Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching

Allert, Malin J.; Kumar, Shivesh; Wang, You; Beese, Lorena S.; Hellinga, Homme W.

doi:10.1038/s42004-023-00982-7

Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching

Journal Article · Sat Aug 19 00:00:00 EDT 2023 · Communications Chemistry

DOI:https://doi.org/10.1038/s42004-023-00982-7· OSTI ID:2423312

^[1]; Kumar, Shivesh ^[2]; Wang, You ^[1]; Beese, Lorena S. ^[1]; ^[1]

Duke Univ., Durham, NC (United States). Medical Center
Washington Univ., St. Louis, MO (United States); Duke Univ., Durham, NC (United States). Medical Center

Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)

Sponsoring Organization:: National Institute of General Medical Sciences (NIGMS); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-05CH11231; AC02-06CH11357

OSTI ID:: 2423312

Journal Information:: Communications Chemistry, Journal Name: Communications Chemistry Journal Issue: 1 Vol. 6; ISSN 2399-3669

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

References (56)

Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching Allert, Malin J.; Kumar, Shivesh; Wang, You Dryad https://doi.org/10.5061/dryad.msbcc2g2x	dataset	January 2023
Molecular Fluorescence Valeur, Bernard; Berberan-Santos, Mário Nuno https://doi.org/10.1002/9783527650002	book	April 2012
Monitoring Ligand‐Induced Conformational Changes for the Identification of Estrogen Receptor Agonists and Antagonists Mayer‐Wrangowski, Svenja C.; Rauh, Daniel Angewandte Chemie International Edition, Vol. 54, Issue 14 https://doi.org/10.1002/anie.201410148	journal	February 2015
Dual Emission: Classes, Mechanisms, and Conditions Behera, Santosh Kumar; Park, Soo Young; Gierschner, Johannes Angewandte Chemie International Edition, Vol. 60, Issue 42 https://doi.org/10.1002/anie.202009789	journal	June 2021
Evaluation of the Interaction between Bax and Hsp70 in Cells by Using a FRET System Consisting of a Fluorescent Amino Acid and YFP as a FRET Pair Park, Seong‐Hyun; Ko, Wooseok; Park, Sang‐Hyun ChemBioChem, Vol. 21, Issue 1-2 https://doi.org/10.1002/cbic.201900293	journal	September 2019
Principles of Fluorescence Spectroscopy Lakowicz, Joseph R. Springer New York, NY https://doi.org/10.1007/978-0-387-46312-4	book	January 2006
The Concept of λ-Ratiometry in Fluorescence Sensing and Imaging Demchenko, Alexander P. Journal of Fluorescence, Vol. 20, Issue 5 https://doi.org/10.1007/s10895-010-0644-y	journal	April 2010
The 1.9 A x-ray structure of a closed unliganded form of the periplasmic glucose/galactose receptor from Salmonella typhimurium. Flocco, M. M.; Mowbray, S. L. Journal of Biological Chemistry, Vol. 269, Issue 12 https://doi.org/10.1016/S0021-9258(17)37057-6	journal	March 1994
Synthesis, spectral properties, and use of 6-acryloyl-2-dimethylaminonaphthalene (Acrylodan). A thiol-selective, polarity-sensitive fluorescent probe. Prendergast, F. G.; Meyer, M.; Carlson, G. L. Journal of Biological Chemistry, Vol. 258, Issue 12 https://doi.org/10.1016/S0021-9258(18)32211-7	journal	June 1983
Dielectric properties of glucose in bulk aqueous solutions: Influence of electrode polarization and modeling Yoon, Gilwon Biosensors and Bioelectronics, Vol. 26, Issue 5 https://doi.org/10.1016/j.bios.2010.10.009	journal	January 2011
Multi-day pre-clinical demonstration of glucose/galactose binding protein-based fiber optic sensor Weidemaier, Kristin; Lastovich, Alexander; Keith, Steven Biosensors and Bioelectronics, Vol. 26, Issue 10 https://doi.org/10.1016/j.bios.2011.04.007	journal	June 2011
