New and unexplored dimension in the study of protein-protein interactions

December 7, 2020

Many proteins are required to maintain the structure, and to preserve the genetic integrity, of DNA. Sliding clamps are proteins that increase the efficiency of DNA replication. Without these proteins, cells would not be able to carry out continuous DNA synthesis, and organisms, from bacteria to humans, would not survive.

Sliding clamps are ring-shaped proteins that encircle DNA and bind to the DNA polymerase, the enzyme that performs the actual DNA replication. They effectively organize and orient the DNA and its ancillary proteins so as to enable replication. Sliding clamps are oligomeric proteins; they are made up of more than one identical copy of individual proteins called monomers. Marcia Levitus, associate professor in the School of Molecular Sciences and faculty member of the Biodesign Center for Single Molecule Biophysics. Download Full Image

The bacterial E. coli clamp, called beta, is made up of two identical monomers. Human cells contain clamps called PCNA, which are made up of three identical monomers. Strong intermolecular forces between these identical monomers ensure that the rings are stable in solution and do not fall off the DNA during replication.

The self-assembly of the monomers of sliding clamps into a stable doughnut-shape ring is controlled by ionic and other intermolecular forces. It is known that assembly of these structures can be influenced by the presence of salts, but other forms of molecular control over this self-assembly are not well understood. In an effort to understand the molecular basis for clamp self-assembly, Associate Professor Marcia Levitus from Arizona State University's School of Molecular Sciences and co-workers have now found that these protein doughnuts assemble in previously unknown ways when exposed to molecules that bacteria typically use to tolerate high levels of salt in the environment.

Specifically, potassium glutamate (KGlu) and glycine betaine are found to promote self-assembly of beta and PCNA clamps into structures containing many doughnuts stacked face-to-face. These structures resemble tubes of doughnuts, and are only observed in the presence of compounds that cells produce when they need to tolerate high-salt concentrations in the growing medium.

Their research, which has just been published in the Biophysical Journal, is a result of a long-standing collaboration with Professor Linda Bloom, who works in the department of biochemistry and molecular biology at the University of Florida.

“In this study we examine non-Coulombic effects on the self-assembly properties of sliding clamps,” Levitus explained. “We determined relative diffusion coefficients of two sliding clamps using fluorescence correlation spectroscopy. Although so far we worked with two sliding clamps, our results suggest that our findings are not specific to these proteins and may be generalizable to a wide range of protein-protein interactions.” Levitus is also part of the Biodesign Center for Single Molecule Biophysics.

Cells accumulate glutamate and related molecules under stress, and so formation of high-order protein assemblies under these conditions has important biological implications. Specifically, this would represent a mechanism by which the presence of stressor compounds in the cell could control DNA replication.

Ian Gould contributed to this story.

Jenny Green

Clinical associate professor, School of Molecular Sciences


No-notice deployment, two moves and a marriage: ASU Online grad did it all while pursuing degree

December 7, 2020

Editor's note: This story is part of a series of profiles of notable fall 2020 graduates.

Iiae Braham always loved school and learning new things. So it’s no surprise she began her studies at 17 at a local community college in her hometown of Lincoln, Illinois. While a psychology degree was her main goal initially, after taking a sociology course taught by an amazing professor, Braham knew her path. And this month, she will be graduating with a degree in sociology and a minor in organizational leadership from Arizona State University. ASU Online student, 2020 graduate Iiae Hess Download Full Image

While taking classes back in her hometown, finances proved difficult, so Braham joined the U.S. Air Force to help pay for her degree. It was joining the Air Force that also introduced her to ASU. Braham was stationed in Arizona for the first five years of her Air Force career. Although there were other options for her in and around Tucson, ASU’s military-friendly reputation ultimately helped her land at ASU Online and while learning more about herself in the Air Force, she became interested in leadership roles, which led to her decision to add a minor in organizational leadership. 

As an online student, she did the majority of her coursework in the comfort of her home at the kitchen table around her work schedule, but that’s not always where deep thinking happened. “Most of my reflection about life or the material I was reading would happen on long walks outside.”

As graduation day approaches, Braham loves the recognition that comes with saying "I pursued a degree with ASU," and enjoys sharing that experience and knowledge with others who may be interested in pursuing a degree but don’t know where to begin. In fact, Braham has also inspired her husband to pursue a degree at ASU. “Getting to say we are a Sun Devil power couple makes me so happy,” she said. 

Aside from graduating summa cum laude, Braham has decided to continue her educational career with a master’s degree in management and leadership she will start next year. For those still pursuing a degree, Braham believes, “The important thing is to never give up, take what life throws at you and do the best that you can and eventually that degree will be in hand and all the bumps along the way will have been worth it!”

Question: What’s something you learned while at ASU — in the classroom or otherwise — that surprised you or changed your perspective?

Answer: There have been so many things I’ve learned here! Realizing that everything must be evaluated in the context or culture it is found in, rather than our perspectives has changed a lot of my beliefs and judgements and made me a more understanding person. Learning about the facets of leadership has really changed how I operate at work and made me a better leader as well.

Q: Which professor taught you the most important lesson while at ASU?

A: Definitely Dr. Carlsen-Landy. I took a sociology course with her then ended up being her TA for two additional courses. I learned that attention to detail matters, academically and in real life. Her course was challenging but really made me sit down and focus on my coursework and what I was reading.

Q: What’s the best piece of advice you’d give to those still in school?

A: Remember your “why." It gets hard and stressful but remember WHY you are pursuing the degree you are pursuing and remind yourself that you’ll only get there if you put in the work.

Q: What are your plans after graduation?

A: I have already been accepted to a master’s program for management and leadership that I will begin next year. After graduation, I will be packing up the house and waiting for my husband to return from South Korea so we can move across the country to our new base in South Carolina.

Q: If someone gave you $40 million to solve one problem on our planet, what would you tackle?

A: That’s a tough one! Although I don’t think $40 million would be enough to solve a problem, I think it would help fund some of the change that needs to happen with racial inequality. The money could be used in a number of ways, however I think targeting a few major cities and restructuring the law enforcement system would help spur change across the county. Bringing in a force of not just police officers, but mental health professionals, social workers, health care workers, etc. to respond to calls with the appropriate agency. Taking this big step would show that this country is taking steps towards changing for the better, and taking the problems of racial inequality and injustice seriously.

Written by Tuesday Mahrle, earned media specialist for EdPlus at Arizona State University