Dr. John Pezacki

Modification of Ago2 using photoactivatable unnatural amino acids for new functionalities

My project will use genetic code expansion to add a site-specific crosslinking capacity to the RNA binding protein Ago2 for high throughput crosslinking and immunoprecipitation to profile Ago2 RNA targets by methodologies such as sequencing. Current methods such as HITS-CLIP and PAR-CLIP use non-selective crosslinking which can damage cells and lead to non-specific crosslinking with RNA and DNA. The use of unnatural amino acids can lead to cleaner and more selective crosslinking.

Cooking and gardening.

Ottawa, Ontario, Canada

Dr. Jean-François Couture and Dr. Jyh-Yeuan Lee

Understand 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 on how ABCG proteins transport cholesterol into cells. Using protein engineering tools and structural determination techniques, and under the 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 love the outdoors and sports with friends like hiking, biking and stargazing. I enjoy table tennis, watching movies, reading, traveling to new places and learning about different cultures and history. I also do some voiceovers and sing in my free time.

Giza, Egypt

Dr. Joelle Pelletier

Development of algorithms for predictive simulations of biocatalytic applications of Cytochrome P450 enzymes

Cytochrome P450 BM3 of bacterial origin is an enzyme known for its specific oxidation of an alkyl group to a hydroxyl group. Such a specific hydroxylation reaction, both regio- and stereoselective, presents a significant advantage for the synthesis of several pharmaceutical compounds. This enzymatic reaction allows better performance at low costs, while reducing the time and effort invested compared to traditional chemical synthesis methods. To test the potential chemical molecules that can benefit from this enzymatic reaction, predictive computer simulations would be favorable to minimize costs and to find molecules that can react with this enzyme. Thus, this project will be based on the development of an algorithm for the prediction of biocatalytic substrates of interest for the pharmaceutical field, compatible with variants of the CYP450 BM3 enzyme.

Read, play sports (soccer and basketball), listen to music and cook.

Montréal, Québec, Canada

Dr. Joelle Pelletier

Determination of the resistance of DfrBH proteins and their homology to DfrBs

Antibiotic resistance has been observed with trimethoprim, a synthetic antibiotic used clinically to inhibit the enzyme chromosomal dihydrofolate reductase (cDfr) found in bacteria. Resistance to trimethoprim has been associated with type A and type B dihydrofolate reductases (DfrA and DfrB). Where DfrAs are mutants of cDfr, but DfrB are not genetically or structurally related to cDfr. Using metagenomic data, 5 uncharacterized proteins were identified as distant homologs to DfrB, namely DfrBH, where the latter have predicted structural homology to DfrB. The objective of the project is to characterize the DfrBH; can they confer resistance to trimethoprim? Do they have dihydrofolate reductase activity? Finally, to verify the possibility of homology between DfrBH and DfrB, inhibition of DfrBH with DfrB inhibitors would indicate structural homology.

Soccer, skiing, reading.

Piedmont, Québec, Canada

Dr. Corrie daCosta

Statistical analysis of ligand-dependent ion channel coupling

My project will use Statistical Coupling Analysis (SCA) to obtain information about groups of coevolutionary amino acids called "protein sectors" in pentameric ligand ion channels (pLGIC), which I can then manipulate experimentally using techniques of protein engineering and electrophysiology to study the relative contributions of the network of interacting residues to the trigger activation of the pLGIC channel upon agonist binding.

Art, cinema, computer programming, and gardening, among other interests.

 Ottawa, Ontario, Canada

Dr. John Pezacki

Functional profiling of SARS-CoV-2 Nsp13 helicase

The SARS-CoV-2 Nsp13 helicase is an important component involved in the replication of the coronavirus. Although this multifunctional protein is known to be able to disentangle DNA and double-stranded RNA in an NTP-dependent manner, the binding activity and unwinding mechanism are not well known. Thus, this project will involve the engineering of Nsp13 proteins with photoactivatable unnatural amino acids as a means to study helicase function and to screen for potential inhibitors.

Reading, painting, photography and hiking.

Ottawa, Ontario, Canada

Dr. Elizabeth Meiering & Dr. Subha Kalyaanamoorthy

Rational engineering of a thermostable cutinase

The pervasive use and sustainability of polyethylene terephthalate (PET) in the environment threatens the health of many ecosystems. To make matters worse, current recycling methods can create toxic byproducts / substandard PET; therefore, the enzymatic degradation of PET is being considered as a more environmentally friendly alternative. Several enzymes (cutinases, PETase) have the ability to degrade PET at varying rates, but none can function effectively at the temperatures required for industrial scale recycling. Thus, in our project, we strive to rationally design an already thermostable cutinase for enhanced PET degradation activity using a combined strategy of bioinformatics, modeling and experimentation.

Sports, hiking, climbing, strategy games, music.

Maple Ridge, British Columbia, Canada

Dr. Andrew Woolley

Switchable affibody engineering

Antibodies are widely useful reagents with applications ranging from basic science to therapy. The fabrication of photo-controlled antibodies / monibodies would improve their utility by allowing applications to dynamic processes. However, current strategies have drawbacks, notably the 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 efficient light-switchable affibodies.

Play volleyball and read (especially books related to history).

Nghe An, Viet Nam

Dr. Jeffrey Keillor

Directed evolution of a nylon hydrolase

The accumulation of non-biodegradable plastics in the environment poses a significant threat to the health of ecosystems. The degradation of these plastics can 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 that catalyzes the formation of amide bonds, and in particular catalyzes the hydrolysis of these bonds in the reverse direction, for its potential for degrading nylon. The iterative modification of the residues will seek to improve the affinity of the enzyme for the nylon-like fractions, towards a more efficient and selective biocatalyst.

I love to draw, paint, make music, and find cats.

Kitchener-Waterloo, Ontario, Canada

Dr. Nicolas Doucet

Demonstration of structural and functional differences of eosinophilic ribonucleases using ancestral sequence reconstruction

Eosinophil-like ribonucleases (RNases) 2 and 3 play an important role in host defense in humans. These two enzymes are subject to a process of considerably rapid evolutionary divergence and appear to have emerged about 50 million years ago as a result of a gene duplication event. In the present study, the reconstruction of the ancestral sequence of RNases 2 and 3 was carried out in collaboration with the group of Mike Harms (U. Oregon). Using PhyML software, ancestors were deduced from a phylogenetic tree constructed from 26 canonical sequences of distinct vertebrate RNases, including fish and sauropsid sequences. Experimental techniques including recombinant expression, folding and purification of proteins will allow us to "resuscitate" this putative ancestor in order to study its biological function and structural properties. Crystallographic and molecular dynamics studies, as well as the antibacterial and cytotoxic characterization of this ancestral RNase, will allow a better understanding of the role of the specific modifications of the residues which have appeared during evolution, in addition to contributing to a better understanding of the structure-activity relationships within the RNase A superfamily.

Cooking and gardening.

Vietnam