The Gradinaru Lab - Publications

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 (2024), 128, 4354-4366

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 (2023), 39(12), btad739

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 and C.C. Gradinaru), P. Tompa, S.C.E. Tosatto, and A.M. Monzon, Nucleic Acids Res (2023), 52(D1), D536-D544

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 (2023), 127, 7472–7486

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

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 (2022), 121, 3049–3060

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. (2022), 9:910956

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

Ligand Modulation of the Conformational Dynamics of the A_2A Adenosine Receptor Revealed by Single-Molecule Fluorescence
D.D. Fernandes, C. Neale, G.-N.W. Gomes, Y. Li, A. Malik, A. Pandey, A.P. Orazietti, X. Wang, L. Ye, R.S. Prosser, and C.C. Gradinaru, Scientific Reports (2021), 11, 5910

PED in 2021: A Major Ipdate of the Protein Ensemble Database for Intrinsically Disordered Proteins
T. Lazar, E. Martínez-Pérez, F. Quaglia, A. Hatos, L.B. Chemes, J.A. Iserte, N.A. Méndez, N.A. Garrone, T.E. Saldaño, J. Marchetti, A.J. Velez Rueda, P. Bernadó, M. Blackledge, T.N. Cordeiro, E. Fagerberg, J.D. Forman-Kay, M.S. Fornasari, T.J. Gibson, G.-N.W. Gomes, C.C. Gradinaru, T. Head-Gordon, M. Ringkjøbing Jensen, E.A. Lemke, S. Longhi, C. Marino-Buslje, G. Minervini, T. Mittag, A. Miguel Monzon, R.V. Pappu, G. Parisi, S. Ricard-Blum, K.M. Ruff, E. Salladini, M. Skepö, D. Svergun, S.D. Vallet, M. Varadi, P. Tompa, S.C.E. Tosatto, D. Piovesan, Nucleic Acids Research (2020), gkaa1021

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

Non-cooperative 4E-BP2 Folding with Exchange between eIF4E-binding and binding-incompatible States allows for Tuning of CAP-dependent Translation Inhibition
J.E. Dawson, A. Bah, R.M. Vernon, Z. Zhang, H. Lin, N. Sonenberg, C.C. Gradinaru and J.D. Forman-Kay, Nat. Commun. (2020), 11, 3146

Extended Experimental Inferential Structure Determination Method for Evaluating the Structural Ensembles of Disordered Protein States
J. Lincoff, M. Haghighatlari, M. Krzeminski, J.M.C. Teixeira, G.-N. W. Gomes, C.C. Gradinaru, J.D. Forman-Kay and T. Head-Gordon, Commun. Chem. (2020), 3, 74

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

Exocyst dynamics during vesicle tethering and fusion
S.M. Ahmed, H. Nishida-Fukuda, Y. Li, W.H. McDonald, C.C. Gradinaru and I.G. Macara, Nat. Comm. (2018), 9:5140

Ligand-Induced Coupling between Oligomers of the M₂ Receptor and the G_i1 Protein in Live Cells
Y. Li, R.V. Shivnaraine, F. Huang, J.W. Wells and C.C. Gradinaru, Biophys. J. (2018), 115, 881-895

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

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

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

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

Single-Molecule Analysis of the Supramolecular Organization of the M₂ Muscarinic Receptor and the Ga_i1 Protein
R.V. Shivnaraine*, D.D. Fernandes, H. Ji, Y. Li, Z. Zhang, B. Kelly, N. Han, F. Huang, K.S. Sankar, D.N. Dubbins, J.V. Rocheleau, J.W. Wells and C.C. Gradinaru, J. Am. Chem. Soc. (2016), 138 (36), 11583-11598

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

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

Allosteric modulation in monomers and oligomers of a G protein-coupled receptor
R.V. Shivnaraine, B. Kelly, K.S. Sankar, D.S. Redka, Y.R. Han, F. Huang, G. Elmslie, D. Pinto, Y. Li, J.V. Rocheleau, C.C. Gradinaru, J. Ellis and J.W. Wells, eLife (2016), 10.7554/eLife.11685

