1
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Elayan IA, Brown A. Non-Degenerate Two-Photon Absorption of Fluorescent Protein Chromophores. J Phys Chem A 2024; 128:7511-7523. [PMID: 39192559 DOI: 10.1021/acs.jpca.3c08402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Two-photon absorption (2PA), where a pair of photons are absorbed simultaneously, is recognized as a potent bioimaging technique, which depends on the quantified 2PA probability, defined as cross-section (σ2PA). The absorbed photons either have equivalent (ω1 = ω2) or different frequencies (ω1 ≠ ω2), where the former is degenerate 2PA (D-2PA) and the latter is nondegenerate 2PA (ND-2PA). ND-2PA is of particular interest since it is a promising imaging technology with flexibility of photon frequencies and enhanced cross sections, however, it remains a relatively unexplored area compared to D-2PA. This work utilizes time-dependent density functional theory (TD-DFT) and second-order approximate coupled-cluster with the resolution-of-identity approximation (RI-CC2), for the excitation from S0 to S1, to investigate σD-2PA and σND-2PA of FP chromophore models. Interestingly, comparing CAM-B3LYP with the RI-CC2 computations shows qualitative and, in fact, near quantitative agreement in the computed improvements of σND-2PA for comparable (relative) frequency detunings, despite the known underestimations of 2PA cross sections, for TD-DFT results relative to RI-CC2 values. As expected from the 2-state model, the computed values of σND-2PA are quantitatively larger than σD-2PA, where chromophores with the largest values of σD-2PA show greater potential for σND-2PA improvement. Anionic chromophores demonstrated improvements up to 14%, while substantial enhancements were observed in neutral chromophores with some achieving a 30% increase. This work investigates the ND-2PA photophysical characteristics of FP chromophores and identifies qualitative patterns in the computed properties of ND-2PA relative to D-2PA.
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Affiliation(s)
- Ismael A Elayan
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
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2
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Lampkin BJ, Goldberg BJ, Kritzer JA. BenzoHTag, a fluorogenic self-labeling protein developed using molecular evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.29.564634. [PMID: 38617361 PMCID: PMC11014480 DOI: 10.1101/2023.10.29.564634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Self-labeling proteins are powerful tools in chemical biology as they enable the precise cellular localization of a synthetic molecule, often a fluorescent dye, with the genetic specificity of a protein fusion. HaloTag7 is the most popular self-labeling protein due to its fast labeling kinetics and the simplicity of its chloroalkane ligand. Reaction rates of HaloTag7 with different chloroalkane-containing substrates is highly variable and rates are only very fast for rhodamine-based dyes. This is a major limitation for the HaloTag system because fast labeling rates are critical for live-cell assays. Here, we report a molecular evolution system for HaloTag using yeast surface display that enables the screening of libraries up to 108 variants to improve reaction rates with any substrate of interest. We applied this method to produce a HaloTag variant, BenzoHTag, which has improved performance with a fluorogenic benzothiadiazole dye. The resulting system has improved brightness and conjugation kinetics, allowing for robust, no-wash fluorescent labeling in live cells. The new BenzoHTag-benzothiadiazole system has improved performance in live-cell assays compared to the existing HaloTag7-silicon rhodamine system, including saturation of intracellular enzyme in under 100 seconds and robust labeling at dye concentrations as low as 7 nM. It was also found to be orthogonal to the silicon HaloTag7-rhodamine system, enabling multiplexed no-wash labeling in live cells. The BenzoHTag system, and the ability to optimize HaloTag for a broader collection of substrates using molecular evolution, will be very useful for the development of cell-based assays for chemical biology and drug development.
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3
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Lampkin BJ, Kritzer JA. Engineered fluorogenic HaloTag ligands for turn-on labelling in live cells. Chem Commun (Camb) 2023; 60:200-203. [PMID: 38048049 PMCID: PMC10835756 DOI: 10.1039/d3cc05536a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Recent years have seen dramatic improvements in the design of organic fluorophores based on limiting non-radiative decay pathways. We sought to extend this understanding to benzothiadiazoles that have been used as turn-on fluorescent substrates for the self-labeling protein HaloTag. When conjugated to HaloTag, the benzothiadiazoles reside in a narrow tunnel that precludes twisted internal charge transfer, which allowed us to explore steric and electronic effects on other non-radiative decay pathways. By minimizing both non-radiative decay and nonspecific interactions with cellular components, we produced improved turn-on dyes with 136-fold increase in fluorescence over background in cells.
