Areas of expertise
Enzymatic engineering , Molecular dynamics involved in the catalytic activity of enzymes , NMR and dynamics
- INRS Professor
- Scientific co-leader of Nuclear Magnetic Resonance Spectroscopy Laboratory
Interested research topics
Understanding the importance of residue motion in enzyme activity may eventually allow us to develop methods to modify, modulate and/or design new protein functions, which would have far-reaching implications in biotechnology, protein engineering, nanotechnology and drug design.
The main goal of our research is to successfully modify enzyme biocatalysts aimed at environmental and pharmaceutical applications, with a broader interest focused on understanding the role between structure, function and flexibility in various enzymatic systems.
To address this important problem, our research strategy combines directed evolution experiments coupled with biochemical and biophysical characterization such as nuclear magnetic resonance (NMR), molecular biology, enzyme kinetics, and molecular modeling. Using this approach, we specifically focus on achieving the following aims:
- To understand how the amino acid sequence and local structural environment of conserved residues determine the motional and functional properties of enzymes.
- To investigate how functionally and structurally related enzymes retain their motional properties within similar folds.
- To modify, reproduce and apply this ‘structure-function’ and ‘flexibility-function’ information to the design of new and improved molecular biocatalysts.
Dr. Nicolas Doucet obtained his B.S. in biochemistry from Université Laval (B.S. Biochemistry, 2000) and successively completed a master’s degree (M.S. Biochemistry, 2004) and a doctoral thesis in enzyme engineering at the Université de Montréal (Ph.D. Biochemistry, 2007). After completing a protein NMR postdoctoral fellowship in the Department of Chemistry at Yale University (with J. Patrick Loria, 2007-2010), Dr. Doucet joined the faculty at INRS-Institut Armand-Frappier in 2010.
Submitted and Under Review
67. Rueda AM, López de los Santos Y, Vincent AT, Létourneau M, Hernández I, Sánchez CI, Molina DV, Ospina SA, Veyrier FJ & Doucet N* (2020) Genome sequencing and functional characterization of a Dictyopanus pusillus fungal extract offers a promising alternative for lignocellulose pretreatment of oil palm residues. bioRxiv, doi: https://doi.org/10.1101/2019.12.23.887034.
66. Narayanan C, Bernard DN, Létourneau M, Gagnon J, Gagné D, Bafna K, Calmettes C, Couture JF, Agarwal PK & Doucet N (2020) Insights into structural and dynamical changes experienced by human RNase 6 upon ligand binding. Biochemistry, 59(6):755-765.
65. Parent-Michaud M, Dufresne PJ, Fournier E, Folch B, Martineau C, Moreira S, Doucet N, de Repentigny L & Dufresne SF (2020) Prevalence and mechanisms of azole resistance in clinical isolates of Aspergillus section Fumigati species in a Canadian tertiary care center, 2000 to 2013, Journal of Antimicrobial Chemotherapy, In Press.
64. Golbaghi G, Pitard I, Lucas M, Haghdoost MM, López de Los Santos Y, Doucet N, Patten SA, Sanderson JT, Castonguay A. (2020) Synthesis and biological assessment of a ruthenium(II) cyclopentadienyl complex in breast cancer cells and on the development of zebrafish embryos. European Journal of Medicinal Chemistry, 188, 112030.
63. López de Los Santos Y, Chew-Fajardo YL, Brault G & Doucet N* (2019) Dissecting the evolvability landscape of the CalB active site toward aromatic substrates, Scientific Reports, 9, 15588.
62. Dulcey CE, López de Los Santos Y, Létourneau M, Déziel E* & Doucet N* (2019) Semi-rational evolution of the 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA to improve rhamnolipid production in Pseudomonas aeruginosaand Burkholderia glumae. FEBS Journal, 86(20), 4036-4059.
61. Chatenet D, Doucet N, St-Pierre Y & Vladoiu MC (2019) Inhibitors of prototypic galectin dimerization and uses thereof. United States Patent and Trademark Office, Patent US15/576,609.
