Infrastructures and research platforms

Scientific platforms supported by PROTEO

1. Identification Platform
(Coordinator: Prof. Christian Landry)

The identification and quantification of biomarkers and new proteins in a variety of contexts is a fundamental facet of academic and industrially-applied protein science. PROTEO has established a network of facilities and services providing quick and efficient access to genomic and proteomic characterization.

Major Platforms: State-of-the-art instrumentation for genomic and proteomic identification at the Centre for Structural and Functional Genomics and CBAMS (Concordia University), proteomics and bioinformatic facilities at Laval and Sherbrooke Universities, the Génome Québec Innovation Centre (McGill University), the IBIS sequencing services (Laval University), as well as proteomic, transcriptomic and metabolomic facilities at TransBiotech.

2. Bioproduction Platform
(Coordinator: Prof. Alain Garnier)

The bioproduction platform makes it possible to produce virtually any protein at several scales, from bench scale to a pilot-scale fermenter. The production of proteins can be undertaken in various host organisms, providing access to post-translational modifications. Major infrastructures include CNETE’s specialized facilities and Laval University’s bioprocess engineering facilities.

Major instrumentation: Fermenters (1, 2, 5, 10, 30, 50 and 500 litres), a high-flow atomizer (3 kg/h), freeze dryers (including a high capacity instrument at 50 litres per batch), incubators, bench and pilot scale filtration systems (MF, UF, NF, OI technologies; membranes: flat, tubular, hollow fibre); purification systems (HPLC, FPLC, AKTA Explorer).

Host organisms available: Bacteria: Bacillus subitilis (different strains), Lactobacillus (different species), Escherichia coli (different strains); Yeast: Saccharomyces (different species), Pichia pastoris (various mutations).

3. Biophysics Platform
(Coordinator: Prof. Nicolas Doucet)

The biophysics platform includes a wide variety of equipment to study protein conformation, changes and stability. For example, one can study the effect of various parameters on the stability of a biocatalyst, determine the long-term stability of a therapeutic protein in diverse formulations and identify regions that modulate the stability of proteins and enzymes of interest.

Major instrumentation: Spectrofluorometers, FTIR, ATR, polarized ATR spectrometers, confocal Raman spectrometers, PM-IRRAS, resonance Raman microscope, stop-flow spectrophotometer, circular dichroism spectropolarimeters (CD), oriented circular dichroism, regular and oriented solid-state NMR, dynamic light scattering, preparative and analytical ultracentrifugation, liquid NMR spectrometers, membrane conductivity isothermal calorimetry (ITC), mass spectrometry (MS). Includes the QANUC platform (McGill), the BIOFINS platform (Concordia), and the biophysics platform (Laval University).

4. Interactions Platform
(Coordinator: Prof. Steve Bourgault)

Proteins and enzymes do not act alone, they constantly interacs with several molecules. These interactions with other proteins and mediators are vital for protein activity and regulation, for metabolism and even for cell survival. This platform includes all necessary instrumentation to identify and to characterize protein interactions, as well as for the effect of various bioactive molecules on these important phenomena.

Major instrumentation: Isothermal titration calorimetry (ITC), differential scanning micro-calorimeter, surface plasmon resonance analysis (SPR), mass spectrometry (Orbitrap Fusion, TripleTOF 5600+6500, QTRAP, LTQ, MassPrep, ProXPress 4800, MALDI TOF-TOF Tempo LC, MALDI 4000, QTRAP, MS/MS/QQQ, MS/MS QTOF/IMS), bioinformatics. Located at BIOFINS facilities (Concordia University), UQAM, and Laval University.

5. In Silico Platform
(Coordinator: Prof. Patrick Lagüe)

In silico approaches to protein research are increasingly used to complement experimental methods. PROTEO provides high-end expertise in bioinformatics and access to high performance computing centres to carry out ultra-sophisticated bioinformatics for protein science, from the design of new enzymes for biocatalysis to the characterization of protein interactions.

Major instrumentation: 3D screening, virtual screening, rational drug design, molecular recognition and docking (FlexAID, MOE, Autodock, Gold, ICM); binding site similarities and cross-reactivity (IsoCleft and IsoMIF), protein engineering and thermostability prediction (ENCoM); molecular dynamics simulations (MOE, CHARMM); quantum calculations (Gamess, Gaussian and WebMO). Also available: biomarker identification and expertise in systems biology and metabolic networks to identify potential therapeutic targets. Located at Laval University and Université de Montréal.

6. Structural Platform
(Coordinator: Prof. Pierre Lavigne)

Protein function is intimately related to its molecular structure. PROTEO provides state-of-the-art expertise and instrumentation in protein structure characterization. Thanks to national and international collaborations, members have access to the 900 MHz solid-state NMR spectrometer at the National Ultrahigh-field NMR Facility for Solids in Ottawa and the 950 MHz liquid NMR spectrometer at the IBS in Grenoble.

Major instrumentation: High-field solution NMR spectrometers: 500 MHz (2), 600 MHz (4), 800 MHz, multi-nuclei probes including F; solid-state spectrometers: 300, 400, and 600 MHz for regular and oriented samples; X-ray and SAXS diffractometers; bioinformatics; DLS. Located at the Quebec/Eastern Canada High Field NMR Facility (QANUC), the protein NMR laboratories (Laval University), the Ultrahigh-field NMR Facility for Solids (CNRC – Ottawa), Laval University and McGill University crystallography laboratories, and the Institute of Structural Biology (IBS) facilities in Grenoble.