV electron microscope, which would cost over $5 million in federal grants and university funds. A more powerful microscope would allow even better image visualization.

Lawson and Hudson hope to continue their mission of archiving and curating the increasing volume of Cryo-EM data — convincing other scientists of the importance of sharing their raw data.

“Every published structure from the last 50 years is available online for free in the PDB. Not moldering on a tape, in a pile, in a lab, in a format they no longer make hardware to read anymore — which is where a lot of this data would end up,” Hudson said.

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