Van Andel Institute Trains Next Generation of Cryo-EM Structural Biologists

September 20, 2018 § 2 Comments

By George Van Den Driessche

Cryo-electron microscopy, or cryo-EM, is structural biology’s golden ticket these days. Since the game-changing technology won the 2017 chemistry Nobel Prize, it feels like there is no problem that cannot be solved by cryo-EM.

Do you have a large protein that won’t crystallize? Are you studying transporter channels or membrane signaling proteins and have no idea what the protein looks like?  Or are you designing new antiviral agents and need the viral capsid structure? Then, at least the current trend suggests, you should consider using cryo-EM, a technique that flash freezes proteins in liquid nitrogen and analyzes electron diffraction patterns to determine the molecular structure of proteins.

The Van Andel Institute, a nonprofit biomedical research facility in Grand Rapids, Michigan, invested more than $10 million dollars to install the David Van Andel Advanced Cryo-EM Suite in 2016. Last year, VAI celebrated the opening of its new facility with a conference about cryo-EM’s advancement of structural biology. This year, VAI hosted a special cryo-EM training workshop for graduate students, postdocs and new faculty. (Full disclosure: VAI awarded travel scholarships to workshop attendees, and I was one of them.)

Attendees at the Van Andel Research Institute’s cryo-EM training workshop this summer.
Van Andel Research Institute

Huilin Li, the VAI cryo-EM core director, designed the workshop so attendees could learn about cryo-EM theory and research advances on the first day and then spend the remaining time working with the microscopes, discussing protein-preparation techniques and reviewing image processing software. “This is a privately endowed research institute. We do research, collaboration, outreach and training. This workshop is part of the training,” Li said.

VAI assistant professor Juan Du, one of the presenters, studies TRPM4 channel proteins. TRPM4 is a calcium-activated nonselective (CAN) cation channel that monitors cellular charge by measuring calcium ion concentration. When the cell’s charge becomes too positive, calcium ions bind to TRPM4, and single-charged cations, such as sodium or potassium ions, flow through the channel. This process decreases the cell’s overall positive charge.

Du’s team determined the structure of TRPM4 and identified key calcium and modulator binding sites using single-particle cryo-EM. Their work appears in Nature. She advised attendees, “We are structural biologists, so we use all kinds of tools to solve problems, and very soon cryo-EM will be equal to X-ray crystallography, and, when that day comes, success will depend on who has a sample in hand. So, remember that biochemistry is the key to success.”

Keynote speaker Steve Ludtke, a professor of biochemistry and molecular biology at Baylor College of Medicine, presented his lab’s research streamlining cryo-electron tomography (cryo-ET) image annotation.

Cryo-ET allows researchers to see the dynamic interactions of frozen macromolecules and offers insight into the native environments of cells. Traditional cryo-EM requires protein purification, and this raises the possibility of disrupting a protein from its natural orientation.

Preparing grids for Titan Krios microscope: (left) loading grids prepared in liquid nitrogen, (top right) an unprepared grid, and (bottom right) the microscope
George Van Den Driessche

However, a major hurdle facing cryo-ET is the time required for image annotation. Image annotation is a task where scientists identify all the individual macromolecules by hand in a series images. A fully annotated cryo-ET image takes about a week to complete.

Ludkte is training deep learning models to overcome the image annotation time barrier. These models are capable of learning a wide-range of macromolecule features (such as distinguishing double-membrane mitochondria from single-membrane organelles) and require minimal training. Each model needs only 10 human annotated training images before the algorithm can begin recognizing patterns in the cryo-ET image.

Georgia Institute of Technology graduate student Kasahun Neselu said he enjoyed the hands-on training and was leaving feeling excited and filled with ideas to test on his own research projects.

Fatemeh Abbasi Yeganeh, a graduate student at Florida State University, said she enjoyed learning more about cryo-EM, meeting new people who share her passion for structural biology, and gaining confidence in the field.

“Currently, EM is the main focus of my Ph.D. project, and I take any opportunity to learn more and meet new people in the field,” Yeganeh said. “So, what can be better for a graduate student than attending a workshop that pays all your expenses, teaches you about your favorite field of study, and, also, gives you the opportunity to meet and talk to experts in the field?”

