Publications
2024
Rakotoharisoa RV, Seifinoferest B, Zarifi N, Miller JDM, Rodriguez JM, Thompson MC* & Chica RA* (2024) Design of efficient artificial enzymes using crystallographically-enhanced conformational sampling. Journal of the American Chemical Society, in press.
Preprint available on bioRxiv.
Chica RA* & Ferruz N* (2024) What does it take for an 'AlphaFold Moment' in functional protein engineering and design? Nature Biotechnology, 42, 173-174. Invited correspondence for the "Spotlight on protein structure design" special issue.
2023
St-Jacques AD, Rodriguez JM, Eason MG, Foster SM, Khan ST, Damry AM, Goto NK, Thompson MC, Chica RA* (2023) Computational Remodeling of an Enzyme Conformational Landscape for Altered Substrate Selectivity. Nature Communications, 14, 6058.
Preprint available on bioRxiv.
2022
Slobodyanyuk M, Banda-Vazquez JA, Thompson MJ, Dean RA, Baenziger JE, Chica RA*, daCosta CJB* (2022) Origin of Acetylcholine Antagonism in ELIC, a Bacterial Pentameric Ligand-gated Ion Channel. Communications Biology, 5, 1264.
Legault S, Fraser-Halberg DP, McAnelly RL, Eason MG, Thompson MC, Chica RA* (2022) Generation of Bright Monomeric Red Fluorescent Proteins via Computational Design of Enhanced Chromophore Packing. Chemical Science, 13, 1408-1418.
2021
Keller BA, Laight BJ, Varette O, Broom A, Wedge ME, McSweeney B, Cemeus C, Petryk J, Lo B, Burns B, Nessim C, Ong M, Chica RA, Atkins HL, Diallo JS, Ilkow CS, Bell JC* (2021) Personalized Oncology and BRAF K601N Melanoma: Model Development, Drug Discovery, and Clinical Correlation. Journal of Cancer Research and Clinical Oncology, 147, 1365-1378.
2020
Eason MG, Pandelieva AT, Mayer MM, Khan ST, Garcia HG & Chica RA* (2020) Genetically-Encoded Fluorescent Biosensor for Rapid Detection of Protein Expression. ACS Synthetic Biology 9, 2955–2963.
Preprint available on bioRxiv.
Broom A, Rakotoharisoa RV, Thompson MC, Zarifi N, Nguyen E, Mukhametzhanov N, Liu L, Fraser JS & Chica RA* (2020) Ensemble-Based Enzyme Design Can Recapitulate the Effects of Laboratory Directed Evolution In Silico. Nature Communications 11, 4808.
Highlighted in Nature Catalysis
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Parmeggiani F, Turner NJ & Chica RA* (2020) One-Pot Biocatalytic Synthesis of D-Tryptophan Derivatives from Substituted Indoles and L-Serine. In: Whittall J & Sutton PW (Ed.) Applied Biocatalysis: The Chemist's Enzyme Toolbox, (pp. 435-441). Wiley.
2019
Damry AM, Mayer MM, Broom A, Goto NK & Chica RA* (2019) Origin of Conformational Dynamics in a Globular Protein. Communications Biology 2, 433.
Chica RA* (2019) Designer Sense-Response Systems. Science 366, 952-953. Invited "Perspective" commentary article.
Parmeggiani F, Rué Casamajo A, Colombo D, Ghezzi MC, Galman JL, Chica RA, Brenna E & Turner NJ* (2019) Biocatalytic Retrosynthesis Approaches to D-(2,4,5-trifluorophenyl)alanine, Key Precursor of the Antidiabetic Sitagliptin. Green Chemistry 21, 4368-4379.
St-Jacques AD, Eyahpaise MEC & Chica RA* (2019) Computational Design of Multisubstrate Enzyme Specificity. ACS Catalysis 9, 5480-5485.
Parmeggiani F, Rué Casamajo A, Walton CJW, Galman JL, Turner NJ & Chica RA* (2019) One-Pot Biocatalytic Synthesis of Substituted D-Tryptophans from Indoles Enabled by an Engineered Aminotransferase. ACS Catalysis 9, 3482–3486.
2018
Chica RA* (2018) Designer Proteins Activate Fluorescence. Nature 561, 471-472. Invited "News and Views" commentary article.
Walton CJW, Thiebaut F, Brunzelle JS, Couture JF* & Chica RA* (2018) Structural Determinants of the Stereoinverting Activity of Pseudomonas stutzeri D-Phenylglycine Aminotransferase. Biochemistry 57, 5437-5446.
Wang CY, Chang PM, Ary ML, Allen BD, Chica RA, Mayo SL & Olafson BD* (2018) ProtaBank: A Repository for Protein Design and Engineering Data. Protein Science 27, 1113-1124.
Preprint available on bioRxiv.
St-Jacques AD, Gagnon O & Chica RA* (2018) Computational Enzyme Design: Successes, Challenges and Future Directions. In: Williams G & Hall M (Ed.) Modern Biocatalysis: Advances Towards Synthetic Biological Systems (pp. 88-116). Cambridge, UK. Royal Society of Chemistry.
Walton CJW, Parmeggiani F, Barber JEB, McCann JL, Turner NJ & Chica RA* (2018) Engineered Aminotransferase for the Production of D-Phenylalanine Derivatives using Biocatalytic Cascades. ChemCatChem 10, 470-474.
2017
Davey JA, Damry AM, Goto NK* & Chica RA* (2017) Rational Design of Proteins that Exchange on Functional Timescales. Nature Chemical Biology 13, 1280-1285.
Highlighted by H1 Connect.
