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Shweta H, Gupta K, Zhou Y, Cui X, Li S, Lu Z, Goldman YE, Dantzig JA. Characterization and structural basis for the brightness of mCLIFY: a novel monomeric and circularly permuted bright yellow fluorescent protein. RESEARCH SQUARE 2024:rs.3.rs-4638282. [PMID: 39070629 PMCID: PMC11276004 DOI: 10.21203/rs.3.rs-4638282/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
We present mCLIFY: a monomeric, bright, yellow, and long-lived fluorescent protein (FP) created by circular permutation of YPet, the brightest yellow FP from Aequorea Victoria for use in cellular and in vitro single molecule studies. mCLIFY retains the enhanced photophysical properties of YPET as a monomer at concentrations ≤ 40 μM. In contrast, we determined that YPet has a dimerization dissociation constant (K D 1-2) of 3.4 μM. Dimerization of YPet can cause homo-FRET, which underlies quantitative errors due to dimerization and homo-FRET. We determined the atomic structure of mCLIFY at 1.57 Å resolution and used its similarity with Venus for guided chromophore-targeted substitution studies to provide insights into its enhanced photophysical properties. The mutation V58L within the chromophore pocket improved quantum yield and extinction coefficient, making mCLIFY ~30% brighter than Venus. The extensive characterization of the photophysical and structural properties of YPet and mCLIFY presented here allowed us to reveal the basis of their long lifetimes and enhanced brightness and the basis of YPet's dimerization.
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Affiliation(s)
- Him Shweta
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Center for Engineering Mechanobiology (CEMB), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Present address: Departments of Pharmacology and Cellular and Molecular Biology, University of California, Davis, CA-95616
| | - Kushol Gupta
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Yufeng Zhou
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Xiaonan Cui
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Selene Li
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Zhe Lu
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Yale E. Goldman
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Center for Engineering Mechanobiology (CEMB), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Present address: Departments of Pharmacology and Cellular and Molecular Biology, University of California, Davis, CA-95616
| | - Jody A. Dantzig
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
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Xu M, Wang H, Tian X, Li B, Wang S, Zhao X, He H. Opsin-Free Activation of Bmp Receptors by a Femtosecond Laser. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308072. [PMID: 38239021 PMCID: PMC10933676 DOI: 10.1002/advs.202308072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/13/2023] [Indexed: 03/14/2024]
Abstract
Bone morphogenetic protein (BMP) signaling plays a vital role in differentiation, organogenesis, and various cell processes. As a member of TGF-β superfamily, the BMP initiation usually accompanies crosstalk with other signaling pathways and simultaneously activates some of them. It is quite challenging to solely initiate an individual pathway. In this study, an opsin-free optical method to specifically activate BMP receptors (BMPR) and subsequent pSmad1/5/8 cascades by a single-time scan of a tightly-focused femtosecond laser in the near infrared range is reported. Via transient two-photon excitation to intrinsic local flavins near the cell membrane, the photoactivation drives conformational changes of preformed BMPR complexes to enable their bonding and phosphorylation of the GS domain in BMPR-I by BMPR-II. The pSmad1/5/8 signaling is initiated by this method, while p38 and pSmad2 are rarely perturbed. Based on a microscopic system, primary adipose-derived stem cells in an area of 420 × 420 µm2 are photoactivated by a single-time laser scanning for 1.5 s and exhibit pSmad1/5/8 upregulation and osteoblastic differentiation after 21 days. Hence, an opsin-free, specific, and noninvasive optical method to initiate BMP signaling, easily accomplished by a two-photon microscope system is reported.
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Affiliation(s)
- Manjun Xu
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Haipeng Wang
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Xiaoying Tian
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Bingyi Li
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Shaoyang Wang
- School of Biomedical EngineeringHainan UniversityHaikou570228China
| | - Xiaohui Zhao
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
| | - Hao He
- School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200031China
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3
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Khoroshyy P, Martinez-Seara H, Myšková J, Lazar J. Dynamics of transition dipole moment orientation in representative fluorescent proteins. Phys Chem Chem Phys 2023; 25:22117-22123. [PMID: 37560975 DOI: 10.1039/d3cp01242e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Molecules of fluorescent proteins (FPs) exhibit distinct optical directionality. This optical directionality is characterized by transition dipole moments (TDMs), and their orientation with respect to the molecular structures. Although our recent observations of FP crystals allowed us to determine the mean TDM directions with respect to the framework of representative FP molecules, the dynamics of TDM orientations within FP molecules remain to be ascertained. Here we describe the results of our investigations of the dynamics of TDM directions in the fluorescent proteins eGFP, mTurquoise2 and mCherry, through time-resolved fluorescence polarization measurements and microsecond time scale all-atom molecular dynamics (MD) simulations. The investigated FPs exhibit initial fluorescence anisotropies (r0) consistent with significant differences in the orientation of the excitation and emission TDMs. However, based on MD data, we largely attribute this observation to rapid (sub-nanosecond) fluorophore motions within the FP molecular framework. Our results allow improved determinations of orientational distributions of FP molecules by polarization microscopy, as well as more accurate interpretations of fluorescence resonance energy transfer (FRET) observations.
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Affiliation(s)
- Petro Khoroshyy
- Inst. of Organic Chemistry and Biochemistry CAS, Flemingovo nám. 2, 160 00, Prague 6, Czech Republic
- 1st Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague 2, Czech Republic.
| | - Hector Martinez-Seara
- Inst. of Organic Chemistry and Biochemistry CAS, Flemingovo nám. 2, 160 00, Prague 6, Czech Republic
| | - Jitka Myšková
- 1st Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague 2, Czech Republic.
| | - Josef Lazar
- Inst. of Organic Chemistry and Biochemistry CAS, Flemingovo nám. 2, 160 00, Prague 6, Czech Republic
- 1st Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague 2, Czech Republic.
