Trainees

2019 - 2021

Louise Connell

MSc Candidate
Dept. of Chemistry & Biomolecular
Sciences, University of Ottawa

Supervisor:

Dr. Corrie daCosta

Project:

Ancestral reconstruction for examining subunit compatibility in ion channels

Description:

Human muscle-type acetylcholine receptors are a type of pentameric ligand-gated ion channels, which can be made from multiple arrangements of subunits, from five identical subunits to five different ones. However, some subunit combinations are not compatible, and the specific amino acid determinants of this compatibility remains unknown. I will be studying the human muscle-type acetylcholine receptor using an evolutionary biochemistry approach with the goal of uncovering these determinants of compatibility.

Hobbies:

Rock climbing, reading, knitting, painting, canoeing, camping.

Hometown:

Toronto, Ontario, Canada


Sandrine Legault

MSc Candidate
Dept. of Chemistry & Biomolecular
Sciences, University of Ottawa

Supervisor:

Dr. Roberto Chica

Project:

Brighter red fluorescent proteins via engineering of reduced structural dynamics

Description:

Red Fluorescent Proteins (RFPs) are extensively used in biological research due to their longer emission wavelengths, which reduce phototoxicity and allow deeper imaging. However, they tend to be dimmer than other fluorescent proteins. Using a combination of nuclear magnetic resonance spectroscopy and mutagenesis, my project aims to investigate an alternate approach to engineer brighter RFPs which relies on rigidification of chromophore dynamics through the introduction of site-specific distal mutations.

Hobbies:

I am a theatre play enthusiast who loves to cook, dance (jazz/contemporary) and travel.

Hometown:

Gatineau, Québec, Canada


Adem Parisien

MSc Candidate
Dept. of Chemistry, Université de Montréal

Supervisor:

Dr. Joelle Pelletier

Project:

Antibody-drug conjugation assisted by microbial transglutaminase

Description:

Transglutaminase is a highly versatile enzyme that allows the formation of amide bonds between amino compounds and glutamine on the surface of a protein. Although the exact mechanism that explains the selectivity of this enzyme for specific glutamines is still poorly understood, this enzyme is already used in several industries, such as the food industry.  Subsequent studies on transglutaminase-reactive mutants may provide important information on the selectivity of this enzyme.

Hobbies:

Lecture, swimming, camping, music and comedy.

Hometown:

Montréal, Québec, Canada


Max Reed

MSc Candidate
Dept. of Chemistry, University of Toronto

Supervisor:

Dr. Andrew Woolley

Project:

Engineered PYP for creation of a general-use photosensitive tool

Description:

Proteins that change their structure and function based on light-exposure offer substantial promise in the engineering of biological systems, as they can respond to a non-invasive and easily modified stimulus. However, the ability to create new photo-switchable protein-protein interactions is currently limited. This project hopes to create a general way of engineering a binding partner that can interact with an arbitrary target in a light-controlled manner. The project will accomplish this by displaying the light-responsive protein PYP on phage, and using alternating rounds of panning for affinity to a target in the light and dark. This will allow for the selection of an interaction that occurs in only one of the two light conditions.

Hobbies:

Studying history, theatre.

Hometown:

Guelph, Ontario, Canada


Julia Steckner

MSc Candidate
Dept. of Chemistry, University of Waterloo

Supervisor:

Dr. Elizabeth Meiering

Project:

Engineering the scaffold of 10Fn3 binding proteins

Description:

The 10th human fibronectin type III (Fn3) domain proteins are small, stable β-sandwich immunoglobulin-like proteins that can bind diverse targets with affinity and specificity rivalling those seen in antibodies. They bind their targets with three loops at the sandwich interface that are analogous to those of antibody complementarity-determining regions; the 10Fn3 structure tolerates alterations to these loop regions remarkably well. This project will investigate the structural features of the 10Fn3 core scaffold that are necessary for global and local stability, and the impact of core scaffold attributes on binding specificity and affinity. Experimental data on 10Fn3 thermal stability, binding energy, and 10Fn3-target complex structure and dynamics will be collected on a library of variants using differential scanning calorimetry, isothermal titration calorimetry, and NMR spectroscopy, respectively. These data will inform computational models with the aim of rationally designing a robust scaffold that will form a foundation for binding engineering endeavours.