60. Hudon Thibeault AA, López de Los Santos Y, Doucet N, Sanderson JT, Vaillancourt C (2019) Serotonin and serotonin reuptake inhibitors alter placental aromatase, Journal of Steroid Biochemistry and Molecular Biology, 195, 105470.
59. Antunes VU, Llontop E, Vasconcelos FNDC, López de Los Santos Y, Oliveira RJ, Lincopan N, Farah CS, Doucet N, Mittermaier AK & Favaro DC (2019) Importance of the β5-β6 Loop for the structure, catalytic efficiency, and stability of the carbapenem-hydrolyzing class D β-lactamase subfamily OXA-143. Biochemistry, 58(34), 3604-3616.
58. Doucet N* (2019) Enzyme catalysis under pressure. Nature Catalysis, 2, 646-647.
57. Bafna K, Narayanan C, Chennubhotla SC, Doucet N, Agarwal PK (2019) Nucleotide substrate binding characterization in human pancreatic-type ribonucleases. PLOS ONE, 14(8), e0220037.
56. Gobeil SMC, Ebert MCCJC, Park J, Gagné D, Doucet N, Berghuis AM, Pleiss J & Pelletier JN (2019) The structural dynamics of engineered β-lactamases vary broadly on three timescales yet sustain native function.Scientific Reports, 9(1), 6656.
55. Golbaghi G, Haghdoost MM, Yancu D, López de los Santos Y, Doucet N, Patten SA, Sanderson JT & Castonguay A (2019) Organoruthenium(II) complexes bearing an aromatase inhibitor: synthesis, characterization, in vitrobiological activity and in vivo toxicity in zebrafish embryos. Organometallics,38(3), 702-711.
54. Debbabi S, Groleau MC, Létourneau M, Narayanan C, Gosselin LL, Iddir M, Gagnon J, Doucet N, Déziel E & Chatenet D (2018) Antibacterial properties of the pituitary adenylate cyclase-activating polypeptide: A new human antimicrobial peptide. PLOS ONE, 13(11), e0207366.
53. Gagné D, Narayanan C, Bafna K, Charest LA, Agarwal PK & Doucet N* (2018) Correction to: Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin. Biomolecular NMR Assignments, 12(2), 365-367.
52. Dionne U, Chartier FJM, López de los Santos Y, Lavoie N, Bernard DN, Banerjee SL, Otis F, Jacquet K, Tremblay MG, Jain M, Bourassa S, Gish GD, Gagné JP, Poirier GG, Laprise P, Voyer N, Landry CR, Doucet N & Bisson N (2018) Direct phosphorylation of SRC homology 3 domains by tyrosine kinase receptors disassembles ligand-induced signaling networks. Molecular Cell, 70(6), 995-1007.
51. Narayanan C, Bernard DN, Bafna K, Gagné D, Agarwal PK & Doucet N*(2018) Ligand-induced variations in structural and dynamical properties within an enzyme superfamily. Frontiers in Molecular Biosciences, 5, 54.
50. St-Pierre Y, Doucet N & Chatenet D (2018) A new approach to inhibit prototypic galectins. Trends in Glycoscience and Glycotechnology, 30(172), SE155-SE165.
49. Narayanan C, Bernard DN, Bafna K, Gagné D, Chennubhotla CS, Doucet N* & Agarwal PK* (2018) Conservation of dynamics associated with biological function in an enzyme superfamily. Structure, 26(3), 426-436.
Article previewed in: Uversky VN (2018) Conserved functional dynamics: I like to move it, move it! Structure, 26(3), 371-373.
48. Gagné D, Narayanan C, Bafna K, Charest LA, Agarwal PK & Doucet N*(2017) Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin. Biomolecular NMR Assignments, 11(2) 143-149.
47. Narayanan C, Bafna K, Roux LD, Agarwal PK, Doucet N* (2017) Applications of NMR and computational methodologies to study protein dynamics. Archives of Biochemistry and Biophysics, 628, 71-80.
46. Narayanan C, Gagné D, Reynolds KA & Doucet N* (2017) Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily. Scientific Reports, 7, 3207.
