An example of a system of interest for our lab is the carboxysome: a ~100 nm microcompartment found in autotrophic bacteria. The carboxysome is responsible for housing the carbon-fixation enzyme Rubisco and creating a high local concentration of CO2 to optimize the selectivity and efficiency of the carbon fixation reaction for higher-order metabolism. Due to the sheer number of autotrophic bacteria across the planet, it is estimated that approximately 10% of all organic carbon on Earth was fixed by a carboxysome.

We are interested in a molecular-scale, mechanistic understanding of carboxysome assembly and internal carboxysome dynamics. This object is the result of thousands of individual proteins spontaneously coming together, each evolved to support the compartment’s overall function. Studying the interactions of shell proteins, enzymes, and disordered scaffolding proteins would allow us to understand why these objects come together and how that logic can be applied to synthetic microcompartments. Equally important, we are interested in how small organic molecules can navigate the crowded protein interior, stumble into the corresponding enzyme active sites, and then escape from the carboxysome. This second aim will require us to also determine the flexibility or fluidity of the interior compartment.

Our approach to answering the above questions leans on our expertise from single-particle spectroscopy (see example data above from Carpenter et al. JCPL 2022). As each object is stochastically assembled from microscopic components, we will be directly observing how individual molecules interact with the carboxysome. Building off recent detailed whole-compartment structures from cryo-electron microscopy, we will aim to elucidate the motions of the molecules comprising these objects. Stay tuned as we get our first results!