An Adequate Account of Excluded Volume Is Necessary To Infer Compactness and Asphericity of Disordered Proteins by Forster Resonance Energy Transfer
J. Song, G.-N. Gomes, C.C. Gradinaru and H.S. Chan, J. Phys. Chem. B (2015), 119, 15191-15202

Single Lipid Bilayer Deposition on Polymer Surfaces Using Bicelles
Q. Saleem, Z. Zhang, A. Petretic, C.C. Gradinaru and P. M. Macdonald, Biomacromolecules (2015), 16 (3), 1032–1039

Multifunctional Perfluorocarbon Nanoemulsions for Cancer Therapy and Imaging
D.A. Fernandes, D.D. Fernandes, Y.J. Wang, Y. Li, C.C. Gradinaru, D. Rousseau and M.C. Kolios, Proc. SPIE 9338 (2015), doi:10.1117/12.2079914

The Effect of Intrachain Electrostatic Repulsion on Conformational Disorder and Dynamics of the Sic1 Protein
B. Liu, D. Chia, V. Csizmok, P. Farber, J.D. Forman-Kay and C.C. Gradinaru, J. Phys. Chem. B (2014), 118 (15), 4088–4097

Isolation of Monovalent Quantum Dot-Nucleic Acid Conjugates Using Magnetic Beads
U. Uddayasankar, Z. Zhang, R.T. Shergill, C.C. Gradinaru and U.J. Krull, Bioconjugate Chem. (2014), 25 (7), 1342–1350

The Advanced Interdisciplinary Research Laboratory: A Student Team Approach to the Fourth-Year Research Thesis Project Experience
P.A.E. Piunno, C. Boyd, V. Barzda, C.C. Gradinaru, U.J. Krull, S. Stefanovic and B. Stewart, J. Chem. Educ. B (2014), 91 (5), 655–661

Electrostatics-Dependent Shape of the Intrinsically-Disordered Protein Sic1: How Big Is It? What Does It Look Like?
G-N.W. Gomes, B. Liu, V. Csizmok, J.D. Forman-Kay and C.C. Gradinaru, Physics in Canada (2013), Vol. 69 (3-4), 149–152

Liposome-Coated Hydrogel Spheres: Delivery Vehicles with Tandem Release from Distinct Compartments
Q. Saleem, Z. Zhang, C.C. Gradinaru and P. M. Macdonald, Langmuir (2013), 29 (47), 14603–14612

Sub-Diffusion Decays in Fluorescence Correlation Spectroscopy: Dye Photophysics or Protein Dynamics?
A. Mazouchi, A. Bahram and C.C. Gradinaru, J. Phys. Chem. B (2013), 117 (38), 11100–11111

Ultrasensitive On-Column Laser-Induced Fluorescence in Capillary Electrophoresis using Multiparameter Confocal Detection
A. Mazouchi, B.J. Dodgson, D.W. Wegman, S.N. Krylov and C.C. Gradinaru, Analyst (2012), 137(23), 5538-5545

Phosphopeptide Selective Coordination Complexes as Promising Src Homology 2 Domain Mimetics
J.A. Drewry, E. Duodu, A. Mazouchi, P. Spagnuolo, S. Burger, C.C. Gradinaru, P. Ayers, A.D. Schimmer and P.T. Gunning, Inorg. Chem. (2012), 51(15), 8284-8291

Detection of a Thousand Copies of miRNA without Enrichment or Modification
B.J. Dodgson, A. Mazouchi, D.W. Wegman, C.C. Gradinaru and S.N. Krylov, Anal. Chem. (2012), 84(13), 5470-74

Src Homology 2 Domain Proteomimetics: Developing Phosphopeptide Selective Receptors
J.A. Drewry, S. Burger, A. Mazouchi, E. Duodu, P. Ayers, C.C. Gradinaru and P.T. Gunning, MedChemComm (2012), 3(7), 763-770

Artificially Induced Protein-Membrane Anchorage with Cholesterol-based Recognition Agents: Towards a New Therapeutic Concept
M. Avadisian, S. Fletcher, B. Liu, W. Zhao, X. Zhang, P. Yue, D. Badali, W. Xu, A.D. Schimmer, J. Turkson, C.C. Gradinaru and P.T. Gunning, Angew. Chem. Int. Ed. (2011), 50(28), 6248-6253