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Affiliation(s)
- Bryan J Lampkin
- Department of Chemistry, Tufts University, 62 Talbot Rd, Medford, MA 02155, USA.
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Rd, Medford, MA 02155, USA.
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4
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Nandi R, Orieshyna A, Amdursky N. Molecular-Doped Protein-Based Elastomers as a Versatile Platform for Energy-Transfer Studies and Emissive Down-Converting Polymers for Light-Emitting Applications. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37486807 DOI: 10.1021/acsami.3c05839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Much effort is being employed for designing "green" environmental emissive materials that are capable of color-tuning, i.e., down-converting the emission, and white-light generation (WLG). Here, we introduce a protein-based elastomer that can noncovalently bind a variety of chromophores while preventing their aggregation. Such binding capabilities are unique to the albumin-based materials that we use here in a process we refer to as "molecular doping". In the first part of this study, we explore the energy transfer across five different chromophores within the protein matrix, where the closely packed chromophore organization enables high energy-transfer efficiencies among them. In the second part, we show the easy control of blue, green, and red chromophores within the biopolymer, resulting in tunable emission properties of the film and WLG. The highly affordable chosen protein and the straightforward molecular doping strategy make our protein elastomers an attractive choice for an emissive material, as either a scaffold for investigating energy transfer in proteins or possible integration in light-emitting applications.
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Affiliation(s)
- Ramesh Nandi
- Schulich Faculty of Chemistry, Technion─Israel Institute of Technology, Haifa 3200003, Israel
| | - Anna Orieshyna
- Schulich Faculty of Chemistry, Technion─Israel Institute of Technology, Haifa 3200003, Israel
| | - Nadav Amdursky
- Schulich Faculty of Chemistry, Technion─Israel Institute of Technology, Haifa 3200003, Israel
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5
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Ghosh S, Ross U, Chizhik AM, Kuo Y, Jeong BG, Bae WK, Park K, Li J, Oron D, Weiss S, Enderlein J, Chizhik AI. Excitation Intensity-Dependent Quantum Yield of Semiconductor Nanocrystals. J Phys Chem Lett 2023; 14:2702-2707. [PMID: 36892266 PMCID: PMC10026174 DOI: 10.1021/acs.jpclett.3c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
One of the key phenomena that determine the fluorescence of nanocrystals is the nonradiative Auger-Meitner recombination of excitons. This nonradiative rate affects the nanocrystals' fluorescence intensity, excited state lifetime, and quantum yield. Whereas most of the above properties can be directly measured, the quantum yield is the most difficult to assess. Here we place semiconductor nanocrystals inside a tunable plasmonic nanocavity with subwavelength spacing and modulate their radiative de-excitation rate by changing the cavity size. This allows us to determine absolute values of their fluorescence quantum yield under specific excitation conditions. Moreover, as expected considering the enhanced Auger-Meitner rate for higher multiple excited states, increasing the excitation rate reduces the quantum yield of the nanocrystals.
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Affiliation(s)
- Subhabrata Ghosh
- Third Institute
of Physics − Biophysics, Georg August
University Göttingen, Friedrich-Hund Platz 1, 37077 Göttingen, Germany
| | - Ulrich Ross
- IV. Physical
Institute - Solids and Nanostructures, Georg
August University Göttingen, Friedrich-Hund Platz 1, 37077 Göttingen, Germany
| | - Anna M. Chizhik
- Third Institute
of Physics − Biophysics, Georg August
University Göttingen, Friedrich-Hund Platz 1, 37077 Göttingen, Germany
| | - Yung Kuo
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los Angeles, California 90095, United States
| | - Byeong Guk Jeong
- School of
Chemical and Biomolecular Engineering, Pusan
National University, Busan 46241, Republic
of Korea
| | - Wan Ki Bae
- SKKU Advanced
Institute of Nanotechnology (SAINT), Sungkyunkwan
University, Suwon 16419, Republic
of Korea
| | - Kyoungwon Park
- Korea Electronics
Technology Institute, Seongnam-si, Gyeonggi-do 13509, Republic of Korea
| | - Jack Li
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los Angeles, California 90095, United States
| | - Dan Oron
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shimon Weiss
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los Angeles, California 90095, United States
- California
NanoSystems Institute, University of California
Los Angeles, Los Angeles, California 90095, United States
- Department
of Physiology, University of California
Los Angeles, Los Angeles, California 90095, United States
- Department
of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Jörg Enderlein
- Third Institute
of Physics − Biophysics, Georg August
University Göttingen, Friedrich-Hund Platz 1, 37077 Göttingen, Germany
- Cluster
of Excellence “Multiscale Bioimaging: from Molecular Machines
to Networks of Excitable Cells,” (MBExC), Georg August University of Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany
| | - Alexey I. Chizhik
- Third Institute
of Physics − Biophysics, Georg August
University Göttingen, Friedrich-Hund Platz 1, 37077 Göttingen, Germany
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6
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Kikuchi K, Adair LD, Lin J, New EJ, Kaur A. Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy. Angew Chem Int Ed Engl 2023; 62:e202204745. [PMID: 36177530 PMCID: PMC10100239 DOI: 10.1002/anie.202204745] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 02/02/2023]
Abstract
Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.
