Dr. John Pezacki
Modifying Ago2 using photoactivatable unnatural amino acids for novel functionalities
My project will use genetic code expansion to add site-specific crosslinking ability to RNA-binding protein Ago2 for high throughput crosslinking and immunoprecipitation to profile RNA targets of Ago2 by sequencing methodologies. Current methods such as HITS-CLIP and PAR-CLIP use non-selective crosslinking that can damage cells and lead to non-specific crosslinking with RNA and DNA. Using unnatural amino acids may result in cleaner and more selective crosslinking.
Reading, tennis, and finding a new recipe to cook (and accidentally burn).
Ottawa, Ontario, Canada
Dr. Jean-François Couture & Dr. Jyh-Yeuan Lee
Understanding the structure-function relationship of ATP binding cassette (ABC) transporters
Several members of ABCG proteins (a subfamily of ABC proteins) facilitate the transport of lipids and sterols across the cell membrane. Despite such a versatile role in pathophysiology, molecular details remain elusive about how ABCG proteins carry out cholesterol transport in cells. Using protein engineering tools and structural determination techniques, and under co-supervision of Drs. Jean-François Couture and Jyh-Yeuan (Eric) Lee, the objective of this project is to study the structural and functional characteristics of ABCG proteins.
I like outdoor activities and sports with friends like hiking, cycling and stargazing. I enjoy table tennis, watching movies, reading, travelling to new places and learn about different cultures and history. I do some voiceover and singing in my spare time as well.
Dr. Joelle Pelletier
Development of Algorithms for Predictive Simulations of Biocatalytic Applications of Cytochrome P450 Enzymes
The bacterial cytochrome P450 BM3 is known for its specific oxidation of an alkyl group into a hydroxyl. A hydroxylation reaction with such precision and specificity is a great advantage for the synthesis of multiple pharmaceutical compounds. This enzymatic reaction offers better yields at lower costs, while also saving time and labor from traditional chemical synthesis. In order to test which potential drug candidates could benefit from this biocatalytic hydroxylation, computer simulations could offer valuable input as to which molecules are more likely to react with this enzyme. Thus, this project will be focused on developing a computer algorithm capable of predicting de novo biocatalytic substrates and products of interest for the pharmaceutical domain using thevariants of the CYP450 BM3 enzyme.
Reading, sports (soccer and basketball), music and cooking.
Montréal, Québec, Canada
Dr. Joelle Pelletier
Determination of the DfrBH proteins resistance and their homology with DfrBs
Antibiotic resistance has been observed with trimethoprim, a synthetic antibiotic used clinically to inhibit the chromosomal dihydrofolate reductase enzyme (cDfr) found in bacteria. Resistance to trimethoprim has been associated with type A and type B dihydrofolate reductases (DfrAs and DfrBs). Where DfrAs are mutants of cDfr, DfrBs are not related to cDfr, genetically and structurally. Using metagenomic data, five non-characterized proteins have been identified as distant homologs to DfrBs (DfrBHs), were they all have a predicted structural homology with the DfrBs. The goal of the project is to characterize the DfrBHs; can they confer resistance to trimethoprim? Do they have dihydrofolate reductase activity? Finally, to verify the possible homology between the DfrBHs and the DfrBs, inhibition of the DfrBHs with DfrBs inhibitors will indicate a structural homology.
Soccer, ski, reading.
Dr. Corrie daCosta
Statistical coupling analysis of ligand-gated ion channels
My project uses statistical coupling analysis (SCA) to gain insights into groups of coevolving amino acids called “protein sectors” in pLGICs, which I can then experimentally manipulate using protein engineering and electrophysiology techniques to study the relative contributions of the interacting network of residues to pLGIC channel gating activation upon agonist binding.
Art, film, computer programming, and gardening, among other interests.
Ottawa, Ontario, Canada
Dr. John Pezacki
Functional profiling of the SARS-CoV-2 Nsp13 helicase
The SARS-CoV-2 Nsp13 helicase is an important component involved in coronavirus replication. While this multi-functional protein is known to be able to unravel double-stranded DNA and RNA in an NTP-dependent fashion, the binding activity and mechanism of unwinding are not well known. Thus, this project will involve engineering Nsp13 proteins with photoactivatable unnatural amino acids as a way to study helicase function and screen for potential inhibitors.
Reading, painting, photography, and hiking.
Ottawa, Ontario, Canada
Dr. Elizabeth Meiering & Dr. Subha Kalyaanamoorthy
Rational engineering of a thermostable cutinase
Pervasive use and durability of polyethylene terephthalate (PET) in the environment threatens the health of many ecosystems. To aggravate the situation, current recycling methods can create toxic by-products/inferior PET; hence, enzymatic PET degradation is being vetted as a greener alternative. Several enzymes (cutinases, PETase) have the ability to degrade PET at varying rates, however, none can operate efficiently at the required temperatures for industrial-scale recycling. Thus, in our project, we strive to rationally engineer an already thermostable cutinase for improved PET degradation activity using combined bioinformatics, modelling, and experimental strategy.
Sports, hiking, climbing, strategy games, music.
Maple Ridge, BC
Dr. Andrew Woolley
Engineering of photoswitchable affibodies
Antibodies are broadly useful reagents with applications ranging from basic science to therapeutics. Making photo-controlled antibodies/monobodies would enhance their usefulness by enabling applications to dynamic processes. However, current strategies have drawbacks including lack of reversibility and the presence of intramolecular disulfide bonds. We aim to circumvent these drawbacks by developing a general approach to the engineering of effective light switchable affibodies.
Playing volleyball and reading (especially history-related books).
Nghe An, Viet Nam
Dr. Jeffrey Keillor
Directed evolution of a nylon hydrolase
Accumulation of non-biodegradable plastics in the environment poses a significant threat to the health of ecosystems. Degradation of such plastics may be achieved through biocatalysis, a potentially greener alternative to industrial recycling or pyrolysis. In this project, we seek to evaluate bacterial transglutaminase (bTG), an enzyme which catalyses the formation of amide bonds, and notably catalyses the hydrolysis of those bonds in the reverse direction, for its potential to degrade nylon. Iterative modification of residues will seek to improve the affinity of the enzyme for nylon-like moieties, towards a more efficient and selective biocatalyst.
I love drawing, painting, making music, and catspotting.
Dr. Nicolas Doucet
Teasing apart the structural and functional differences of eosinophil ribonucleases using ancestral sequence reconstruction
The two eosinophil Ribonucleases (RNase), RNase 2 and 3 playing important roles in human host defense emerged from a gene duplication event about 50 million years ago and experienced a divergence process with considerable high evolutionary speed. In this study, Ancestral sequence reconstruction of RNase 2 and 3 was performed in collaboration with the group of Mike Harms (U. Oregon). Using the PhyML software, ancestors were deduced from a phylogenetic tree constructed from 26 different canonical RNase sequences, including fish and sauropsid sequences. Experimental techniques including recombinant expression, refolding and protein purification will allow us to "resuscitate" this putative ancestor to study its biological function and structural properties. Further crystallographic and molecular dynamics studies, as well as antibacterial and cytotoxic characterization of this ancestral RNase will offer insights into the role of specific residue changes occurring through evolution and contributing to our better understanding of structure-activity relationships within the RNase A superfamily.
Cooking and gardening.