45. Herrero C, Nguyen-Thi N, Hammerer F, Banse F, Gagné D, Doucet N, Mahy JP & Ricoux R (2016) Photoassisted oxidation of sulfides catalyzed by artificial metalloenzymes using water as an oxygen source. Catalysts, 6(12), 202.
44. Agarwal PK, Doucet N, Chennubhotla CS, Ramanathan A & Narayanan C (2016) Conformational sub-states and populations in enzyme catalysis.Methods in Enzymology, 578, 273-297.
43. Gagné D, Narayanan C, Nguyen-Thi N, Roux LD, Bernard DN, Brunzelle JS, Couture JF, Agarwal PK & Doucet N* (2016) Ligand binding enhances millisecond conformational exchange in xylanase B2 from Streptomyces lividans. Biochemistry, 55(30), 4184–4196.
42. Narayanan C, Bernard DN & Doucet N* (2016) Role of conformational motions in enzyme function: selected methodologies and case studies. Catalysts, 6(6), 81.
41. Gobeil SMC, Gagné D, Doucet N & Pelletier JN (2016) 15N, 13C and 1H backbone resonance assignments of an artificially engineered TEM-1/PSE-4 Class A β-lactamase chimera and its deconvoluted mutant. Biomolecular NMR Assignments, 10(1), 93-99.
40. Nguyen Thi N & Doucet N* (2016) Combining chitinase C and N-acetylhexosaminidase from Streptomyces coelicolor A3(2) provides an efficient way to synthesize N-acetylglucosamine from crystalline chitin. Journal of Biotechnology, 220, 25-32.
39. Gagné D, French RL, Narayanan C, Simonović M, Agarwal PK & Doucet N* (2015) Perturbation of the conformational dynamics of an active-site loop alters enzyme activity. Structure, 23(12), 2256-2266.
38. Vladoiu M, Labrie M, Létourneau M, Egesborg P, Gagné D, Billard E, Grosset AA, Doucet N, Chatenet D & St-Pierre Y (2015) Design of a peptidic inhibitor that targets the dimer interface of a prototypic galectin. Oncotarget, 6(38), 40970-40980.
37. Ndoti-Nembe A, Vu KD, Han J, Doucet N & Lacroix M (2015) Antimicrobial effects of nisin, essential oil, and γ-irradiation treatments against high load of Salmonella typhimurium on mini-carrots. Journal of Food Science, 80(7), M1544-M1548.
36. Egesborg P, Carlettini H, Volpato JP & Doucet N* (2015) Combinatorial active-site variants confer sustained clavulanate resistance in BlaC β-lactamase from Mycobacterium tuberculosis. Protein Science, 24(4), 534-544.
35. Gagné D, Narayanan C & Doucet N* (2015) Network of long-range concerted chemical shift displacements upon ligand binding to human angiogenin. Protein Science, 24(4), 525-533.
34. Ndoti-Nembe A, Vu KD, Doucet N & Lacroix M (2015) Antimicrobial effects of essential oils, nisin, and irradiation treatments against Listeria monocytogenes on ready-to-eat carrots. Journal of Food Science, 80(4), M795-M799.
33. Gagné D & Doucet N* (2015) Sequence-specific backbone 1H, 13C, and 15N resonance assignments of human ribonuclease 4. Biomolecular NMR Assignments, 9(1), 181-185.
32. Tadevosyan A, Létourneau M, Folch B, Doucet N, Villeneuve LR, Mamarbachi AM, Pétrin D, Hébert TE, Fournier A, Chatenet D, Allen BG, Nattel S (2015) Photoreleasable ligands to study intracrine angiotensin II signalling. Journal of Physiology, 593.3, 521-539.
31. Grosset AA, Labrie M, Gagné D, Vladoiu M, Gaboury L, Doucet N & St-Pierre Y (2014) Cytosolic galectin-7 impairs p53 functions and induces chemoresistance in breast cancer cells. BMC Cancer, 14, 801.
