Claudiu Gradinaru, Ph.D.

Interim Chair & Professor at the Department of Chemical and Physical Sciences

Physics | Biophysics and Physical Chemistry

E-mail:

claudiu.gradinaru@utoronto.ca
Phone:

905 828 3833
Fax:

905 828 5425
Website:

http://www.utm.utoronto.ca/gradinaru-lab/
Mailing Address:

3359 Mississauga Road
Mississauga ON L5L 1C6
Canada

Research Areas:

single-molecule biophysics, intrinsically-disordered proteins, GPCRs, computational methods, bioanalytical chemistry

Research Profile:

Gradinaru biophysics research laboratory uses advanced laser and detection technology to capture conformational dynamics and molecular interactions at the single-molecule level. Single-molecule techniques are widely applied in life sciences and nanotechnology due to their unique ability to go beyond the intrinsic disorder and complexity of biological systems and provide new insights for how they work and for therapeutic intervention. Ultrasensitive microscopes in our lab, designed and built specifically for single-molecule fluorescence imaging and spectroscopy, provide a wide range of photon-level experimental capabilities, making the lab unique in Canada. Currently, the Gradinaru lab focuses on two main directions of research. First, we integrate single-molecule fluorescence data with other structural data (NMR, SAXS) and polymer physics theory to understand the determinants of “fuzzy structures” in biology and how intrinsically-disordered proteins (IDPs) interact with other molecules. Second, we measure nanometer-scale distances and nanosecond-to-second dynamics in G protein coupled-receptors (GPCRs), a large class of membrane proteins that are the main target of medicinal drugs. Our goal is to define how/when/where GPCRs activate and oligomerize in the cell membrane and how their innate structural flexibility couples to quaternary organization and biased signaling.

Courses Taught:

PHY332H5, PHY343H5, and PHY347H5 (undergraduate); PHY2707H1 (graduate)

Publications

Recent:

Diffusion and Oligomerization States of the Muscarinic M1 Receptor in Live Cells – The
Impact of Ligands and Membrane Disruptors. X. Zhou, H. Septien-Gonzalez, S. Husaini, R.J. Ward, G. Milligan, and C.C. Gradinaru, J. Phys. Chem. B virtual special issue Advances in Cellular Biophysics (2024) doi.org/10.1021/acs.jpcb.4c01035

Local Disordered Region Sampling (LDRS) for Ensemble Modeling of Proteins with
Experimentally Undetermined or Low Confidence Prediction Segments. Z.H. Liu, J.M.C. Teixeira, O. Zhang, T.E. Tsangaris, J. Li, C.C. Gradinaru, T. Head-Gordon, and J.D. Forman-Kay, Bioinformatics, 39(12), DOI: 10.1093/bioinformatics/btad739 (2023)

Delineating Structural Propensities of the 4E-BP2 Protein via Integrative Modeling and
Clustering. T.E. Tsangaris, S. Smyth, G.W. Gomes, Z.H. Liu, M. Milchberg, A. Bah, G.A. Wasney, J.D.
Forman-Kay, and C.C. Gradinaru, J. Phys. Chem. B 127, 7472–7486 (2023)

PED in 2024: Improving the Community Deposition of Structural Ensembles for Intrinsically
Disordered Proteins. H. Ghafouri, T. Lazar, A. Del Conte, L.G. Tenorio Ku, PED Consortium (incl. T.E. Tsangaris & C.C. Gradinaru), P. Tompa, S.C.E. Tosatto, A.M. Monzon, Nucleic Acids Research
doi.org/10.1093/nar/gkad947 (2023)

Multisite Phosphorylation and Binding Alter Conformational Dynamics of the 4E-BP2 Protein S. Smyth, Z. Zhang, A. Bah, T.E. Tsangaris, J. Dawson, J.D. Forman-Kay, and C.C. Gradinaru, Biophysical Journal 121, 3049–3060 (2022)

Single-molecule Counting Applied to the Study of GPCR Oligomerization J.N. Milstein, D.F. Nino, X. Zhou, and C.C. Gradinaru*, Biophysical Journal, 121, 3175-3187 (2022)

Integrative Conformational Ensembles of Sic1 Using Different Initial Pools and Optimization Methods G.-N.W. Gomes, A. Namini, and C. C. Gradinaru, Front. Mol. Biosci. 9:910956 (2022)

Naullage, P. M., Haghighatlari, M., Namini, A., Teixeira, J. M. C., Li, J., Zhang, O., Gradinaru, C. C., Forman-Kay, J. D., and Head-Gordon, T. Protein Dynamics to Define and Refine Disordered Protein Ensembles. J. Phys. Chem. B 126, 1885-1894 (2022)

Fernandes, D.D., Neale, C., Gomes, G.-N.W., Li, Y., Malik, A., Pandey, A., Orazietti, A.P., Wang, X., Ye, L., Prosser, R.S. and Gradinaru, C. C., Ligand modulation of the conformational dynamics of the A2A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports (Nature) 2021, 11: 5910.

Fernandes, D.A., Fernandes, D.D., Malik, A., Gomes, G.-N.W., Appak-Baskoy, S., Berndl, E. Gradinaru, C. C., and Kolios, M.C. Multifunctional nanoparticles as theranostic agents for therapy and imaging of breast cancer. Journal of Photochemistry and Photobiology B: Biology 2021, 218: 112110.

