The Students

The Big Picture

Tools to investigate the effects of tensile force on protein conformational dynamics in vitro and in silico

AlphaFold has made protein structure prediction accessible to anybody with a browser and an amino acid sequence. But, proteins are more complicated than a single snapshot can show; they’re dynamic and flexible, and for many proteins these conformational dynamics define their function. This is especially true for mechanosensitive proteins, the class of molecules that mediates our ability to sense and respond to forces through dynamic structural rearrangements. Investigating these molecules at equilibrium is critically important, but things get really exciting when you subject them to tensile forces. Scientists have come up with clever ways to pull on these molecules one at a time, both in silico (e.g., molecular dynamics simulations) and in vitro (e.g., optical tweezers). But many of our most informative characterization methods, including hydrogen-deuterium exchange mass spectrometry (HDXMS), rely on examining an ensemble of many proteins at once to gain insight into the statistical mechanics across an entire population. Unfortunately, to our knowledge there are no established techniques to apply a uniform tensile force across many proteins at once.

In my work, I hope to fill that gap by developing a device that can subject an ensemble of proteins to a uniform, tunable tensile force. I'm using this device to perform HDX on enhanced green fluorescent protein (EGFP) as a model system, comparing data for pulled and unpulled samples. I will then use my device to perform HDX on three biologically interesting mechanosensitive proteins. Together, this work will present a novel strategy to probe the conformational dynamics of protein species under tension, enabling scientists to ask new questions that are currently unavailable to the research community.