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4
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Borges-Araújo L, Monteiro ME, Mil-Homens D, Bernardes N, Sarmento MJ, Coutinho A, Prieto M, Fernandes F. Impact of Ca 2+-Induced PI(4,5)P 2 Clusters on PH-YFP Organization and Protein-Protein Interactions. Biomolecules 2022; 12:912. [PMID: 35883468 PMCID: PMC9312469 DOI: 10.3390/biom12070912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Despite its low abundance, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is a key modulator of membrane-associated signaling events in eukaryotic cells. Temporal and spatial regulation of PI(4,5)P2 concentration can achieve localized increases in the levels of this lipid, which are crucial for the activation or recruitment of peripheral proteins to the plasma membrane. The recent observation of the dramatic impact of physiological divalent cation concentrations on PI(4,5)P2 clustering, suggests that protein anchoring to the plasma membrane through PI(4,5)P2 is likely not defined solely by a simple (monomeric PI(4,5)P2)/(protein bound PI(4,5)P2) equilibrium, but instead depends on complex protein interactions with PI(4,5)P2 clusters. The insertion of PI(4,5)P2-binding proteins within these clusters can putatively modulate protein-protein interactions in the membrane, but the relevance of such effects is largely unknown. In this work, we characterized the impact of Ca2+ on the organization and protein-protein interactions of PI(4,5)P2-binding proteins. We show that, in giant unilamellar vesicles presenting PI(4,5)P2, the membrane diffusion properties of pleckstrin homology (PH) domains tagged with a yellow fluorescent protein (YFP) are affected by the presence of Ca2+, suggesting direct interactions between the protein and PI(4,5)P2 clusters. Importantly, PH-YFP is found to dimerize in the membrane in the absence of Ca2+. This oligomerization is inhibited in the presence of physiological concentrations of the divalent cation. These results confirm that cation-dependent PI(4,5)P2 clustering promotes interactions between PI(4,5)P2-binding proteins and has the potential to dramatically influence the organization and downstream interactions of PI(4,5)P2-binding proteins in the plasma membrane.
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Affiliation(s)
- Luís Borges-Araújo
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Marina E. Monteiro
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (M.E.M.); (M.J.S.)
| | - Dalila Mil-Homens
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Nuno Bernardes
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Maria J. Sarmento
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (M.E.M.); (M.J.S.)
- Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Avenida Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Ana Coutinho
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Manuel Prieto
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Fábio Fernandes
- IBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal; (L.B.-A.); (D.M.-H.); (N.B.); (A.C.); (M.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
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Nunthaboot N, Tanaka F, Borst JW, Visser AJ. Simultaneous analyses of fluorescence decay and anisotropy decay in green fluorescent protein dimer from jellyfish Clytia gregaria: FRET and molecular dynamics simulation. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2021.113584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Saha P, Moitra P, Bhattacharjee U, Bhattacharya S. Selective pathological and intracellular detection of human serum albumin by photophysical and electrochemical techniques using a FRET-based molecular probe. Biosens Bioelectron 2022; 203:114007. [DOI: 10.1016/j.bios.2022.114007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/25/2021] [Accepted: 01/13/2022] [Indexed: 12/31/2022]
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7
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Tsubota H, Takayama A, Takeda Y, Yamada N, Hosoi H. Three Simultaneous Fluorescence Resonance Energy Transfer Processes and Structural Relaxation of Enhanced Yellow Fluorescent Protein Observed by Picosecond Time-Resolved Fluorescence Anisotropy. J Phys Chem B 2021; 125:7997-8009. [PMID: 34259526 DOI: 10.1021/acs.jpcb.1c03906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescent proteins (FPs) have been widely used to visualize biological processes in living cells. It is essential to understand the underlying fluorescence mechanism to develop novel FPs and to interpret imaging data appropriately. Enhanced yellow fluorescent protein (eYFP) is one of the most typical FPs; however, several reports to date have been limited to individual discussion, which is insufficient to understand the full picture of the dynamics involved. In this study, we focused on the fluorescence resonance energy transfer (FRET) and dimerization behavior and performed picosecond time-resolved fluorescence measurements of eYFP and its A206K mutant, which does not form a dimer. The combination of the dissociation constant and the acid dissociation constant rationally explains the mechanism of ultrafast homo-FRET and ultrafast hetero-FRET. It is also shown that structural relaxation occurs in the dimer after excited-state proton transfer. The formation efficiencies and quaternary structures of dimers consisting of different protonation states are shown to be different. Furthermore, under high-concentration conditions, "slow" homo-FRET with tens of nanoseconds timescale occurs between monomers and dimers. The findings from this study will be applied to other fluorescent proteins such as Aequorea victoria green FP and its mutants and various red FPs with longer conjugation lengths.
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Affiliation(s)
- Hiroki Tsubota
- Department of Biomolecular Science, Faculty of Sciences, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Aimi Takayama
- Department of Biomolecular Science, Faculty of Sciences, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Yuri Takeda
- Department of Biomolecular Science, Faculty of Sciences, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Natsumi Yamada
- Department of Biomolecular Science, Faculty of Sciences, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Haruko Hosoi
- Department of Biomolecular Science, Faculty of Sciences, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
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8
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Aplin CP, Miller RC, Kay TM, Heikal AA, Boersma AJ, Sheets ED. Fluorescence depolarization dynamics of ionic strength sensors using time-resolved anisotropy. Biophys J 2021; 120:1417-1430. [PMID: 33582140 DOI: 10.1016/j.bpj.2021.01.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/17/2020] [Accepted: 01/20/2021] [Indexed: 10/22/2022] Open
Abstract
Eukaryotic cells exploit dynamic and compartmentalized ionic strength to impact a myriad of biological functions such as enzyme activities, protein-protein interactions, and catalytic functions. Herein, we investigated the fluorescence depolarization dynamics of recently developed ionic strength biosensors (mCerulean3-linker-mCitrine) in Hofmeister salt (KCl, NaCl, NaI, and Na2SO4) solutions. The mCerulean3-mCitrine acts as a Förster resonance energy transfer (FRET) pair, tethered together by two oppositely charged α-helices in the linker region. We developed a time-resolved fluorescence depolarization anisotropy approach for FRET analyses, in which the donor (mCerulean3) is excited by 425-nm laser pulses, followed by fluorescence depolarization analysis of the acceptor (mCitrine) in KE (lysine-glutamate), arginine-aspartate, and arginine-glutamate ionic strength sensors with variable amino acid sequences. Similar experiments were carried out on the cleaved sensors as well as an E6G2 construct, which has neutral α-helices in the linker region, as a control. Our results show distinct dynamics of the intact and cleaved sensors. Importantly, the FRET efficiency decreases and the donor-acceptor distance increases as the environmental ionic strength increases. Our chemical equilibrium analyses of the collapsed-to-stretched conformational state transition of KE reveal that the corresponding equilibrium constant and standard Gibbs free energy changes are ionic strength dependent. We also tested the existing theoretical models for FRET analyses using steady-state anisotropy, which reveal that the angle between the dipole moments of the donor and acceptor in the KE sensor are sensitive to the ionic strength. These results help establish the time-resolved depolarization dynamics of these genetically encoded donor-acceptor pairs as a quantitative means for FRET analysis, which complement traditional methods such as time-resolved fluorescence for future in vivo studies.
