Research

Current Projects

Structural characterization of novel biocatalysts

In collaboration with other labs in Biozone and Concordia University, we pursue studies into structural and molecular mechanisms of action of enzymes of industrial utility, including carbohydrate active enzymes (i.e. GH5, GH10 and GH62 glycosyl hydrolyses), X, Y and Z. We pursue structural charactesation of fungal and bacterial representatives of these enzyme families, which will advance our understanding of their substrate specificity, stability and other enzymatic properties of these industrially important proteins.

nserc_IBN_logo_small

Structural genomics of antibiotic resistance

Antibiotic resistance is a serious and growing health concern. Due to misuse or overuse of antibiotics, bacteria have evolved various mechanisms to reduce the effectiveness of these drugs.  Many clinically-relevant species, including the ESKAPE pathogens Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species contain either plasmids or chromosomal genes that produce enzymes with activities rendering antibiotics inactive.

In our lab, we are carrying out many structure-function and inhibition studies of enzymes conferring antibiotic resistance to the glycopeptide drug of last resort vancomycin, aminoglycosides, streptogramin compounds and other antibiotics. We use X-ray crystallography as our primary tool to produce detailed insights into molecular structure of these enzymes and use this information to guide design of potent inhibitory scaffolds that can be used as antibiotic adjuvants for combined antimicrobial therapy.

This work is funded by the National Institute of Allergy and Infectious Diseases (NIAID, http://www.niaid.nih.gov) through the Center for Structural Genomics of Infectious Diseases (CSGID, http://www.csgid.org and the Ontario Research Fund.

NIH_NIAID_Master_Logo_Alpha orf

Bacterial structural genomics

We are integral member of the Center for Structural Genomics of Infectious Diseases (CSGID, http://www.csgid.org), where our lab operates a full recombinant cloning, purification, crystallization and structure determination platform. Using optimized parallel methodology this platform is sued for large-scale structural characterization of proteins from various bacteria of health relevance, such as Bacillus anthracis, Chlamydia trichomatis, Clostridium difficle, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Vibrio cholerae and Yersinia pestis. Obtained structural information is released to the unrestricted public use through the Protein Databank (PDB, www.rcsb.org/) to aid in research efforts dedicated to understanding the molecular basis of the infectious activity of these bacteria.

csgid_title_leftNIH_NIAID_Master_Logo_Alpha

Past Projects

Protein Structure Initiative (PSI), PSI-Biology and Midwest Center for Structural Genomics

Our lab was a central component of the now-closed Midwest Center for Structural Genomics, a collaboration of labs participating in the NIH-funded Protein Structure Initiative (PSI) and PSI-Biology projects. This effort forms the core of our experience and historical record of high-throughput structure determination, as our lab determined the structures of 527 bacterial proteins.  These structures have involved numerous research studies and publications and have been deposited into the PDB.

PSI_Logo MCSG

Genozymes

The Genozymes project (Genozymes for Bioproducts and Bioprocesses Development) started ran from October 2009 to September 2014. It was funded primarily by Genome Canada, Genome Quebec, and Genome Alberta. The project involved various academic and industrial partners.

Fungal enzymes are being used widely in industry. They are versatile and can be deployed in challenging environments. Genozymes used functional genomic and ancillary approaches to identify and characterize fungal enzymes for industrial and environmental applications including the conversion of woody biomass to biofuels and other bioproducts. The Genozymes project examined evolutionarily diverse fungal species chosen for their ability to grow at environmental extremes and their known ability in biodegradation, bioremediation and biocatalysts.” – from www.fungalgenomics.ca

Our lab’s involvement in this project was 3D structure determination of carbohydrate-degrading enzymes.  We successfully determined crystal structures of 17 enzymes, including members of the GH5 (glycoside hydrolase family 5), GH10, GH11, GH12, GH61, GH62, GH93, GH105, CE3 (carbohydrate esterase family 3) and CE16 families.  These structures have lead to numerous publications and have been disseminated into the public domain in the Protein Databank.

400px-Genozymes2

MAMBA (Marine Metagenomics for New Biotechnological Applications)

“MAMBA stands for “Marine Metagenomics for New Biotechnological Applications”, a collaborative project to mine for and use of new microbial activities, in particular for targeted production of fine chemicals, antioxidants and anti-cancer drugs.

This Project builds up on the previous efforts of European Framework Programs and National research initiatives for exploiting the catalytic activities of marine microorganisms and microbial communities and to gain the new knowledge on the mechanisms of survival of living organisms in extreme environments.” – from http://mamba.bangor.ac.uk

Our lab’s involvement in this project was 3D structure determination of novel hydrolase/esterase enzymes.  We successfully crystallized 6 novel esterases which informed substrate screening and functional studies performed by partner labs.  These structures led to publications in Biochemical Journal and Environmental Microbiology.

Screen Shot 2017-02-02 at 10.38.19 AM