Keeping Protein Structure Analysis in the Family - ACS Axial

Keeping Protein Structure Analysis in the Family

If you’ve ever browsed through an academic family tree you, know there are plenty of similarities between families in the home and the found families researchers discover in their labs. The head of a lab often forms a special bond with their students and post-docs, sharing wisdom and helping to shape their careers. A recent Perspective in the Journal of Chemical Information and Modeling saw both kinds of families combine to explore an intergenerational and interdisciplinary topic.

The Perspective, “From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses” was authored by Professor Saraswathi Vishveshwara, her daughter Professor Smitha Vishveshwara, and Saraswathi’s former Ph.D. advisee Dr. Vasundhara Gadiyaram – whom she calls an “academic daughter.” It provides an examination of graph spectral analysis of protein structures going back to its early days, while also looking at the field’s future and potential applications, including improving our understanding of the biological functions of diseases such as HIV. But it could never have come together without the diverse interests of three women, and the bonds they share.

Meet the Family

Professor Saraswathi Vishveshwara

Professor Saraswathi Vishveshwara’s lab at the Indian Institute of Science, Bangalore, focuses on computational approaches to understand the relationship between the structure and function of macromolecules, especially proteins. She began her career in biochemistry, before getting her Ph.D. in quantum chemistry and then working with Sir John Pople, who would go on to win the 1998 Nobel Prize in Chemistry for his work developing computational methods in quantum chemistry. Her work has always stood at the crossroads of several different disciplines, so she knows how to balance multiple approaches in pursuit of answers.

“Biology is so fascinating and complex. But the main problem in biology is that it has to be optimal and flexible,” Saraswathi says. “That makes it very difficult for computational people to take care of, in the sense that you can’t keep optimizing because you are losing flexibility at some other position, which will not be suitable for function. You have to struggle a lot and keep the balance.”

Professor Smitha Vishveshwara

Likewise, her daughter, Professor Smitha Vishveshwara of the University of Illinois at Urbana-Champaign, has long seen the value in exploring different fields. Her work as a theoretical physicist focuses on quantum condensed matter, and strongly correlated states of matter, such superconductors and nanotubes. But in addition to collaborating with her mother, she maintains ties to the art world. Smitha teaches a class on the intersection of art and physics, c0-created an original performance piece called Quantum Voyages that explores physics principles on the stage, and is working on a popular science book based on letters between her and her late father, C. V. Vishveshwara, who pioneered predicting the quasinormal modes of black holes.

Dr. Vasundhara Gadiyaram

Dr. Vasundhara Gadiyaram studied mathematics and computer applications before joining Saraswathi’s lab in 2012 under the Institute Mathematics Initiative, which looks to promote interdisciplinary applications of mathematics. She says she initially wanted to go into neuroscience, but since that field is heavily experimental, she reasoned that it wouldn’t have the work-life balance she was looking for. That led her to explore opportunities that better fit her lifestyle, even if they were a little less familiar.

“I had never heard of protein structures,” she says, but Saraswathi was more than willing to teach her what she needed to know so that Vasundhara could apply her considerable computational expertise to the questions that lab was exploring. “She has been continuously teaching me all these different problems in biology, and it was a fantastic experience.”

Working Together

Both Smitha and Vasundhara note that Saraswathi runs her lab like an extended family, full of discussion and collaboration, but also caring and flexibility. It’s not uncommon that she’ll have students over to home, to continue scientific discussions in an informal setting that sparks creativity. It was on one of these visits, over tea and snacks, that Vasundhara met her advisor’s daughter and bonded over the challenges of being a scientist with young children. These meetings would plant the seeds for a collaboration between the three of them.

Smitha has collaborated with her mother and her mother’s students a few times over the past decade but adds that her collaborations with her mother tend to pick up whenever she visits India.  It was during one such visit that Saraswathi heard about JCIM’s call for papers for a Special Issue on Women in Computational Chemistry, giving her the idea of writing a Perspective piece on the graph spectral approach to protein structure analyses.

But JCIM”s Special Issue submission deadline meant they didn’t have a lot of time to write the paper. Vasundhara says she was on vacation when the idea hit and could only offer limited contributions during the writing phase, though the final article ended up reflecting months of work she’d done earlier.

In the end, the pressure may have helped the project get off the ground. “I feel like almost with the limited time we were able to really distill the essence of what we wanted to say,” Smitha says.

Looking Forward

Smitha adds that this collaboration with her mother has sparked new ideas for both of them, and is likely to lead to more intergenerational work being done down the line.

“We’re energized to bring in more concepts from physics, and we see some very clear directions,” says Smitha. “For example, there’s percolation, and also related,  the concept of localization/delocalization, which asks, when you’re in a very disordered system, can a particle get from one side of the system to the other? Physics offers a lot of insights into this issue and its approaches could perhaps apply very concretely to biological system. Because whatever the entity is – it could be a molecule or it could just be an electronic signal — whether it could get from one end to the other could be quite crucial in the functioning of some proteins.”

Do you have an interesting story about collaborating with your lab family? Submit your research to ACS Publications journals and consider telling your story on ACS Axial.

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