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Affiliation(s)
- Cody P Aplin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Robert C Miller
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - Taryn M Kay
- Department of Physics and Astronomy, University of Minnesota Duluth, Duluth, Minnesota
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota.
| | - Arnold J Boersma
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany.
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota.
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Myšková J, Rybakova O, Brynda J, Khoroshyy P, Bondar A, Lazar J. Directionality of light absorption and emission in representative fluorescent proteins. Proc Natl Acad Sci U S A 2020; 117:32395-32401. [PMID: 33273123 PMCID: PMC7768707 DOI: 10.1073/pnas.2017379117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescent molecules are like antennas: The rate at which they absorb light depends on their orientation with respect to the incoming light wave, and the apparent intensity of their emission depends on their orientation with respect to the observer. However, the directions along which the most important fluorescent molecules in biology, fluorescent proteins (FPs), absorb and emit light are generally not known. Our optical and X-ray investigations of FP crystals have now allowed us to determine the molecular orientations of the excitation and emission transition dipole moments in the FPs mTurquoise2, eGFP, and mCherry, and the photoconvertible FP mEos4b. Our results will allow using FP directionality in studies of molecular and biological processes, but also in development of novel bioengineering and bioelectronics applications.
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Affiliation(s)
- Jitka Myšková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Olga Rybakova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Molecular Genetics, Czech Academy of Sciences, 14220 Prague 4, Czech Republic
| | - Petro Khoroshyy
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
| | - Alexey Bondar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
| | - Josef Lazar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic;
- Institute of Microbiology, Czech Academy of Sciences, 37333 Nové Hrady, Czech Republic
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Gordon F, Elcoroaristizabal S, Ryder AG. Modelling Förster resonance energy transfer (FRET) using anisotropy resolved multi-dimensional emission spectroscopy (ARMES). Biochim Biophys Acta Gen Subj 2020; 1865:129770. [PMID: 33214128 DOI: 10.1016/j.bbagen.2020.129770] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 12/01/2022]
Abstract
BACKGROUND Förster Resonance Energy Transfer (FRET) is widely used to study the structure and dynamics of biomolecular systems and also causes the non-linear fluorescence response observed in multi-fluorophore proteins. Accurate FRET analysis, in terms of measuring changes in donor and acceptor spectra and energy transfer efficiency is therefore critical. METHODS We demonstrate a novel quantitative FRET analysis using anisotropy resolved multidimensional emission spectroscopy (ARMES) in a Human Serum Albumin (HSA) and 1,8-anilinonaphathalene sulfonate (ANS) model. ARMES combines 4D measurement of polarized excitation emission matrices (pEEM) with multivariate data analysis to spectrally resolve contributing fluorophores. Multivariate analysis (Parallel Factor, PARAFAC and restricted Tucker3) was used to resolve fluorophore contributions and for modelling the quenching of HSA emission and the HSA-ANS interactions. RESULTS pEEM spectra were modelled using Tucker3 which accommodates non-linearities introduced by FRET and a priori chemical knowledge was used to optimise the solution, thus resolving three components: HSA emission, ANS emission from indirect FRET excitation, and ANS emission from direct excitation. Perpendicular emission measurements were more sensitive to indirectly excited acceptor emission. PARAFAC modelling of HSA, donor emission, separated ANS FRET interacting (Tryptophan) and non-interacting (Tyrosine) components. This enabled a new way of calculating quenching constants using the multi-dimensional emission of individual donor fluorophores. CONCLUSIONS FRET efficiency could be calculated using the multi-dimensional, resolved emission of the interacting donor fluorophores only which yielded higher ET efficiencies compared to conventional methods. GENERAL SIGNIFICANCE Shows the potential of multidimensional fluorescence measurements and data analysis for more accurate FRET modelling in proteins.
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Affiliation(s)
- Fiona Gordon
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, Galway, Galway H91 CF50, Ireland.
| | - Saioa Elcoroaristizabal
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, Galway, Galway H91 CF50, Ireland.
| | - Alan G Ryder
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, Galway, Galway H91 CF50, Ireland.
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11
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Slocum JD, Palmer AE, Jimenez R. Intramolecular Fluorescent Protein Association in a Class of Zinc FRET Sensors Leads to Increased Dynamic Range. J Phys Chem B 2019; 123:3079-3085. [PMID: 30942588 DOI: 10.1021/acs.jpcb.9b02479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genetically encoded Förster resonance energy transfer (FRET) sensors enable the visualization of ions, molecules, and processes in live cells. However, despite their widespread use, the molecular states that determine sensor performance are usually poorly understood, which limits efforts to improve them. We used dynamic light scattering (DLS) and time-resolved fluorescence anisotropy to uncover the sensing mechanism of ZifCV1.173, a Zn2+ FRET sensor. We found that the dynamic range (DR) of ZifCV1.173 was dominated by the high FRET efficiency of the Zn2+-free state, in which the donor and acceptor fluorescent proteins were closely associated. Mutating the donor-acceptor interface revealed that the DR of ZifCV1.173 could be increased or decreased by promoting or disrupting the donor-acceptor interaction, respectively. Adapting the same mutations to a related sensor showed the same pattern of DR tuning, supporting our sensing mechanism and suggesting that DLS and time-resolved fluorescence anisotropy might be generally useful in the biophysical characterization of other FRET sensors.