Top and side view of the TRPM4 calcium channel
George Van Den Driessche

George Van Den Driessche (gavanden@ncsu.edu) is a graduate research assistant in the Fourches lab at North Carolina State University.

NCATS issues awards to repurpose shelved compounds

June 18, 2013 § Leave a comment

The National Institutes of Health announced today that it has awarded $12.7 million to nine academic research groups matched with pharmaceutical companies to explore new uses for some of the companies’ shelved compounds. One of the awards was issued to ASBMB member Stephen M. Strittmatter and his team at Yale University School of Medicine.

Strittmatter, along with Haakon Berge Nygaard and Christopher H. Van Dyck, will explore the use of a compound from AstraZeneca called saracatinib, or AZD0530. The team recently characterized, using a mouse model, a pathway in which beta amyloid damages neurons in Alzheimer’s disease; they found that inhibiting the Fyn kinase in that pathway reduced symptoms. The new study will test the use of saracatinib as a Fyn inhibitor, first in mice and later in humans, for safety. Previously, AstraZeneca had tested the compound in humans with cancer.

Another group based at Baylor College of Medicine will study saracatinib in a lung disease called lymphangioleiomyomatosis.

The award program, called Discovering New Therapeutic Uses for Existing Molecules, is led by the National Center for Advancing Translational Sciences and is funded by the NIH Common Fund. In late May 2012, NCATS made available information about more than 50 shelved compounds and solicited proposals about new uses from academic researchers. Those proposals were peer-reviewed, and then cooperative agreements between the winning institutions and the pharmaceutical companies were forged.

During a news teleconference today, NCATS officials indicated that they’d aimed to fund about six projects through the program but ended up having enough money to fund more because the funding requests from the winning proposals were lower than expected.

NCATS Director Christopher P. Austin said during the telebriefing: “These companies have invested between $10 (million) to even $100 million in these drugs to get them to this point. We around here talk about football. This is an analogy of the drug-development process … Some of these drugs have been taken all the way to the 10-yard line or the 5-yard line, and we’re hoping that we can have a new special team come in and even run a play or two and have a touchdown formation. So we’re really hopeful one of these will result in the end zone really soon.”

 

This is a guest post by Angela Hopp, editor of ASBMB Today.

Science funding through crowdsourcing

March 15, 2012 § 1 Comment

Image from http://www.public-domain-image.com/miscellaneous/money/slides/penny-pennies-coins-money.html

Did your or your adviser’s grant get rejected from a federal agency despite scoring well because of tight purse strings? Well, maybe it’s time to turn to your neighbors, family members, friends and interested strangers for some cold, hard cash.

The idea isn’t bizarre. Kickstarter made its name a few years ago for setting up a mechanism so people with ideas for creative projects could request funds from anybody by describing their ideas and proposing a budget. Folks checked out the projects and, if one caught their fancy, pledged some of their own money, anywhere from a few dollars and up, to help the project come to life.

Now that idea has crossed over from the arts to science. The two examples I’ve come across that emulate the Kickstarter model are the SciFund Challenge and PetriDish.

The SciFund Challenge, established by two ecologists,  Jai Ranganathan and Jarrett Byrnes, has been around since last summer. The PetriDish was founded by Matt Salzberg, who previously worked at Bessemer Venture PartnersIt appeared on the scene earlier this year.

Last year, SciFund Challenge scientists raised $76,230 for their research. From the first round of funding, SciFund Challenge’s Ranganathan and Byrnes compiled some stats on how the SciFund Challenge has fared so far in terms of raising money for projects. One interesting tidbit: The median contribution from a person was $25, but most of the money for a project came from a few large contributions.

In both cases, I didn’t seem to find any fundamental molecular biology or biochemisty projects. There are quite a few ecology and marine biology types of projects. It will be interesting to see how these kinds of projects fare in the crowdsourcing world. Is there anyone out there willing to give it a shot?

As with getting money from anywhere, you have to make a compelling argument as to why you deserve the funding. Remember, you are not selling your idea to fellow scientists familiar with the jargon and context for the research. You have to able to sell your pitch to intelligent people who don’t have the same scientific know-how as you do about your area of work but are interested in what your science has to offer. It’s an important skill to have!

The SciFund Challenge is calling for projects for its second round of crowdsourcing. The deadline for proposals is March 31. PetriDish appears to solicit project ideas at all times.

Enjoy!

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