Hobbies:

Hiking, board games, crocheting, reading.

Hometown:

Kilbride, Ontario, Canada


Gabriel Sullivan

MSc Candidate
Dept. of Chemistry & Biomolecular
Sciences, University of Ottawa

Supervisor:

Dr. John Pezacki

Project:

Adapting the CRISPR/Cas9 system for novel functionalities

Description:

One approach that I will explore will be to engineer Cas9 complex so that the Cas9-guide RNA that is used to target specific genomic sequences for editing will be covalently crosslinked. This will allow for easier delivery of gene editing tools that reliably contain all components of the gene editing complex.

Hobbies:

Running, foodie, mixology, guitar.

Hometown:

Aylmer, Québec, Canada


Mike Tarasca

MSc Candidate
Dept. of Chemistry, University of Waterloo

Supervisor:

Dr. Elizabeth Meiering

Project:

Characterizing protein aggregate structures using quenched amide exchange

Description:

I am acquiring data using quenched amide exchange nuclear magnetic resonance experiments on naturally aggregating proteins, in order to determine the structure of the protein aggregate. I will use this data to then design proteins that will aggregate into specific structures.

Hobbies:

I spend my spare time playing ice hockey, baking, and reading.

Hometown:

Bolton, Ontario, Canada


Niayesh Zarifi

MSc Candidate
Dept. of Chemistry & Biomolecular
Sciences, University of Ottawa

Supervisor:

Dr. Roberto Chica

Project:

In-silico directed evolution of the tryptophan synthase β-subunit towards stand-alone activity

Description:

This project aims to address current drawbacks in the field of enzyme design through the development of a genuinely In Silico Directed Evolution protocol, referred to as "InSiDE". The InSiDE protocol will be employed to efficiently design enzymes by accurately considering all the catalytically relevant states, as well as the protein conformational dynamics. This computational protocol will combine meta-multistate design (meta-MSD), a computational approach developed in the Chica lab to design states over an entire reaction coordinate, with an extensive evaluation of the enzyme’s conformational dynamics using enhanced molecular dynamics (MD) simulations. To validate the designed computational approach, the InSiDE method will be used to tune tryptophan synthase allostery by tailoring its β-subunit towards highly active stand-alone catalytic efficiency.

Hobbies:

Reading, swimming, photography, cycling.

Hometown:

Kish Island, Iran


Claudèle Lemay-St-Denis

PhD Candidate
Dept. of Chemistry, Université de Montréal

Supervisor:

Dr. Joelle Pelletier

Project:

Is the protein dynamics of ß-lactamases related to the acquisition of antibiotic resistance?

Description:

Bacteria have developed a predominant mechanism of resistance against penicillin and its derivatives, notably by producing ß-lactamases. An understanding of the implication of dynamism in the adaptability of ß-lactamases could be applied to the design of more efficient approaches for treating bacterial infections. In addition, the comprehension of the role played by dynamism in protein adaptability to a new function will increase the efficiency of protein engineering.

Hobbies:

Traveling, badminton, reading.

Hometown:

Montréal, Québec, Canada


Rojo Rakotoharisoa

PhD Candidate
Dept. of Chemistry & Biomolecular
Sciences, University of Ottawa

Supervisor:

Dr. Roberto Chica

Project:

Towards a new computational methodology to perform de novo enzyme design

Description:

Enzymes are outstanding catalysts increasingly used in therapeutic and industrial applications. However, natural enzymes perform only a small fraction of commercially or medicinally valuable reactions. As such, the design of artificial enzymes able to perform any desired reaction has been a key goal of Computational Protein Design (CPD) for the past decade. Although several de novo enzymes have been successfully designed, these have failed to reach the efficiency of natural enzymes, requiring multiple rounds of laborious directed evolution to improve their activity. The goal of my project is to implement a computational methodology to design de novo enzymes that reach natural like catalytic efficiency.

Hobbies:

I like travelling, reading historical and science fiction books, outdoor activities as hiking or going out for long walks.

Hometown:

Antananarivo, Madagascar

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Interested in donating or becoming a partner with the CREATE team to help to empower trainees with outstanding research skills in the field of protein engineering? Please contact This email address is being protected from spambots. You need JavaScript enabled to view it. for more information.