Detection of Nav1.5 Conformational Change in Mammalian Cells Using the Noncanonical Amino Acid ANAP Shandell, Mia A.; Quejada, Jose R.; Yazawa, Masayuki Biophysical Journal, Vol. 117, Issue 7 https://doi.org/10.1016/j.bpj.2019.08.028	journal	October 2019
Describing Complex Structure-Function Relationships in Biomolecules at Equilibrium Allert, Malin J.; Hellinga, Homme W. Journal of Molecular Biology, Vol. 432, Issue 7 https://doi.org/10.1016/j.jmb.2019.12.039	journal	March 2020
Practical aspects of wavelength ratiometry in the studies of intermolecular interactions Demchenko, Alexander P. Journal of Molecular Structure, Vol. 1077 https://doi.org/10.1016/j.molstruc.2013.11.045	journal	December 2014
Structure-switching biosensors: inspired by Nature Vallée-Bélisle, Alexis; Plaxco, Kevin W. Current Opinion in Structural Biology, Vol. 20, Issue 4 https://doi.org/10.1016/j.sbi.2010.05.001	journal	August 2010
Fiber optic biosensor for transdermal glucose based on the glucose binding protein Tiangco, Cristina; Fon, Dieudonne; Sardesai, Neha Sensors and Actuators B: Chemical, Vol. 242 https://doi.org/10.1016/j.snb.2016.11.077	journal	April 2017
Monitoring protein interactions and dynamics with solvatochromic fluorophores Loving, Galen S.; Sainlos, Matthieu; Imperiali, Barbara Trends in Biotechnology, Vol. 28, Issue 2 https://doi.org/10.1016/j.tibtech.2009.11.002	journal	February 2010
Mathematics for Machine Learning Deisenroth, Marc Peter; Faisal, A. Aldo; Ong, Cheng Soon https://doi.org/10.1017/9781108679930	book	January 2020
Solvatochromic and Fluorogenic Dyes as Environment-Sensitive Probes: Design and Biological Applications Klymchenko, Andrey S. Accounts of Chemical Research, Vol. 50, Issue 2 https://doi.org/10.1021/acs.accounts.6b00517	journal	January 2017
Wavelength-Dependent Fluorescent Immunosensors via Incorporation of Polarity Indicators near the Binding Interface of Antibody Fragments Islam, Jiaul; Riley, Blake T.; Fercher, Christian Analytical Chemistry, Vol. 91, Issue 12 https://doi.org/10.1021/acs.analchem.9b00445	journal	May 2019
Harnessing Environmental Ca²⁺ for Extracellular Protein Thermostabilization Allert, Malin J.; Hellinga, Homme W. Biochemistry, Vol. 59, Issue 39 https://doi.org/10.1021/acs.biochem.0c00449	journal	September 2020
Discovery of Thermostable, Fluorescently Responsive Glucose Biosensors by Structure-Assisted Function Extrapolation Allert, Malin J.; Hellinga, Homme W. Biochemistry, Vol. 61, Issue 4 https://doi.org/10.1021/acs.biochem.1c00738	journal	January 2022
Unraveling the Conformational Landscape of Ligand Binding to Glucose/Galactose-Binding Protein by Paramagnetic NMR and MD Simulations Unione, Luca; Ortega, Gabriel; Mallagaray, Alvaro ACS Chemical Biology, Vol. 11, Issue 8 https://doi.org/10.1021/acschembio.6b00148	journal	June 2016
Large Amplitude Twisting Motions of an Interdomain Hinge: A Disulfide Trapping Study of the Galactose-Glucose Binding Protein Careaga, Claire L.; Sutherland, Jesse; Sabeti, Jilla Biochemistry, Vol. 34, Issue 9 https://doi.org/10.1021/bi00009a036	journal	March 1995
Open conformation of a substrate-binding cleft: fluorine-19 NMR studies of cleft angle in the D-galactose chemosensory receptor Luck, Linda A.; Falke, Joseph J. Biochemistry, Vol. 30, Issue 26 https://doi.org/10.1021/bi00240a019	journal	July 1991
Synthesis and spectral properties of a hydrophobic fluorescent probe: 6-propionyl-2-(dimethylamino)naphthalene Weber, Gregorio; Farris, Fay J. Biochemistry, Vol. 18, Issue 14 https://doi.org/10.1021/bi00581a025	journal	July 1979