30. Gobeil SMC, Clouthier CM, Park J, Gagné D, Berghuis AM, Doucet N & Pelletier JN (2014) Maintenance of native-like protein dynamics may not be required for engineering functional proteins. Chemistry & Biology, 21, 1330-1340.
Article previewed in: Tokuriki N, Jackson CJ (2014) Enzyme dynamics and engineering: one step at a time. Chemistry & Biology, 21, 1259-1260.
29. Nguyen TTN, Folch B, Létourneau M, Truong NH, Doucet N, Fournier A & Chatenet D (2014) Design of a truncated cardiotoxin-I analog with potent insulinotropic activity. Journal of Medicinal Chemistry, 57(6), 2623–2633.
28. Brault G, Shareck F, Hurtubise Y, Lépine F & Doucet N* (2014) Short-chain flavor ester synthesis in organic media by an E. coli whole-cell biocatalyst expressing a newly characterized heterologous lipase. PLOS ONE, 9(3): e91872.
27. Nguyen Thi N, Offen WA, Shareck F, Davies GJ & Doucet N* (2014) Structure and activity of the Streptomyces coelicolor A3(2) β-N-acetylhexosaminidase provides further insight into GH20 family catalysis and inhibition. Biochemistry, 53, 1789-1800.
26. Chatenet D, Folch B, Feytens D, Létourneau M, Tourwé D, Doucet N & Fournier A (2013) Development and pharmacological characterization of conformationally constrained urotensin II-related peptide agonists. Journal of Medicinal Chemistry, 56(23), 9612-9622.
25. Dulcey CE, Dekimpe V, Fauvelle DA, Milot S, Groleau MC, Doucet N, Rahme LG, Lépine F & Déziel E (2013) The end of an old hypothesis: the Pseudomonas signalling molecules 4-hydroxy-2-alkylquinolines are derived from fatty acids, not 3-keto fatty acids. Chemistry & Biology, 20(12), 1481-1491.
24. Gagné D & Doucet N* (2013) Structural and functional importance of local and global conformational fluctuations in the RNase A superfamily. FEBS Journal, 280(22), 5596-5607.
23. Ndoti-Nembe A, Vu KD, Doucet N & Lacroix M (2013) Effect of combination of essential oils and bacteriocins on the efficacy of gamma radiation against Salmonella Typhimurium and Listeria monocytogenes. IInternational Journal of Radiation Biology, 89, 794-800.
22. Folch B, Déziel E & Doucet N* (2013) Systematic mutational analysis of the putative hydrolase PqsE: Toward a deeper molecular understanding of virulence acquisition in Pseudomonas aeruginosa. PLOS ONE, 8(9): e73727.
21. Garénaux A, Houle S, Folch B, Dallaire G, Truesdell M, Lépine F, Doucet N & Dozois CM (2013) Avian lipocalin expression in chickens following Escherichia coli infection and inhibition of avian pathogenic Escherichia coligrowth by Ex-FABP. Veterinary Immunology and Immunopathology, 152, 156-167.
20. Gagné D, Charest LA, Morin S, Kovrigin EL & Doucet N* (2012) Conservation of flexible residue clusters among structural and functional enzyme homologues. Journal of Biological Chemistry, 287(53), 44289-44300.
19. Clouthier CM, Morin S, Gobeil S, Doucet N, Blanchet J, Nguyen E, Gagné SM & Pelletier JN (2012) Chimeric β-lactamases: global conservation of parental function and fast time-scale dynamics with increased slow motions.PLOS ONE, 7(12): e52283.
18. Doan ND, Létourneau M, Vaudry D, Doucet N, Folch B, Vaudry H, Fournier A & Chatenet D (2012) Design and characterization of novel cell-penetrating peptides from pituitary adenylate cyclase-activating polypeptide. Journal of Controlled Release, 163(2), 256-265.
17. Nguyen TTN, Folch B, Létourneau M, Vaudry D, Truong NH, Doucet N, Chatenet D & Fournier A (2012) Cardiotoxin I: An unexpectedly potent insulinotropic agent. ChemBioChem, 13, 1805-1812.