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12
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Wurm M, Ilhan S, Jandt U, Zeng AP. Direct and highly sensitive measurement of fluorescent molecules in bulk solutions using flow cytometry. Anal Biochem 2019; 570:32-42. [PMID: 30710511 DOI: 10.1016/j.ab.2019.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 12/24/2018] [Accepted: 01/14/2019] [Indexed: 11/25/2022]
Abstract
Utilizing flow cytometry to monitor progress of bulk biochemical reactions and concentration of chemical species normally relies on the utilization of cells carrying intrinsic fluorescence or modified beads. We present a method for a simple measurement of the fluorescent marker molecule fluorescein and GFPuv in bulk solutions with high sensitivity using a CytoFLEX flow cytometer and without the need for modified beads. Polystyrene beads were used to trigger measurements based on their high scatter signal, to detect the fluorescence signal from two different fluorophores present in the sample solution. We report sensitivities of 33 pg/mL for fluorescein and 50 ng/mL for GFPuv. This method is comparable in sensitivity to a typical spectrometric fluorescence assay tested with fluorescein, and approximately ten times more sensitive for the measurement of GFPuv. PEG was added to the sample at a low concentration of 0.001% (w/v) to block unspecific GFPuv binding to the beads. The method was further applied to measure the GFPuv concentration in crude cell lysate samples used for cell free protein expression. An advantage of this method over spectrometric assays is the ability to differentiate signal subpopulations in the sample based on their individual fluorescence intensities.
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Affiliation(s)
- Matthias Wurm
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany
| | - Sibel Ilhan
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany
| | - Uwe Jandt
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany.
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, D-21073, Hamburg, Germany
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13
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Schwarz J, J Leopold H, Leighton R, Miller RC, Aplin CP, Boersma AJ, Heikal AA, Sheets ED. Macromolecular crowding effects on energy transfer efficiency and donor-acceptor distance of hetero-FRET sensors using time-resolved fluorescence. Methods Appl Fluoresc 2019; 7:025002. [PMID: 30690439 DOI: 10.1088/2050-6120/ab0242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Living cells are crowded with macromolecules and organelles, which affect a myriad of biochemical processes. As a result, there is a need for sensitive molecular sensors for quantitative, site-specific assessment of macromolecular crowding. Here, we investigated the excited-state dynamics of recently developed hetero-FRET sensors (mCerulean3-linker-mCitrine) in homogeneous and heterogeneous environments using time-resolved fluorescence measurements, which are compatible with fluorescence lifetime imaging microscopy (FLIM). The linker in these FRET constructs, which tether the mCerulean3 (the donor) and mCitrine (the acceptor), vary in both length and flexibility. Glycerol and Ficoll-70 solutions were used for homogeneous and heterogeneous environments, respectively, at variable concentrations. The wavelength-dependent studies suggest that the 425-nm excitation and the 475-nm emission of the donor are best suited for quantitative assessment of the energy transfer efficiency and the donor-acceptor distance of these FRET probes. Under the same experimental conditions, the enzymatically cleaved counterpart of these probes was used as a control as well as a means to account for the changes in the environmental refractive indices. Our results indicate that the energy transfer efficiency of these FRET probes increases as the linker becomes shorter and more flexible in pure buffer at room temperature. In addition, the FRET probes favor a compact structure with enhanced energy transfer efficiency and a shorter donor-acceptor distance in the heterogeneous, polymer-crowded environment due to steric hindrance. In contrast, the stretched conformation of these FRET probes is more favorable in the viscous, homogeneous environment with a reduced energy transfer efficiency and relatively larger donor-acceptor distance as compared with those in pure buffer, which was attributed to a reduced structural fluctuation of the mCerulean3-mCitrine FRET pair in the viscous, more restrictive glycerol-enriched buffer. Our findings will help to advance the potential of these hetero-FRET probes using FLIM for spatio-temporal assessment of the compartmentalized crowding in living cells.
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Affiliation(s)
- Jacob Schwarz
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN, United States of America
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14
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Bekić SS, Marinović MA, Petri ET, Sakač MN, Nikolić AR, Kojić VV, Ćelić AS. Identification of d-seco modified steroid derivatives with affinity for estrogen receptor α and β isoforms using a non-transcriptional fluorescent cell assay in yeast. Steroids 2018; 130:22-30. [PMID: 29224741 DOI: 10.1016/j.steroids.2017.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 02/06/2023]
Abstract
Synthesis and biological evaluation of steroidal derivatives with anticancer properties is an active area of drug discovery. Here we measured the relative affinities of d-seco modified steroidal derivatives for estrogen receptor α, estrogen receptor β or androgen receptor ligand binding domains using an optimized non-transcriptional fluorescent cell assay in yeast. Ligand binding domains of steroid receptors were expressed in-frame with yellow fluorescent protein in the yeast Saccharomyces cerevisiae. Addition of known steroid ligands to yeast expressing the appropriate cognate receptor results in increased fluorescence intensity, enabling estimation of receptor binding affinities in a dose-response and time-dependent manner. Relative binding affinities of d-seco modified steroidal derivatives 1-4 were then evaluated using this yeast system by live cell fluorimetry and fluorescence microscopy, coupled with in vitro cytotoxicity and in silico molecular docking studies. d-Seco estratriene derivative 2displayed strong affinity for both estrogen receptor α and β ligand binding domains and negligible affinity for the androgen receptor ligand binding domain. Compound 2 also showed moderate cytotoxicity against estrogen receptor positive MCF-7 breast adenocarcinoma cells. In addition to identification of new ligands for steroid receptors, this assay could also be used to filter out compounds with potential for off-target interactions with steroid receptors during the early stages of compound screening.
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Affiliation(s)
- Sofija S Bekić
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Maja A Marinović
- University of Novi Sad, Faculty of Sciences, Department of Biology and Ecology, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Edward T Petri
- University of Novi Sad, Faculty of Sciences, Department of Biology and Ecology, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Marija N Sakač
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Andrea R Nikolić
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Vesna V Kojić
- University of Novi Sad, Faculty of Medicine, Oncology Institute of Vojvodina, Put doktora Goldmana 4, 21204 Sremska Kamenica, Serbia
| | - Andjelka S Ćelić
- University of Novi Sad, Faculty of Sciences, Department of Biology and Ecology, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia.
