Watching “Transporter” Proteins Using Computers

Shriyaa Mittal, Graduate Student, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign

Stories_insci Stories_insci on June 24, 2018

Shriyaa Mittal

In less than 200 words, what main research questions are you working on? Please make sure to first include a brief context and background to your research, articulate your question(s) and conclude with why you think it’s important to study the them (i.e., the potential broader impacts).

Proteins are tiny biological machines that ensure the perfect working of all living cells in our bodies. They come in many shapes and sizes, have several parts, each with a defined set of movements and functions. “Transporter” proteins are attached to a cell membrane that separate the interior of all cells from the outside environment. These proteins catch a small molecule needed within the cell from the exterior and help it to move inwards. Once we eat food, it is broken down into glucose, water, and minerals so that these nutrients can be pulled from the blood into the cell via transporter proteins. Any mis-step by transporter proteins can quickly lead to nutrient deficiency inside the cell.

I study the transporter proteins’ movement using computer modeling. On a computer, I observe the protein starting from recognizing the nutrient small molecule, opening at the top to gobble it up, moving it further down and passing it into the cell’s cytoplasm. Since computers are effective at long calculations, I look at the behavior of proteins over long time as they transport molecules. With the data collected, I compute how fast proteins transport small molecules and whether we can increase this to make them more efficient