16. Brault G, Shareck F, Hurtubise Y, Lépine F & Doucet N* (2012) Isolation and characterization of EstC, a new cold-active esterase from Streptomyces coelicolor A3(2). PLOS ONE, 7(3): e32041.
15. Allard M, Dupont C, Muñoz Robles V, Doucet N, Lledós A, Maréchal JD, Urvoas A, Mahy JP & Ricoux R (2012) Incorporation of manganese complexes into xylanase: new artificial metalloenzymes for enantioselective epoxidation. ChemBioChem, 13, 240-251.
14. Doucet N* (2011) Can enzyme engineering benefit from the modulation of protein motions? Lessons learned from NMR relaxation dispersion experiments. Protein & Peptide Letters, 18, 336-343.
13. Doucet N, Khirich G, Kovrigin EL & Loria JP (2011) Alteration of hydrogen bonding in the vicinity of histidine 48 disrupts millisecond motions in RNase A. Biochemistry, 50, 1723-1730.
12. Doucet N* & Loria JP* (2011) Relaxation dispersion studies of enzyme motions. In: Biomedical Applications of Nuclear Magnetic Resonance Spectroscopy, A. J. Dingley & S. M. Pascal, eds., IOS Press, Amsterdam, 3, 185-202.08.
11. Doucet N, Jayasundera TB, Simonović M & Loria JP (2010) The crystal structure of ribonuclease A in complex with thymidine-3′-monophosphate provides further insight into ligand binding. Proteins: Structure, Function, and Bioinformatics, 78, 2459-2468.
10. Doucet N, Watt ED, & Loria JP (2009) The flexibility of a distant loop modulates active-site motion and product release in ribonuclease A.Biochemistry, 48, 7160–7168.
09. De Wals PY, Doucet N & Pelletier JN (2009) High tolerance to simultaneous active-site mutations in TEM-1 beta-lactamase: Distinct mutational paths provide more generalized beta-lactam recognition. Protein Science, 18, 147-160.
08. Doucet N & Pelletier JN (2011) Gaining insight into enzyme function through correlations with protein motions. In: Protein Engineering Handbook,S. Lutz & U.T. Bornscheuer, eds., Wiley-VCH, Weinheim, Vol. 1, pp. 187-211.
07. Doucet N, Savard PY, Pelletier JN & Gagné SM (2007) NMR investigation of Tyr105 mutants in TEM-1 beta-lactamase: dynamics are correlated with function. J. Biol. Chem., 282 (29), 21448-21459.
06. Doucet N & Pelletier JN (2007) Simulated annealing exploration of an active-site tyrosine in TEM-1 beta-lactamase suggests the existence of alternate conformations. Proteins: Structure, Function, and Bioinformatics, 69, 340–348.
05. Pelletier JN, De Wals PY, Doucet N & Volpato J (2007) Modifying enzyme specificity by combinatorial active site mutations. In: Molecular Interactions: Bringing Chemistry to Life, M. Hicks & C. Kettners, eds., pp. 59-76.
04. Chica RA, Doucet N & Pelletier JN (2005) Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Current Opinion in Biotechnology, 16, 378-384.
03. Doucet N, De Wals PY & Pelletier JN (2004) Site-saturation mutagenesis of Tyr-105 reveals its importance in substrate stabilization and discrimination in TEM-1 beta-lactamase. Journal of Biological Chemistry, 279 (44), 46295-46303.
02. Doucet N & Pelletier JN (2004) Directed evolution of enzymes. Obtaining clean, efficient and biodegradable catalysts. ACCN, the Canadian Chemical News, 56 (4), 20-21.
01. Doucet N & Pelletier JN (2004) Directed evolution: the search for more powerful enzymes. BioTechno Report, 2 (5), 1-12. [Article in French]
Doucet N* Semi-random mutagenesis and dynamic analysis of TEM-1 β-lactamase from Escherichia coli. Université de Montréal, Montréal (QC), 2006. [Partly in French and English]