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15
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Nordenfelt P, Moore TI, Mehta SB, Kalappurakkal JM, Swaminathan V, Koga N, Lambert TJ, Baker D, Waters JC, Oldenbourg R, Tani T, Mayor S, Waterman CM, Springer TA. Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration. Nat Commun 2017; 8:2047. [PMID: 29229906 PMCID: PMC5725580 DOI: 10.1038/s41467-017-01848-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 10/20/2017] [Indexed: 12/31/2022] Open
Abstract
Integrin αβ heterodimer cell surface receptors mediate adhesive interactions that provide traction for cell migration. Here, we test whether the integrin, when engaged to an extracellular ligand and the cytoskeleton, adopts a specific orientation dictated by the direction of actin flow on the surface of migrating cells. We insert GFP into the rigid, ligand-binding head of the integrin, model with Rosetta the orientation of GFP and its transition dipole relative to the integrin head, and measure orientation with fluorescence polarization microscopy. Cytoskeleton and ligand-bound integrins orient in the same direction as retrograde actin flow with their cytoskeleton-binding β-subunits tilted by applied force. The measurements demonstrate that intracellular forces can orient cell surface integrins and support a molecular model of integrin activation by cytoskeletal force. Our results place atomic, Å-scale structures of cell surface receptors in the context of functional and cellular, μm-scale measurements.
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Affiliation(s)
- Pontus Nordenfelt
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Physiology Course, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Program in Cellular and Molecular Medicine, Children's Hospital, and Department of Biological Chemistry and Molecular Pharmacology and Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, 221 84, Sweden
| | - Travis I Moore
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Program in Cellular and Molecular Medicine, Children's Hospital, and Department of Biological Chemistry and Molecular Pharmacology and Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Shalin B Mehta
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Joseph Mathew Kalappurakkal
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Physiology Course, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- National Center for Biological Sciences, Bangalore, 560065, India
| | - Vinay Swaminathan
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Physiology Course, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Cell Biology and Physiology Center, NHLBI, NIH, Bethesda, MD, 20824, USA
| | - Nobuyasu Koga
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Talley J Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - David Baker
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Jennifer C Waters
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Rudolf Oldenbourg
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Tomomi Tani
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Satyajit Mayor
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Physiology Course, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- National Center for Biological Sciences, Bangalore, 560065, India
| | - Clare M Waterman
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Physiology Course, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Cell Biology and Physiology Center, NHLBI, NIH, Bethesda, MD, 20824, USA
| | - Timothy A Springer
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
- Physiology Course, Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
- Program in Cellular and Molecular Medicine, Children's Hospital, and Department of Biological Chemistry and Molecular Pharmacology and Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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16
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Currie M, Leopold H, Schwarz J, Boersma AJ, Sheets ED, Heikal AA. Fluorescence Dynamics of a FRET Probe Designed for Crowding Studies. J Phys Chem B 2017; 121:5688-5698. [DOI: 10.1021/acs.jpcb.7b01306] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Megan Currie
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Hannah Leopold
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Jacob Schwarz
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Arnold J. Boersma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Erin D. Sheets
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Ahmed A. Heikal
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
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17
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Jinno Y, Shoda K, Rial-Verde E, Yuste R, Miyawaki A, Tsutsui H. Engineering a genetically-encoded SHG chromophore by electrostatic targeting to the membrane. Front Mol Neurosci 2014; 7:93. [PMID: 25505870 PMCID: PMC4245886 DOI: 10.3389/fnmol.2014.00093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/08/2014] [Indexed: 11/22/2022] Open
Abstract
Although second harmonic generation (SHG) microscopy provides unique imaging advantages for voltage imaging and other biological applications, genetically-encoded SHG chromophores remain relatively unexplored. SHG only arises from non-centrosymmetric media, so an anisotropic arrangement of chromophores is essential to provide strong SHG signals. Here, inspired by the mechanism by which K-Ras4B associates with plasma membranes, we sought to achieve asymmetric arrangements of chromophores at the membrane-cytoplasm interface using the fluorescent protein mVenus. After adding a farnesylation motif to the C-terminus of mVenus, nine amino acids composing its β-barrel surface were replaced by lysine, forming an electrostatic patch. This protein (mVe9Knus-CVIM) was efficiently targeted to the plasma membrane in a geometrically defined manner and exhibited SHG in HEK293 cells. In agreement with its design, mVe9Knus-CVIM hyperpolarizability was oriented at a small angle (~7.3°) from the membrane normal. Genetically-encoded SHG chromophores could serve as a molecular platform for imaging membrane potential.
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Affiliation(s)
- Yuka Jinno
- Laboratory of Integrative Physiology, Graduate School of Medicine, Osaka University Suita, Japan
| | - Keiko Shoda
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN Wako, Japan
| | - Emiliano Rial-Verde
- Department of Biological Sciences, Neurotechnology Center, Columbia University New York, NY, USA
| | - Rafael Yuste
- Department of Biological Sciences, Neurotechnology Center, Columbia University New York, NY, USA
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN Wako, Japan
| | - Hidekazu Tsutsui
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN Wako, Japan ; Formation of and Information Processing by Neural Networks, and Control, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Japan ; Department of Material Science, Japan Advanced Institute of Science and Technology Nomi, Japan
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18
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Seward HE, Basran J, Denton R, Pfuhl M, Muskett FW, Bagshaw CR. Halide and proton binding kinetics of yellow fluorescent protein variants. Biochemistry 2013; 52:2482-91. [PMID: 23514090 DOI: 10.1021/bi3016839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A T203Y substitution in green fluorescent protein causes a red shift in emission to yield a class of mutants known as yellow fluorescent protein (YFP). Many of these YFP mutants bind halides with affinities in the millimolar range, which often results in the chromophore pK values being shifted into the physiological range. While such sensitivities may be exploited for halide and pH sensors, it is desirable to reduce such environmental sensitivities in other studies, such as in Förster resonance energy transfer probes to measure conformational changes within fusion proteins. Venus and Citrine are two such variants that have been developed with much reduced halide sensitivities. Here we compare the kinetics of halide binding, and the coupled protonation reaction, for several YFP variants and detect slow kinetics (dissociation rate constants in the range of 0.1-1 s(-1)), indicative of binding to an internal site, in all cases. The effective halide affinity for Venus and Citrine is much reduced compared with that of the original YFP 10C construct, primarily through a reduced association rate constant. Nuclear magnetic resonance studies of YFP 10C confirm halide binding occurs on a slow time scale (<4 s(-1)) and that perturbations in the chemical shift occur throughout the sequence and structure.
