Publications#

Pubmed | Google Scholar


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),

Journal link | Paper PDF

Deep mutational scanning of a GTPase uncovers novel allosteric sites Deep mutational scanning of a GTPase uncovers novel allosteric sites

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

  • Selected for a Spotlight in Trends in Biochemical Sciences

  • Featured in an article by UCSF

Profiling the cellular effects of interface mutations in the GTPase Ran/Gsp1 Profiling the cellular effects of interface mutations in the GTPase Ran/Gsp1

A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design.#

PLoS Computational Biology (2021)

Baker JJ, Mathy CJP, & Schaletzky J

Journal link | Pubmed link | Paper PDF


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

Journal link | Pubmed link | Paper PDF


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).

Profiling the cellular effects of interface mutations in the GTPase Ran/Gsp1 Profiling the cellular effects of interface mutations in the GTPase Ran/Gsp1

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