Structural Changes Accompanying Intramolecular Electron Transfer: Focus on Twisted Intramolecular Charge-Transfer States and Structures Grabowski, Zbigniew R.; Rotkiewicz, Krystyna; Rettig, Wolfgang Chemical Reviews, Vol. 103, Issue 10 https://doi.org/10.1021/cr940745l	journal	October 2003
Singlet adiabatic states of solvated PRODAN: a semiempirical molecular orbital study Ilich, Predrag; Prendergast, Franklyn G. The Journal of Physical Chemistry, Vol. 93, Issue 11 https://doi.org/10.1021/j100348a014	journal	June 1989
Direct Binding Assay for the Detection of Type IV Allosteric Inhibitors of Abl Schneider, Ralf; Becker, Christian; Simard, Jeffrey R. Journal of the American Chemical Society, Vol. 134, Issue 22 https://doi.org/10.1021/ja303858w	journal	May 2012
Carbohydrate Affinity for the Glucose–Galactose Binding Protein Is Regulated by Allosteric Domain Motions Ortega, Gabriel; Castaño, David; Diercks, Tammo Journal of the American Chemical Society, Vol. 134, Issue 48 https://doi.org/10.1021/ja3092938	journal	November 2012
Overcoming Compound Fluorescence in the FLiK Screening Assay with Red-Shifted Fluorophores Schneider, Ralf; Gohla, Anne; Simard, Jeffrey R. Journal of the American Chemical Society, Vol. 135, Issue 22 https://doi.org/10.1021/ja403074j	journal	May 2013
Development of a Fluorescent-Tagged Kinase Assay System for the Detection and Characterization of Allosteric Kinase Inhibitors Simard, Jeffrey R.; Getlik, Matthäus; Grütter, Christian Journal of the American Chemical Society, Vol. 131, Issue 37 https://doi.org/10.1021/ja902010p	journal	June 2009
Genetic Incorporation of a Small, Environmentally Sensitive, Fluorescent Probe into Proteins in Saccharomyces cerevisiae Lee, Hyun Soo; Guo, Jiantao; Lemke, Edward A. Journal of the American Chemical Society, Vol. 131, Issue 36 https://doi.org/10.1021/ja904896s	journal	August 2009
Fluorophore Labeling of the Glycine-Rich Loop as a Method of Identifying Inhibitors That Bind to Active and Inactive Kinase Conformations Simard, Jeffrey R.; Getlik, Matthäus; Grütter, Christian Journal of the American Chemical Society, Vol. 132, Issue 12 https://doi.org/10.1021/ja908083e	journal	March 2010
Estimation of the polarity of the protein interior by optical spectroscopy Macgregor, Robert B.; Weber, Gregorio Nature, Vol. 319, Issue 6048 https://doi.org/10.1038/319070a0	journal	January 1986
A new screening assay for allosteric inhibitors of cSrc Simard, Jeffrey R.; Klüter, Sabine; Grütter, Christian Nature Chemical Biology, Vol. 5, Issue 6 https://doi.org/10.1038/nchembio.162	journal	April 2009
A fluorescence lifetime-based fibre-optic glucose sensor using glucose/galactose-binding protein Saxl, Tania; Khan, Faaizah; Ferla, Matteo The Analyst, Vol. 136, Issue 5 https://doi.org/10.1039/C0AN00430H	journal	January 2011
Macro-/micro-environment-sensitive chemosensing and biological imaging Yang, Zhigang; Cao, Jianfang; He, Yanxia Chem. Soc. Rev., Vol. 43, Issue 13 https://doi.org/10.1039/C4CS00051J	journal	January 2014
Polarity-based fluorescence probes: properties and applications Qin, Xiaojun; Yang, Xingye; Du, Lupei RSC Medicinal Chemistry, Vol. 12, Issue 11 https://doi.org/10.1039/D1MD00170A	journal	January 2021
A paradigm of thermal adaptation in penguins and elephants by tuning cold activation in TRPM8 Yang, Shilong; Lu, Xiancui; Wang, Yunfei Proceedings of the National Academy of Sciences, Vol. 117, Issue 15 https://doi.org/10.1073/pnas.1922714117	journal	March 2020
The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors Marvin, J. S.; Corcoran, E. E.; Hattangadi, N. A. Proceedings of the National Academy of Sciences, Vol. 94, Issue 9 https://doi.org/10.1073/pnas.94.9.4366	journal	April 1997