Lazar, T., Martínez-Pérez, E., Quaglia, F., Hatos, A., Chemes, L.B., Iserte, J.A., Méndez, N.A. Garrone, N.A., Saldaño, T.E., Marchetti, J., Velez Rueda, A.J., Bernadó, P., Blackledge, M., Cordeiro, T.N., Fagerberg, E., Forman-Kay, J.D., Fornasari, M.S., Gibson, T.J., Gomes, G.-N. W., Gradinaru, C. C., Head-Gordon,T., Ringkjøbing Jensen, M., Lemke, E.A., Longhi, S., Marino-Buslje, C., Minervini, G., Mittag, T., Miguel Monzon, A., Pappu, R.V., Parisi, G., Ricard-Blum, S., Ruff, K.M., Salladini, E., Skepö, M., Svergun, D., Vallet, S.D., Varadi, M., Tompa, P., Tosatto, S.C.E., and Piovesan, D. PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. Nucleic Acids Research, 2021, 49 (D1), D404–D411.

Gomes, G.-N. W.; Krzeminski, M.; Namini, A.; Martin, E. W.; Mittag, T.; Head-Gordon, T.; Forman-Kay, J. D.; Gradinaru, C. C., Conformational Ensembles of an Intrinsically Disordered Protein Consistent with NMR, SAXS, and Single-Molecule FRET. Journal of the American Chemical Society 2020, 142 (37), 15697-15710.

Dawson, J. E.; Bah, A.; Zhang, Z.; Vernon, R. M.; Lin, H.; Chong, P. A.; Vanama, M.; Sonenberg, N.; Gradinaru, C. C.; Forman-Kay, J. D., Non-cooperative 4E-BP2 folding with exchange between eIF4E-binding and binding-incompatible states tunes cap-dependent translation inhibition. Nature Communications 2020, 11 (1), 3146.

Lincoff, J.; Haghighatlari, M.; Krzeminski, M.; Teixeira, J. M. C.; Gomes, G.-N. W.; Gradinaru, C. C.; Forman-Kay, J. D.; Head-Gordon, T., Extended experimental inferential structure determination method in determining the structural ensembles of disordered protein states. Communications Chemistry 2020, 3 (1), 74.

Garry, J., Li, Y. Shew, B., Gradinaru, C.C., and Rutenberg, A. R., (2020). Bayesian Counting of Photobleaching Steps with Physical Priors. J. Chem. Phys. 152(2): 024110.

Ahmed, S.M., Nishida-Fukuda, H., Li, Y., McDonald, W.H., Gradinaru, C.C., and Macara, I.G. (2018). Exocyst Dynamics during Vesicle Tethering and Fusion. Nature Communications, volume 9, 5140.

Li, Y., Shivnaraine, R.V., Huang, F., Wells, J.W., and Gradinaru, C.C. (2018). Ligand-Induced Coupling between Oligomers of the M2 Receptor and the Gi1 Protein in Live Cells. Biophys. J., 115, 881-895.

Fernandes, D.D., Bamrah, J., Kailasam, S., Li, Y., Gomes, G.-N., Wieden, H.-J., and Gradinaru, C.C. (2017). Characterization of Fluorescein Arsenical Hairpin (FlAsH) as a Probe for Single-Molecule Fluorescence Spectroscopy. Scientific Reports, 7:13063, DOI:10.1038/s41598-017-13427-8.

Song, J., Gomes, G.-N., Shi, T., Gradinaru, C.C., and Chan, H.S. (2017). Conformational Heterogeneity and FRET Data Interpretation for Dimensions of Unfolded Proteins. Biophys. J., 113, 1012-1024.

Gomes, G.-N. and Gradinaru, C.C. (2017). Insights into the Conformations and Dynamics of Intrinsically Disordered Proteins using Single-Molecule Fluorescence. BBA - Proteins and Proteomics, Special Issue “Biophysics in Canada”, 1865, 1696-1706.

Zhang, Z., Yomo, D. and Gradinaru, C. C. (2017). Choosing the Right Fluorophore for Single-Molecule Fluorescence Studies in a Lipid Environment. BBA Biomembranes, 1859, 1242–1253.

Shivnaraine, R.V., Fernandes, D. D., Ji, H., Li, Y., Zhang, Z., Kelly, B., Han, N., Huang, F., Sankar, K. S., Dubbins, D. N., Rocheleau, J. V., Wells, J. W. and Gradinaru, C. C. (2016). Single-Molecule Analysis of the Supramolecular Organization of the M2 Muscarinic Receptor and the G_αi1 Protein. J. Am. Chem. Soc. 138 (36), 11583–11598.

Fernandes, D. A., Fernandes, D. D., Li, Y., Wang, Y., Zhang, Z., Rousseau, D., Gradinaru,* C. C. and Kolios,* M. C. (2016). Synthesis of Stable Multifunctional Perfluorocarbon Nanoemulsions for Cancer Therapy and Imaging. Langmuir, 32, 10870-10880.

Shivnaraine,* R.V., Kelly, B., Sankar, K. S., Redka, D.S., Han, Y. R., Huang, F., Elmslie, G., Pinto, D., Li, Y., Rocheleau, J. V., Gradinaru,* C. C., Ellis,* J. and Wells,* J. W. (2016). Allosteric Modulation in Monomers and Oligomers of a G Protein-Coupled Receptor, eLife, 10.7554/eLife.11685.

Mazouchi, A., Zhang, Z., Bahram, A., Gomes, G.-N., Lin, H., Song, J., Chan, H. S., Forman-Kay, J. D. and Gradinaru, C.C. (2016). Conformations of a Metastable SH3 Domain Characterized by smFRET and an Excluded-Volume Polymer Model. Biophys. J., 110, 1510–1522.