James Davey

Education

• Research Fellow, Harvard Medical School, USA
• Research Associate, University of Ottawa, ON
• NSERC Postdoctoral Fellowship, Georgia Institute of Technology, USA
• Ph.D. Chemistry, University of Ottawa, ON
• M.Sc. Chemistry, Carleton University, ON
• B.Sc. Biochemistry, Honours, Carleton University, ON

Academic Positions

• Department member since 2023

Research Topics:

Computational protein design, molecular modeling, experimental protein engineering, synthetic biology, gene transcription, genetic circuitry, epigenetic modification

Research

Environmentally induced and inherited chemical modifications to DNA are crucial signalling mechanisms involved in epigenetic regulatory processes. These modifications are often implicated as the etiological or intermediating factors directing many disease processes. Inspired by the genome editing revolution, my research program seeks to design and engineer new biotechnologies coordinating the targeted manipulation of epigenetic modifications in living systems. To accomplish this task, my laboratory utilizes an iterative combination of computational and experimental strategies to design and engineer proteins facilitating the targeted recognition, installation, and removal of chemical modifications to DNA. This paired computational and experimental workflow allows my laboratory to develop new methodologies for modeling and predicting protein properties and functions, including: allostery, protein-DNA and protein-protein interactions, enzyme catalysis, and mechanistic processes involved in genetic regulation. Sequence predictions and design hypotheses are then experimentally tested utilizing genetic circuitry to report on the design outcomes of multiple concerted biomolecular functions acting to control gene transcription in a living host. Select protein candidates are then experimentally characterized to validate the accuracy of design hypotheses.

Current Lab Members

Undergraduate and graduate students interested in pursuing computational protein design, experimental protein engineering, and synthetic biology research should contact Dr. James Davey via email.

Publications

1. Davey JA, Damry AM, Goto NK, Chica RA. (2017). Rational design of proteins that exchange on functional timescales. Nature Chemical Biology. 13:1280–1285. [Article]
2. Davey JA, Wilson CJ, (2020). Engineered signal-coupled inducible protooters: measuring the apparent RNA-polymerase resource budget. Nucleic Acids Research. 48:9995–10012. [Article]
3. Lanouette S, Davey JA, Elisma F, Zhibin N, Figeys D, Chica RA. (2015) Couture J-F Discovery of substrates for a SET domain lysine methyltransferase predicted by multistate computational protein design. Structure. 23:206–215.[Article]
4. Davey JA.(2023). Goto NK TReSR: A PCR-compatible DNA sequence design method for engineering proteins containing tandem repeats. PLoS One. 18:e0281228.[Article]