Probing Relationships between Protein Structure and Movement

by Jeff Cutler

Penny Beuning’s research is based on relationships. Proteins, DNA, RNA in a dance of scientific compatibility. A dance that affects life, the fight against disease and understanding how to create new chemical reactions.

An associate professor in Chemistry and Chemical Biology at Northeastern University’s College of Science, Beuning’s groundbreaking efforts were documented recently in a paper published in “Structure.” In it, she detailed how various proteins might act in different situations in the lab.

“There are many examples of proteins of similar structure with similar dynamic behavior, but so far our work is one of very few examples of proteins of similar structure with really different dynamics,” said Beuning.

As she explains it, for a cell to work properly, proteins have to be made correctly every time so that biological information is propagated accurately from the DNA that contains the genetic code to the RNA and protein molecules that carry out the business of cells.

A focus of her research was in trying to understand how cells replicate DNA accurately and how they deal with damage to their DNA. Part of her research involved the proteins that carry out the work, which led to the paper in “Structure.”

“We first looked at the movements of a ring-shaped processivity clamp protein that binds DNA, the protein is like a donut, and the DNA goes through the donut hole. The clamp protein controls which other proteins can bind to it and to the DNA like a ‘traffic cop,’” said Beuning. “One interesting thing about the clamp proteins is that their structures are really similar: whether the clamp is from a bacterium, yeast, plants, or humans, they basically look the same. So we wanted to know if the very dynamic nature of the E. coli (bacterial) clamp would be similar or different in other clamps—they look the same, do they behave the same? And the answer was definitely no.”

Ultimately, she found with the exception of a few similar themes across the clamps, their dynamics were very different. Which led to her conclusion that just because proteins look similar, doesn’t mean that even as something as fundamental as how they move will be similar. However, the relatively minor parts of the proteins that have similar movements are the regions involved in binding DNA, which is something all clamps have in common. This indicates that the movements are important for the biological function of the clamp proteins.

But the life of a college professor and research scientist isn’t all data and theories. Beuning said her paper allowed her to travel to Lithuania as part of the collaborative process. In a profession where free time doesn’t readily present itself, she’s been able to create a network of researchers all over the world as part of her job.

Beuning’s advice for anyone interested in research science is to do what you love. Be creative and think every day. Also to help those who come after you.

The work in this most recent paper was carried out with two Ph.D. students and with Prof. John Engen, also in Chemistry and Chemical Biology, in addition to Beuning’s collaborators in Lithuania. “Northeastern fosters a very collaborative and international research environment, which really increases our impact” said Beuning.

“I would like the work my group does to help people, to lead to a better treatment for a disease, or to improve the natural environment,” said Beuning, “I also feel fortunate to have interacted with wonderful students in my research group, from undergraduate co-op students to graduate students in the Ph.D. program, and hope they will use what they’ve learned to better humanity.”

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Posted in Chemistry and Chemical Biology

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