The Effect of Brownian Motion of Fluorescent Probes on Measuring Nanoscale Distances by Forster Resonance Energy Transfer
D. Badali and C.C. Gradinaru, J. Chem. Phys. (2011), 134, 225102

Lipogels: Single Lipid Bilayer-Enclosed Hydrogel Spheres
Q. Saleem, B. Liu, C.C. Gradinaru and P.M. Macdonald, Biomacromolecules (2011), 12(6), 2364-2374

On the Performance of Bioanalytical Fluorescence Correlation Spectroscopy Measurements in a Multiparameter Photon-Counting Microscope
A. Mazouchi, B. Liu, A. Bahram and C.C. Gradinaru, Anal. Chim. Acta (2011), 688(1), 61-69

Trapping Single Molecules in Liposomes: Surface Interactions and Freeze−Thaw Effects
B. Liu, A. Mazouchi and C.C. Gradinaru, J. Phys. Chem. B (2010), 114(46), 15191-15198

Development of STAT3 as an Accessible Target for Fluorescence-Based Inhibition Assays
D. Badali, B. Liu, A. Mazouchi, M. Avadisian, P.T. Gunning and C.C. Gradinaru, JULS (2010), 4, 18-23

Fluorescence Anisotropy: From Single Molecules to Live Cells
C.C. Gradinaru, D.O. Marushchak, M. Samim and U.J. Krull, Analyst (2010), 135, 452-459

A Mixed Film Composed of Oligonucleotides and Poly(2-Hydroxyethyl methacrylate) Brushes to Enhance Selectivity for Detection of Single Nucleotide Polymorphisms
A.K.Y. Wong, D. Marushchak, C.C. Gradinaru and U.J. Krull, Anal. Chim. Acta (2010), 661(1), 103-110

Coordination Complex SH2 Domain Proteomimetics: An Alternative Approach to Disrupting Oncogenic Protein–Protein Interactions
J.A. Drewry, S. Fletcher, P. Yue, D. Marushchak, W. Zhao, S. Sharmeen, X. Zhang, A. D. Schimmer, C.C. Gradinaru, J. Turkson and P.T. Gunning, Chem. Commun. (2010), 46, 892-894

Triggered Instability of Liposomes Bound to Hydrophobically Modified Core-Shell PNIPAM Hydrogel Beads
N. MacKinnon, G. Guerin, B. Liu, C.C. Gradinaru, J.L. Rubinstein, and P.M. Macdonald, Langmuir (2010), 26(2) 1081–1089

A Photostable, pH-invariant Fluorescein Derivative for Single-Molecule Microscopy
B. Liu, S. Fletcher, M. Avadisian, P.T. Gunning and C.C. Gradinaru, J. Fluoresc. (2009), 19, 915-920

Liposome-Hydrogel Bead Complexes Prepared via Biotin-Avidin Conjugation
N. MacKinnon, G. Guerin, B. Liu, C.C. Gradinaru and P.M. Macdonald, Langmuir (2009), 25(16), 9413-9423

Developing Methods to Study the Conformational Dynamics of Quantum Dot-Oligonucleotide Conjugates by Single Molecule Spectroscopy
W.R. Algar, M.B. Prigozhin, B. Liu, U.J. Krull and C.C. Gradinaru, Proc. SPIE 7386, 73860J (2009)

Single-Molecule Fluorescence Study of the Inhibition of the Oncogenic Functionality of STAT3
B. Liu, D. Badali, S. Fletcher, M. Avadisian, P.T. Gunning and C.C. Gradinaru, Proc. SPIE 7386, 738605 (2009)

Simultaneous Time- and Wavelength-Resolved Fluorescence Microscopy of Single Molecules
A.K. Luong, C.C. Gradinaru, D.W. Chandler and C.C. Hayden, J. Phys. Chem. B 109, 15691-15698 (2005)

Simultaneous Atomic-Force and Two-Photon Fluorescence Imaging of Biological Specimens in vivo
C.C. Gradinaru, P. Martinsson, T.J. Aartsma and Th. Schmidt, Ultramicroscopy 99, 235-245 (2004)