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Affiliation(s)
- Harriet E Seward
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, UK
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19
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Jordan AN, Das S, Siraj N, de Rooy SL, Li M, El-Zahab B, Chandler L, Baker GA, Warner IM. Anion-controlled morphologies and spectral features of cyanine-based nanoGUMBOS--an improved photosensitizer. NANOSCALE 2012; 4:5031-5038. [PMID: 22766774 DOI: 10.1039/c2nr30432e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The ability to control the morphologies and spectral properties of organic low-dimensional nanomaterials is of paramount importance. The research reported herein demonstrates a template-free approach to tailored morphological and optical properties for a novel class of pseudoisocyanine (PIC)-based fluorescent organic nanoparticles derived from a group of uniform materials based on organic salts (GUMBOS). The synthesized nanoscale PIC-based particles (termed nanoGUMBOS), [PIC][NTf(2)] and [PIC][BETI], exhibit interesting adaptability as a function of the associated anion. The diamond-shaped nanostructures of [PIC][NTf(2)] and [PIC][BETI] nanorods exhibit enhanced fluorescence quantum yields relative to the parent compound, [PIC][I]. As supported by fluorescence lifetime measurements, these enhanced spectral properties can be attributed to differences in molecular self-assembly ordering (e.g., H- vs. J-aggregation) and restricted molecular rotation leading to reduced twisted intramolecular charge transfer in the nanoGUMBOS. The electrochemical properties of the PIC-based GUMBOS suggest their potential use in dye-sensitized solar cells.
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Affiliation(s)
- Atiya N Jordan
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, USA
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20
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Hunt J, Keeble AH, Dale RE, Corbett MK, Beavil RL, Levitt J, Swann MJ, Suhling K, Ameer-Beg S, Sutton BJ, Beavil AJ. A fluorescent biosensor reveals conformational changes in human immunoglobulin E Fc: implications for mechanisms of receptor binding, inhibition, and allergen recognition. J Biol Chem 2012; 287:17459-17470. [PMID: 22442150 PMCID: PMC3366799 DOI: 10.1074/jbc.m111.331967] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/08/2012] [Indexed: 11/06/2022] Open
Abstract
IgE binding to its high affinity receptor FcεRI on mast cells and basophils is a key step in the mechanism of allergic disease and a target for therapeutic intervention. Early indications that IgE adopts a bent structure in solution have been confirmed by recent x-ray crystallographic studies of IgEFc, which further showed that the bend, contrary to expectation, is enhanced in the crystal structure of the complex with receptor. To investigate the structure of IgEFc and its conformational changes that accompany receptor binding in solution, we created a Förster resonance energy transfer (FRET) biosensor using biologically encoded fluorescent proteins fused to the N- and C-terminal IgEFc domains (Cε2 and Cε4, respectively) together with the theoretical basis for quantitating its behavior. This revealed not only that the IgEFc exists in a bent conformation in solution but also that the bend is indeed enhanced upon FcεRI binding. No change in the degree of bending was seen upon binding to the B cell receptor for IgE, CD23 (FcεRII), but in contrast, binding of the anti-IgE therapeutic antibody omalizumab decreases the extent of the bend, implying a conformational change that opposes FcεRI engagement. HomoFRET measurements further revealed that the (Cε2)(2) and (Cε4)(2) domain pairs behave as rigid units flanking the conformational change in the Cε3 domains. Finally, modeling of the accessible conformations of the two Fab arms in FcεRI-bound IgE revealed a mutual exclusion not seen in IgG and Fab orientations relative to the membrane that may predispose receptor-bound IgE to cross-linking by allergens.
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Affiliation(s)
- James Hunt
- MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, Guy's Hospital Campus, London SE1 1UL; The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL; The Division of Asthma Allergy and Lung Biology, King's College London, Guy's Hospital Campus, London SE1 1UL
| | - Anthony H Keeble
- MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, Guy's Hospital Campus, London SE1 1UL; The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL; The Division of Asthma Allergy and Lung Biology, King's College London, Guy's Hospital Campus, London SE1 1UL
| | - Robert E Dale
- The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL
| | - Melissa K Corbett
- The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL
| | - Rebecca L Beavil
- MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, Guy's Hospital Campus, London SE1 1UL; The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL; The Division of Asthma Allergy and Lung Biology, King's College London, Guy's Hospital Campus, London SE1 1UL
| | - James Levitt
- The Department of Physics, King's College London, Strand, London WC2R 2LS
| | - Marcus J Swann
- Farfield Group Limited, Voyager, Chicago Avenue, Manchester Airport, Manchester, M90 3DQ, United Kingdom
| | - Klaus Suhling
- The Department of Physics, King's College London, Strand, London WC2R 2LS
| | - Simon Ameer-Beg
- The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL
| | - Brian J Sutton
- MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, Guy's Hospital Campus, London SE1 1UL; The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL
| | - Andrew J Beavil
- MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, Guy's Hospital Campus, London SE1 1UL; The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL; The Division of Asthma Allergy and Lung Biology, King's College London, Guy's Hospital Campus, London SE1 1UL.
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21
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Ansbacher T, Srivastava HK, Stein T, Baer R, Merkx M, Shurki A. Calculation of transition dipole moment in fluorescent proteins--towards efficient energy transfer. Phys Chem Chem Phys 2012; 14:4109-17. [PMID: 22331099 DOI: 10.1039/c2cp23351g] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Förster Resonance Energy Transfer (FRET) between fluorescent proteins (FPs) is widely used to construct fluorescent sensor proteins, to study intracellular protein-protein interactions and to monitor conformational changes in multidomain proteins. Although FRET depends strongly on the orientation of the transition dipole moments (TDMs) of the donor and acceptor fluorophores, this orientation dependence is currently not taken into account in FRET sensor design. Similarly, studies that use FRET to derive structural constrains typically assume a κ(2) of 2/3 or use the TDM of green fluorescent protein, as this is the only FP for which the TDM has been determined experimentally. Here we used time-dependent density functional theory (TD-DFT) methods to calculate the TDM for a comprehensive list of commonly used fluorescent proteins. The method was validated against higher levels of calculation. Validation with model compounds and the experimentally determined TDM of GFP shows that the TDM is mostly determined by the structure of the π-conjugated fluorophore and is insensitive to non-conjugated side chains or the protein surrounding. Our calculations not only provide TDM for most of the currently used FPs, but also suggest an empirical rule that can be used to obtain the TDMs for newly developed fluorescent proteins in the future.