Dielectric Properties of Supersaturated α-D-Glucose Aqueous Solutions at 2450 MHz Liao, X.; Raghavan, V. G. S.; Meda, V. Journal of Microwave Power and Electromagnetic Energy, Vol. 36, Issue 3 https://doi.org/10.1080/08327823.2001.11688455	journal	January 2001
Continuous Glucose Monitoring Using a Novel Glucose/Galactose Binding Protein: Results of a 12-Hour Feasibility Study with the Becton Dickinson Glucose/Galactose Binding Protein Sensor Judge, Kevin; Morrow, Linda; Lastovich, Alexander G. Diabetes Technology & Therapeutics, Vol. 13, Issue 3 https://doi.org/10.1089/dia.2010.0130	journal	March 2011
Structure-based engineering of environmentally sensitive fluorophores for monitoring protein-protein interactions Sloan, D. J.; Hellinga, H. W. Protein Engineering Design and Selection, Vol. 11, Issue 9 https://doi.org/10.1093/protein/11.9.819	journal	September 1998
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Construction of a fluorescent biosensor family De Lorimier, Robert M.; Smith, J. Jeff; Dwyer, Mary A. Protein Science, Vol. 11, Issue 11 https://doi.org/10.1110/ps.021860	journal	November 2002
Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates Rizk, Shahir S.; Cuneo, Matthew J.; Hellinga, Homme W. Protein Science, Vol. 15, Issue 7 https://doi.org/10.1110/ps.062135206	journal	July 2006
Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures Borrok, M. Jack; Kiessling, Laura L.; Forest, Katrina T. Protein Science, Vol. 16, Issue 6 https://doi.org/10.1110/ps.062707807	journal	June 2007
X‐ray structure of glucose/galactose receptor from Salmonella typhimurium in complex with the physiological ligand, (2R)‐glyceryl‐β‐d‐galactopyranoside Sooriyaarachchi, Sanjeewani; Ubhayasekera, Wimal; Boos, Winfried The FEBS Journal, Vol. 276, Issue 7 https://doi.org/10.1111/j.1742-4658.2009.06945.x	journal	March 2009
Probing Protein Electrostatics with a Synthetic Fluorescent Amino Acid Cohen, B. E. Science, Vol. 296, Issue 5573 https://doi.org/10.1126/science.1069346	journal	May 2002
Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein Vyas, N.; Vyas, M.; Quiocho, F. Science, Vol. 242, Issue 4883 https://doi.org/10.1126/science.3057628	journal	December 1988
Physical Biology of the Cell Phillips, Rob; Kondev, Jane; Theriot, Julie https://doi.org/10.1201/9781134111589	book	October 2012
Fluorophore Labeled Kinase Detects Ligands That Bind within the MAPK Insert of p38α Kinase Getlik, Matthäus; Simard, Jeffrey R.; Termathe, Martin PLoS ONE, Vol. 7, Issue 7 https://doi.org/10.1371/journal.pone.0039713	journal	July 2012
Voltage-clamp fluorometry analysis of structural rearrangements of ATP-gated channel P2X2 upon hyperpolarization Andriani, Rizki Tsari; Kubo, Yoshihiro eLife, Vol. 10 https://doi.org/10.7554/eLife.65822	journal	May 2021

Similar Records

Structure-Based Design of Robust Glucose Biosensors using a Thermotoga maritima Periplasmic Glucose-Binding Protein

Journal Article · Sun Dec 31 23:00:00 EST 2006 · Protein Science · OSTI ID:959969

PEGylation of a Maltose Biosensor Promotes Enhanced Signal Response

Journal Article · Wed Dec 31 23:00:00 EST 2008 · Bioconjugate Chemistry · OSTI ID:1078191

Ligand-induced conformational changes in a thermophilic ribose-binding protein

Journal Article · Thu May 21 00:00:00 EDT 2009 · BMC Struct. Biol. · OSTI ID:1007064

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching

Citation Formats

References (56)

Similar Records

Related Subjects