Selective Interaction between Xanthophylls and Chlorophylls in LHCII Probed by Femtosecond Transient Absorption Spectroscopy
C.C. Gradinaru, H. van Amerongen and R. van Grondelle, J. Phys. Chem. B 107, 3938-3943, (2003)

Stark Spectroscopy of the Light-harvesting Complex II in Different Oligomerisation States
M.A. Palacios, R.N. Frese, C.C. Gradinaru, I.H.M. van Stokkum, L.L. Premvardhan, P. Horton, A.V. Ruban, R. van Grondelle and H. van Amerongen, Biochim. Biophys. Acta 1605, 83-95 (2003)

The Primary Photoreaction of Photoactive Yellow Protein (PYP): Anisotropy Changes and Excitation Wavelength Dependence
T. Gensch, C.C. Gradinaru, I.H.M. van Stokkum, J. Hendriks, K.J. Hellingwerf and R. van Grondelle, Chem. Phys. Lett. 356, 347-354 (2002)

An Unusual Pathway of Excitation Energy Deactivation in Carotenoids: Singlet to Triplet Conversion on an Ultrafast Time Scale in a Photosynthetic Antenna
C.C. Gradinaru, J.T.M. Kennis, E. Papagiannakis, I.H.M van Stokkum, R.J. Cogdell, G.R. Fleming, R.A. Niederman and R. van Grondelle, PNAS 98, 2364-2369 (2001)

Energy Transfer in the Peridinin Chlorophyll-a Protein of Amphidinium Carterae Studied by Polarized Transient Absorption and Target Analysis
B.P. Krueger, S.S. Lampoura, I.H.M. van Stokkum, E. Papagiannakis, J.M. Salverda, C.C. Gradinaru, D. Rutkauskas, R.G. Hiller and R. van Grondelle, Biophys. J. 80, 2843-2855 (2001)

Identifying the Pathways of Energy Transfer between Carotenoids and Chlorophylls in LHCII and CP29. A Multicolor Pump-Probe Study
C.C. Gradinaru, I.H.M. van Stokkum, A.A. Pascal, R. van Grondelle and H. van Amerongen, J. Phys. Chem. B 104, 9330-9342 (2000)

Structure and Interactions of the Chlorophyll a Molecules in the Higher Plant Lhcb4 Antenna Protein
A. Pascal, E. Peterman, C.C. Gradinaru, H. van Amerongen and B. Robert, J. Phys. Chem. B 104, 9317-9321 (2000)

Spectroscopic Characterization of the Spinach Lhcb4 Protein (CP29), a Minor Light-Harvesting Complex of Photosystem II
A. Pascal, C.C. Gradinaru, U. Wacker, E. Peterman, F. Calkoen, K.D. Irrgang, P. Horton, G. Renger, R. van Grondelle, B. Robert and H. van Amerongen, Eur. J. Biochem. 262, 817-823 (1999)

The Flow of Excitation Energy in LHCII Monomers. Implications for the Structural Model of the Major Plant Antenna
C.C. Gradinaru, S. Özdemir, D. Gülen, I.H.M. van Stokkum, R. van Grondelle and H. van Amerongen, Biophys. J. 75, 3064-3077 (1998)

Ultrafast Evolution of the Excited States in the Chlorophyll a/b Complex CP29 from Green Plants Studied by Energy-Selective Pump-Probe Spectroscopy
C.C. Gradinaru, A.A. Pascal, F. van Mourik, B. Robert, P. Horton, R. van Grondelle and H. van Amerongen, Biochemistry 37, 1143-1149 (1998)

Energy Transfer in LHCII Monomers at 77K Studied by Sub-Picosecond Transient Absorption Spectroscopy
F. Kleima, C.C. Gradinaru, F. Calkoen, I.H. van Stokkum, R. van Grondelle and H. van Amerongen, Biochemistry 36, 15262-15268 (1997)

Xanthophylls in Light-Harvesting Complex II of Higher Plants: Light Harvesting and Triplet Quenching
E. Peterman, C.C. Gradinaru, F. Calkoen, J.C. Borst, R. van Grondelle, and H. van Amerongen, Biochemistry 36, 12208-12215 (1997)