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Affiliation(s)
- Kai Kikuchi
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liam D Adair
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jiarun Lin
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth J New
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Amandeep Kaur
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
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7
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Adam V, Hadjidemetriou K, Jensen N, Shoeman RL, Woodhouse J, Aquila A, Banneville AS, Barends TRM, Bezchastnov V, Boutet S, Byrdin M, Cammarata M, Carbajo S, Eleni Christou N, Coquelle N, De la Mora E, El Khatib M, Moreno Chicano T, Bruce Doak R, Fieschi F, Foucar L, Glushonkov O, Gorel A, Grünbein ML, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Liang M, Mantovanelli A, Nass K, Nass Kovacs G, Owada S, Roome CM, Schirò G, Seaberg M, Stricker M, Thépaut M, Tono K, Ueda K, Uriarte LM, You D, Zala N, Domratcheva T, Jakobs S, Sliwa M, Schlichting I, Colletier JP, Bourgeois D, Weik M. Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement. Chemphyschem 2022; 23:e202200192. [PMID: 35959919 DOI: 10.1002/cphc.202200192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/25/2022] [Indexed: 01/07/2023]
Abstract
Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.
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Affiliation(s)
- Virgile Adam
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | | | - Nickels Jensen
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany and University Medical Center of Göttingen, Clinic for Neurology, Göttingen, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Göttingen, Germany
| | - Robert L Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Joyce Woodhouse
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Andrew Aquila
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Anne-Sophie Banneville
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Thomas R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Victor Bezchastnov
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Martin Byrdin
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Marco Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1, Rennes, France
| | - Sergio Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Nina Eleni Christou
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Nicolas Coquelle
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Eugenio De la Mora
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Mariam El Khatib
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Tadeo Moreno Chicano
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - R Bruce Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Franck Fieschi
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Oleksandr Glushonkov
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Alexander Gorel
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Marie Luise Grünbein
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Mario Hilpert
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Mark Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Marco Kloos
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Thomas J Lane
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Angela Mantovanelli
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Karol Nass
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Shigeki Owada
- RIKEN SPring-8 Center, Sayo, Japan.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Christopher M Roome
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Matthew Seaberg
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Miriam Stricker
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Michel Thépaut
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Kensuke Tono
- RIKEN SPring-8 Center, Sayo, Japan.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, 980-8577, Japan
| | - Lucas M Uriarte
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille, 59000, France
| | - Daehyun You
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, 980-8577, Japan
| | - Ninon Zala
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Tatiana Domratcheva
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany.,Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany and University Medical Center of Göttingen, Clinic for Neurology, Göttingen, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Göttingen, Germany
| | - Michel Sliwa
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille, 59000, France
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | | | - Dominique Bourgeois
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
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8
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Heesink G, Caron C, van Leijenhorst-Groener K, Molenaar R, Gadella TWJ, Claessens MMAE, Blum C. Quantification of Dark Protein Populations in Fluorescent Proteins by Two-Color Coincidence Detection and Nanophotonic Manipulation. J Phys Chem B 2022; 126:7906-7915. [PMID: 36190918 PMCID: PMC9574928 DOI: 10.1021/acs.jpcb.2c04627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Genetically encoded visible fluorescent proteins (VFPs)
are a key
tool used to visualize cellular processes. However, compared to synthetic
fluorophores, VFPs are photophysically complex. This photophysical
complexity includes the presence of non-emitting, dark proteins within
the ensemble of VFPs. Quantitative fluorescence microcopy approaches
that rely on VFPs to obtain molecular insights are hampered by the
presence of these dark proteins. To account for the presence of dark
proteins, it is necessary to know the fraction of dark proteins (fdark) in the ensemble. To date, fdark has rarely been quantified, and different methods
to determine fdark have not been compared.
Here, we use and compare two different methods to determine the fdark of four commonly used VFPs: EGFP, SYFP2,
mStrawberry, and mRFP1. In the first, direct method, we make use of
VFP tandems and single-molecule two-color coincidence detection (TCCD).