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Affiliation(s)
- Tamar Ansbacher
- Department of Medicinal Chemistry, Institute for Drug Research, The Lise-Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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22
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Two-photon polarization microscopy reveals protein structure and function. Nat Methods 2011; 8:684-90. [PMID: 21725301 DOI: 10.1038/nmeth.1643] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 05/17/2011] [Indexed: 11/08/2022]
Abstract
Membrane proteins are a large, diverse group of proteins, serving a multitude of cellular functions. They are difficult to study because of their requirement of a lipid membrane for function. Here we show that two-photon polarization microscopy can take advantage of the cell membrane requirement to yield insights into membrane protein structure and function, in living cells and organisms. The technique allows sensitive imaging of G-protein activation, changes in intracellular calcium concentration and other processes, and is not limited to membrane proteins. Conveniently, many suitable probes for two-photon polarization microscopy already exist.
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23
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Ganguly S, Clayton AHA, Chattopadhyay A. Organization of higher-order oligomers of the serotonin₁(A) receptor explored utilizing homo-FRET in live cells. Biophys J 2011; 100:361-8. [PMID: 21244832 DOI: 10.1016/j.bpj.2010.12.3692] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/16/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022] Open
Abstract
The serotonin₁(A) receptor is a representative member of the GPCR superfamily and serves as an important drug target. The possible role of GPCR oligomerization in receptor function is an active area of research. We monitored the oligomerization state of serotonin₁(A) receptors using homo-FRET and fluorescence lifetime measurements. Homo-FRET is estimated by a reduction in fluorescence anisotropy and provides a superior approach for exploring oligomerization. In addition, homo-FRET offers the possibility of detecting higher-order oligomers. On the basis of an observed increase in fluorescence anisotropy upon progressive photobleaching and analysis of the difference between the extrapolated anisotropy and the predicted anisotropy of an immobile monomer, we propose the presence of constitutive oligomers of the serotonin₁(A) receptor. To the best of our knowledge, these results constitute the first report of higher-order oligomers for the serotonin₁(A) receptor. We further show that cholesterol depletion and antagonist treatment result in a reduced population of higher-order oligomers. In contrast, agonist stimulation and destabilization of the actin cytoskeleton lead to an increased contribution from higher oligomers. These results provide novel insight into the oligomerization status of the serotonin₁(A) receptor that could enhance the ability to design better therapeutic strategies to combat diseases related to malfunctioning of GPCRs.
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Affiliation(s)
- Sourav Ganguly
- Centre for Cellular and Molecular Biology, Hyderabad, India
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24
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Abraham BG, Tkachenko NV, Santala V, Lemmetyinen H, Karp M. Bidirectional Fluorescence Resonance Energy Transfer (FRET) in Mutated and Chemically Modified Yellow Fluorescent Protein (YFP). Bioconjug Chem 2011; 22:227-34. [DOI: 10.1021/bc100372u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bobin George Abraham
- Department of Chemistry and Bioengineering, Tampere University of Technology, 541, 33101 Tampere, Finland
| | - Nikolai V. Tkachenko
- Department of Chemistry and Bioengineering, Tampere University of Technology, 541, 33101 Tampere, Finland
| | - Ville Santala
- Department of Chemistry and Bioengineering, Tampere University of Technology, 541, 33101 Tampere, Finland
| | - Helge Lemmetyinen
- Department of Chemistry and Bioengineering, Tampere University of Technology, 541, 33101 Tampere, Finland
| | - Matti Karp
- Department of Chemistry and Bioengineering, Tampere University of Technology, 541, 33101 Tampere, Finland
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26
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Espagne A, Erard M, Madiona K, Derrien V, Jonasson G, Lévy B, Pasquier H, Melki R, Mérola F. Cyan Fluorescent Protein Carries a Constitutive Mutation That Prevents Its Dimerization. Biochemistry 2010; 50:437-9. [DOI: 10.1021/bi1015875] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Agathe Espagne
- Laboratoire de Chimie Physique, Université Paris-Sud and CNRS (UMR 8000), 91405 Orsay, France
| | - Marie Erard
- Laboratoire de Chimie Physique, Université Paris-Sud and CNRS (UMR 8000), 91405 Orsay, France
| | - Karine Madiona
- Laboratoire d’Enzymologie et Biochimie Structurales, CNRS (UPR 3082), 91198 Gif-sur-Yvette, France
| | - Valérie Derrien
- Laboratoire de Chimie Physique, Université Paris-Sud and CNRS (UMR 8000), 91405 Orsay, France
| | - Gabriella Jonasson
- Laboratoire de Chimie Physique, Université Paris-Sud and CNRS (UMR 8000), 91405 Orsay, France
| | - Bernard Lévy
- Laboratoire de Chimie Physique, Université Paris-Sud and CNRS (UMR 8000), 91405 Orsay, France
| | - Hélène Pasquier
- Laboratoire de Chimie Physique, Université Paris-Sud and CNRS (UMR 8000), 91405 Orsay, France
| | - Ronald Melki
- Laboratoire d’Enzymologie et Biochimie Structurales, CNRS (UPR 3082), 91198 Gif-sur-Yvette, France
| | - Fabienne Mérola
- Laboratoire de Chimie Physique, Université Paris-Sud and CNRS (UMR 8000), 91405 Orsay, France
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Distribution of resting and ligand-bound ErbB1 and ErbB2 receptor tyrosine kinases in living cells using number and brightness analysis. Proc Natl Acad Sci U S A 2010; 107:16524-9. [PMID: 20813958 DOI: 10.1073/pnas.1002642107] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ligand-driven dimerizations of ErbB receptor subunits fulfill a fundamental role in their activation. We have used the number and brightness analysis technique to investigate the existence of preformed ligand-independent dimers and clusters and to characterize the initial steps in the activation of ErbB1 and ErbB2. In cells expressing 50,000-200,000 receptors, ErbB1 was monomeric in the absence of ligand stimulation, whereas in CHO cells with receptor levels >500,000 as much as 30% of ErbB1 was present as preformed dimers. EGF induced the formation of ErbB1 dimers as well as larger clusters (up to pentamers) that colocalized with clathrin-coated pits. The distribution of unstimulated ErbB2 in cells expressing 3·10(5)-10(6) receptors was fundamentally different, in that this receptor was present in preformed homoassociated aggregates containing 5-10 molecules. These constitutive ErbB2 homoclusters colocalized with caveolae, increased in size at subphysiological temperatures, but decreased in size upon EGF stimulation. We conclude that these ErbB2 clusters are promoted primarily by membrane-mediated interactions and are dispersed upon ligand stimulation.