Chica RA* & Goto NK (2017) Rational Design of Protein Dynamics: Making Proteins Dance. Cell Systems, 5: 428–430. Invited commentary article.
Eason MG, Damry AM & Chica RA* (2017) Structure-Guided Rational Design of Red Fluorescent Proteins: Towards Designer Genetically-Encoded Fluorophores. Current Opinion in Structural Biology 45, 91-99.
Davey JA & Chica RA* (2017) Multistate Computational Protein Design with Backbone Ensembles. Methods in Molecular Biology 1529, 161-179.
2016
Davey JA & Chica RA* (2016) Turning a Negative into a Positive: Conversion of a Homodimer into a Heterodimer using Negative State Repertoires. Structure 24, 496-497. Invited commentary article.
Pandelieva AT, Baran MJ, Calderini GF, McCann JL, Tremblay V, Sarvan S, Davey JA, Couture JF* & Chica RA* (2016) Brighter Red Fluorescent Proteins by Rational Design of Triple-Decker Motif. ACS Chemical Biology 11, 508-517.
St-Jacques AD, Rachel NM, Curry DR, Gillet SMFG, Clouthier CM, Keillor JW, Pelletier JN & Chica RA* (2016) Specificity of Transglutaminase-Catalyzed Peptide Synthesis. Journal of Molecular Catalysis B: Enzymatic 123, 53-61.
2015
Davey JA, Damry AM, Euler CK, Goto NK & Chica RA* (2015) Prediction of Stable Globular Proteins using Negative Design With Non-Native Backbone Ensembles. Structure 23, 2011-2021.
Chica RA* (2015) Protein Engineering in the 21st Century. Protein Science 24, 431-433. Commentary article.
Davey JA & Chica RA* (2015) Optimization of Rotamers Prior to Template Minimization Improves Stability Predictions Made by Computational Protein Design. Protein Science 24, 545-560.
Lanouette S, Davey JA, Elisma F, Ning Z, Figeys D, Chica RA* & Couture JF* (2015) Discovery of Substrates for a SET Domain Lysine Methyltransferase Predicted by Multistate Computational Protein Design. Structure 23, 206-215.
Commentary on this article can be found here.
2014
Barber JEB, Damry AM, Calderini GF, Walton CJW & Chica RA* (2014) Continuous Colorimetric Screening Assay for Detection of D-Amino Acid Aminotransferase Mutants Displaying Altered Substrate Specificity. Analytical Biochemistry 463, 23-30.
Davey JA & Chica RA* (2014) Improving the Accuracy of Protein Stability Predictions With Multistate Design Using a Variety of Backbone Ensembles. Proteins: Structure, Function and Bioinformatics 82, 771-784.
2013
Mironov GG, St.-Jacques AD, Mungham A, Eason MG, Chica RA* & Berezovski MV* (2013) Bioanalysis for Biocatalysis: Multiplexed Capillary Electrophoresis–Mass Spectrometry Assay for Aminotransferase Substrate Discovery and Specificity Profiling. Journal of the American Chemical Society 135, 13728-13736.
Walton CJW & Chica RA* (2013) A High-Throughput Assay for Screening L- or D-amino Acid Specific Aminotransferase Mutant Libraries. Analytical Biochemistry 441, 190–198.
2012
Moore MM, Oteng-Pabi SK, Pandelieva AT, Mayo SL & Chica RA* (2012) Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design. PLoS One 7: e52463.
Davey JA & Chica RA* (2012) Multistate Approaches in Computational Protein Design. Protein Science 21, 1241-1252.
Postdoctoral Research
Privett HK, Kiss G, Lee TM, Blomberg R, Chica RA, Thomas LM, Hilvert D, Houk KN & Mayo SL (2012) Iterative Approach to Computational Enzyme Design. Proceedings of the National Academy of Science of the USA 109, 3790-3795.
Hemmert AC, Otto TC, Chica RA, Wierdl M, Edwards JS, Lewis SL, Edwards CC, Tsurkan L, Cadieux CL, Kasten SA, Cashman JR, Mayo SL, Potter PM, Cerasoli DM & Redinbo MR (2011) Nerve Agent Hydrolysis Activity Designed into a Human Drug Metabolism Enzyme. PLoS One 6, e17441.
Chica RA, Moore MM, Allen BD & Mayo SL (2010) Generation of Longer Emission Wavelength Red Fluorescent Proteins Using Computationally Designed Libraries. Proceedings of the National Academy of Science of the USA 107, 20257-20262.
Highlighted by H1 Connect.
Graduate Research
Pardin C, Roy I, Chica RA, Bonneil E, Thibault P, Lubell WD, Pelletier JN & Keillor JW (2009) Photolabeling of Tissue Transglutaminase Reveals the Binding Mode of Potent Cinnamoyl Inhibitors. Biochemistry 48, 3346-53.
Keillor JW, Chica RA, Chabot N, Vinci V, Pardin C, Fortin E, Gillet SMFG, Nakano Y, Kaartinen MT, Pelletier JN & Lubell WD (2008) The Bioorganic Chemistry of Transglutaminase: From Mechanism to Inhibition and Engineering. Canadian Journal of Chemistry 86, 271-276.
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.
Chica RA, Gagnon P, Keillor JW & Pelletier JN (2004) Tissue Transglutaminase Acylation: Proposed Role of Conserved Active Site Tyr and Trp Residues Revealed by Molecular Modelling of Peptide Substrate Binding. Protein Science 13, 979-991.
Gillet SMFG, Chica RA, Keillor JW & Pelletier JN (2004) Expression and Rapid Purification of Highly Active Hexahistidine-Tagged Guinea Pig Liver Transglutaminase. Protein Expression & Purification 33, 256-264.
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