The second method relies on comparing the bright state fluorescence
quantum yield obtained by photonic manipulation to the ensemble-averaged
fluorescence quantum yield of the VFP. Our results show that, although
very different in nature, both methods are suitable to obtain fdark. Both methods show that all four VFPs contain
a considerable fraction of dark proteins. We determine fdark values between 30 and 60% for the different VFPs.
The high values for fdark of these commonly
used VFPs highlight that fdark has to
be accounted for in quantitative microscopy and spectroscopy.
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Affiliation(s)
- Gobert Heesink
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| | - Cécile Caron
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| | - Kirsten van Leijenhorst-Groener
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| | - Robert Molenaar
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| | - Theodorus W J Gadella
- Section of Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, P.O. Box 94215, 1090 GEAmsterdam, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
| | - Christian Blum
- Nanobiophysics (NBP), MESA+ Institute for Nanotechnology and Technical Medical Centre, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AEEnschede, The Netherlands
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9
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Mukherjee S, Jimenez R. Photophysical Engineering of Fluorescent Proteins: Accomplishments and Challenges of Physical Chemistry Strategies. J Phys Chem B 2022; 126:735-750. [DOI: 10.1021/acs.jpcb.1c05629] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
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Devos O, Ghaffari M, Vitale R, de Juan A, Sliwa M, Ruckebusch C. Multivariate Curve Resolution Slicing of Multiexponential Time-Resolved Spectroscopy Fluorescence Data. Anal Chem 2021; 93:12504-12513. [PMID: 34494422 DOI: 10.1021/acs.analchem.1c01284] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time-resolved fluorescence spectroscopy (TRFS), i.e., measurement of fluorescence decay curves for different excitation and/or emission wavelengths, provides specific and sensitive local information on molecules and on their environment. However, TRFS relies on multiexponential data fitting to derive fluorescence lifetimes from the measured decay curves and the time resolution of the technique is limited by the instrumental response function (IRF). We propose here a multivariate curve resolution (MCR) approach based on data slicing to perform tailored and fit-free analysis of multiexponential fluorescence decay curves. MCR slicing, taking as a basic framework the multivariate curve resolution-alternating least-squares (MCR-ALS) soft-modeling algorithm, relies on a hybrid bilinear/trilinear data decomposition. A key feature of the method is that it enables the recovery of individual components characterized by decay profiles that are only partially describable by monoexponential functions. For TRFS data, not only pure multiexponential tail information but also shorter time delay information can be decomposed, where the signal deviates from the ideal exponential behavior due to the limited time resolution. The accuracy of the proposed approach is validated by analyzing mixtures of three commercial dyes and characterizing the mixture composition, lifetimes, and associated contributions, even in situations where only ternary mixture samples are available. MCR slicing is also applied to the analysis of TRFS data obtained on a photoswitchable fluorescent protein (rsEGFP2). Three fluorescence lifetimes are extracted, along with the profile of the IRF, highlighting that decomposition of complex systems, for which individual isomers are characterized by different exponential decays, can also be achieved.
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Affiliation(s)
- Olivier Devos
- Univ. Lille, CNRS, UMR 8516 - LASIRE - Laboratory of advanced spectroscopy, interactions, reactivity and environment, Cité scientifique, Bâtiment C5, 59000 Lille, France
| | - Mahdiyeh Ghaffari
- Univ. Lille, CNRS, UMR 8516 - LASIRE - Laboratory of advanced spectroscopy, interactions, reactivity and environment, Cité scientifique, Bâtiment C5, 59000 Lille, France
| | - Raffaele Vitale
- Univ. Lille, CNRS, UMR 8516 - LASIRE - Laboratory of advanced spectroscopy, interactions, reactivity and environment, Cité scientifique, Bâtiment C5, 59000 Lille, France
| | - Anna de Juan
- Chemometrics Group, Dept. of Chemical Engineering and Analytical Chemistry, Universitat de Barcelona, Martí I Franquès, 1, 08028 Barcelona, Spain
| | - Michel Sliwa
- Univ. Lille, CNRS, UMR 8516 - LASIRE - Laboratory of advanced spectroscopy, interactions, reactivity and environment, Cité scientifique, Bâtiment C5, 59000 Lille, France
| | - Cyril Ruckebusch
- Univ. Lille, CNRS, UMR 8516 - LASIRE - Laboratory of advanced spectroscopy, interactions, reactivity and environment, Cité scientifique, Bâtiment C5, 59000 Lille, France
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