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Photophysics and Spectroscopy of Fluorophores in the Green Fluorescent Protein Family. SPRINGER SERIES ON FLUORESCENCE 2010. [DOI: 10.1007/978-3-642-04702-2_11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Szentpetery Z, Balla A, Kim YJ, Lemmon MA, Balla T. Live cell imaging with protein domains capable of recognizing phosphatidylinositol 4,5-bisphosphate; a comparative study. BMC Cell Biol 2009; 10:67. [PMID: 19769794 PMCID: PMC2755470 DOI: 10.1186/1471-2121-10-67] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 09/21/2009] [Indexed: 11/24/2022] Open
Abstract
Background Phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] is a critically important regulatory phospholipid found in the plasma membrane of all eukaryotic cells. In addition to being a precursor of important second messengers, PtdIns(4,5)P2 also regulates ion channels and transporters and serves the endocytic machinery by recruiting clathrin adaptor proteins. Visualization of the localization and dynamic changes in PtdIns(4,5)P2 levels in living cells is critical to understanding the biology of PtdIns(4,5)P2. This has been mostly achieved with the use of the pleckstrin homology (PH) domain of PLCδ1 fused to GFP. Here we report on a comparative analysis of several recently-described yeast PH domains as well as the mammalian Tubby domain to evaluate their usefulness as PtdIns(4,5)P2 imaging tools. Results All of the yeast PH domains that have been previously shown to bind PtdIns(4,5)P2 showed plasma membrane localization but only a subset responded to manipulations of plasma membrane PtdIns(4,5)P2. None of these domains showed any advantage over the PLCδ1PH-GFP reporter and were compromised either in their expression levels, nuclear localization or by causing peculiar membrane structures. In contrast, the Tubby domain showed high membrane localization consistent with PtdIns(4,5)P2 binding and displayed no affinity for the soluble headgroup, Ins(1,4,5)P3. Detailed comparison of the Tubby and PLCδ1PH domains showed that the Tubby domain has a higher affinity for membrane PtdIns(4,5)P2 and therefore displays a lower sensitivity to report on changes of this lipid during phospholipase C activation. Conclusion These results showed that both the PLCδ1PH-GFP and the GFP-Tubby domain are useful reporters of PtdIns(4,5)P2 changes in the plasma membrane, with distinct advantages and disadvantages. While the PLCδ1PH-GFP is a more sensitive reporter, its Ins(1,4,5)P3 binding may compromise its accuracy to measure PtdIns(4,5)P2changes. The Tubby domain is more accurate to report on PtdIns(4,5)P2 but its higher affinity and lower sensitivity may limit its utility when phospholipase C activation is only moderate. These studies also demonstrated that similar changes in PtdIns(4,5)P2 levels in the plasma membrane can differentially regulate multiple effectors if they display different affinities to PtdIns(4,5)P2.
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Affiliation(s)
- Zsofia Szentpetery
- Sections on Molecular Signal Transduction, Program for Developmental Neuroscience, NICHD, National Institutes of Health, Bethesda, MD 20892, USA.
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Seward HE, Bagshaw CR. The photochemistry of fluorescent proteins: implications for their biological applications. Chem Soc Rev 2009; 38:2842-51. [DOI: 10.1039/b901355p] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Balance between ultrafast parallel reactions in the green fluorescent protein has a structural origin. Biophys J 2008; 95:1902-12. [PMID: 18469081 DOI: 10.1529/biophysj.108.129957] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fluorescence photocycle of the green fluorescent protein is functionally dependent on the specific structural protein environment. A direct relationship between equilibrium protein side-chain conformation of glutamate 222 and reactivity is established, particularly the rate of ultrafast proton transfer reactions in the fluorescence photocycle. We show that parallel transformations in the photocycle have a structural origin, and we report on the vibrational properties of responsive amino acids on an ultrafast timescale. Blue excitation of GFP drives two parallel, excited-state deuteron transfer reactions with 10 ps and 75 ps time constants to the buried carboxylic acid side chain of glutamate 222 via a hydrogen-bonding network. Assignment of 1456 cm(-1) and 1441 cm(-1) modes to nu(sym) and assignment of 1564 cm(-1) and 1570 cm(-1) features to nu(asym) of E222 in the 10 ps and 75 ps components, respectively, was possible from the analysis of the transient absorption data of an E222D mutant and was consistent with photoselection measurements. In contrast to the wild-type, measurements of E222D can be described with only one difference spectrum, with the nu(sym) mode at 1435 cm(-1) and the nu(asym) mode at 1567 cm(-1), also correlating a large Deltanu(asym-sym) with slow excited-state proton transfer kinetics. Density Functional Theory calculations and published model compound and theoretical studies relate differences in Deltanu(asym-sym) to the strength and number of hydrogen-bonding interactions that are detected via equilibrium geometry and COO- stretching frequency differences of the carboxylate. The correlation of photocycle kinetics with side-chain conformation of the acceptor suggests that proton transfer from S205 to E222 controls the rate of the overall excited-state proton transfer process, which is consistent with recent theoretical predictions. Photoselection measurements show agreement for localized C=O vibrations of chromophore, Q69, and E222 with Density Functional Theory and ab initio calculations placed in the x-ray geometry and provide their vibrational response in the intermediates in the photocycle.
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