The next generation

The second generation of graduate students have completed their PhDs! Congratulations to Dr. Zijian Zhang, Dr. David Ryoo, Dr. Andrew Pang, and Dr. Katie Kuo for making it to the end! Or is it just the beginning? That’s for each of them to discover!

A reunion of sorts

We just had our first *full* in-person gathering as a group in over two years! It was bittersweet however, as we got together to send off Atanu Acharya, who’s leaving to start his own lab in the Department of Chemistry at Syracuse University. Good luck to Atanu in his new career as an Assistant Professor – Syracuse will be lucky to have him!

Over a year of coronavirus simulations

Like many computational labs, at the start of the pandemic in the US in early 2020, we turned our attention to SARS-CoV-2, aided by a rapidly growing amount of structural data. Since then, as a community, we have learned a tremendous amount about the biophysics of the virus and the proteins it uses to infect and replicate. Our lab in particular has focused on protonation states of the main protease (Mpro), the closed-to-open transition of the spike protein, and its binding to the receptor ACE2 (see our coronavirus page for more). The last year and a half have also demonstrated a tremendous degree of communication and cooperation amongst the scientific community and especially the computational chemistry community, including in two ACS symposia at the spring meeting (“A Call to Action: The Many Roles of Computational Chemistry in Addressing COVID-19” organized by JC Gumbart and Rommie Amaro) and the fall meeting (“Computational Chemistry of COVID-19: Lessons Learned and Future Directions” organized by Katarzyna Świderek and Carlos Simmerling). What discoveries will the next year and a half bring?

A bacterial weapon

Bacteria are often in battle with each other, fighting over limited resources. One of the weapons they bring into battle is a toxin delivery system known as Contact-Dependent growth Inhibition (CDI). Composed of two proteins, a toxin called CdiA is delivered via a transporter in the bacterial outer membrane called CdiB. In collaboration with structural biologists at NIH, Zijian, Karl, and JC determined how CdiB can be primed for subsequent delivery in a recent paper in eLife. They calculated the energy required to extract the helix that plugs CdiB in its resting state, finding it to be relatively modest. This energy could be provided, for example, by the binding of CdiA prior to its export.

Simbac at Biophysics 2020

David, Anna, Katie, Jinchan, Atanu, and JC stand in front of the Gaslamp Quarter (Andrew is not pictured here).

The group just finished a successful trip to the 2020 Biophysical Society meeting in San Diego! David presented a poster on autotransporters; Anna gave a talk on HBV; Katie, Andrew, and Jinchan presented posters on BamA and the BAM complex; Atanu presented a poster on Aβ; and JC gave a talk on the multidrug efflux pump AcrAB-TolC. Next, it’s on to Boston for BPS 2021!