Publications#
A complete allosteric map of a GTPase switch in its native network.#
Cell Systems (2023)
Mathy CJP, Mishra P, Flynn JM, Perica T, Mavor D, Bolon DNA, & Kortemme T
Mathy et al., A complete allosteric map of a GTPase switch in its native cellular network, Cell Systems (2023),
Systems-level effects of allosteric perturbations to a model molecular switch.#
Nature (2021)
Perica T*, Mathy CJP*, Xu J, Jang GΜ, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, & Kortemme T
* co-first authors
Journal link | Pubmed link | Paper PDF | Supplement PDF
A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design.#
PLoS Computational Biology (2021)
Baker JJ, Mathy CJP, & Schaletzky J
The Global Phosphorylation Landscape of SARS-CoV-2 Infection.#
Cell (2020)
Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, …, Mathy CJP, … Krogan NJ
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.#
Nature (2020)
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O’Meara MJ, Rezelj VV, …, Mathy CJP, … Krogan NJ.
Journal link | Pubmed link | Paper PDF | Supplement PDF
Our collaborators in the Krogan lab mapped the interactions between human and SARS-COV-2 proteins, and looked to our group for structural interpretation. I discovered a conserved interaction motif in the C-terminal end of Orf6 and modeled it with Rosetta (see figure, purple peptide), using as a template a previously solved crystal structure of the Nup98-Rae1 complex bound to a protein from an unrelated virus, VSV (Quan et al 2014). The analysis predicted a methionine in the viral motif was key to the interaction, and mutations to this methionine were later shown to disrupt Orf6 binding to the complex (Miorin et al 2020).
Other work#
My previous work on growth factor engineering in Jennifer Cochran’s lab was accepted for an undergraduate honors thesis:
Mathy, CJP (2016) Engineering the NK1 Fragment of the Human Hepatocyte Growth Factor for Dual Use as a Potent Agonist and a Gene Therapy Delivery Vehicle. Stanford Digital Repository | link