Research

How much of a protein is actually free to vary, and what would tell you? Alignment statistics, language-model likelihoods, force fields and strain are four different answers, and they disagree. Which disagreement matters depends on what you need the protein to do.

Publications

  1. Structurally distributed surface sites tune allosteric regulation

    James W. McCormick, Marielle AX Russo, Samuel Thompson, Aubrie Blevins, Kimberly A. Reynolds · eLife 10, e68346 (2021)

  2. Local disorder is associated with enhanced catalysis in an engineered photoswitch

    James W. McCormick, Jerry C. Dinan, Marielle AX Russo, Kimberly A. Reynolds · bioRxiv Preprint (2024)

  3. Determining the mechanisms of the allosteric architecture of DHFR

    James W. McCormick, Jerry C. Dinan, Marielle AX Russo, Kimberly A. Reynolds · Biophysical Journal 122(3), 49a (2023)

  4. Cell cycle–independent integration of stress signals by Xbp1 promotes Non-G1/G0 quiescence entry

    Orlando Argüello-Miranda, Ashley J. Marchand, Taylor Kennedy, Marielle A.X. Russo, Jungsik Noh · Journal of Cell Biology 221(1), e202103171 (2022)

  5. Complete Genome Sequence of Xanthomonas Phage Pagan

    Marielle Russo, Tram Le, Russell Moreland, Carlos F. Gonzalez, Mei Liu, Jolene Ramsey · Microbiology Resource Announcements 8(39), e01031-19 (2019)

ORCID 0000-0001-6147-7871

At the bench

Where I learned what selection actually costs — which is a claim a purely computational designer cannot make, and the reason the tooling above is built the way it is.

Graduate Researcher

Sculpting Evolution, Media Lab, Massachusetts Institute of Technology ·

  • Characterized a library of TEV protease variants using PRANCE, evaluating their activity and specificity across a panel of four diverse peptide substrates, presenting findings at the Molecular Mechanisms of Evolution Gordon Research Conference.
  • Debugged and improved a PyHamilton PRANCE experimental script, incorporating continuous well-mixing for enhanced culture homogeneity.

Research Assistant I

Reynolds Lab, Department of Bioinformatics, UT Southwestern Medical Center ·

  • Developed strategies, outlined assays, and deployed proposed schema to refine the purification of a unique putatively light-dependent recombinant protein, eliminating contamination that disrupted crystallization efforts.
  • Performed the initial hardware configuration, proposed and conducted assessments, and elaborated SOPs for the eVOLVER, an open-source continuous culture framework incorporating Python and Arduino scripting.

Research Technician II

Danhuser/Schmid Lab, Department of Cell Biology, UT Southwestern Medical Center ·

  • Developed and executed experiments examining quiescence entry and cell cycle in S. cerevisiae via genetic manipulation and fluorescence microscopy imaging coupled with computational analysis.
  • Independently managed lab databases and stock, including solutions and media, and coordinated planning for ongoing and frequently shifting research projects.

The bench layer of the stack

Talks and posters

Full CV