1
|
Gebhardt C, Lehmann M, Reif MM, Zacharias M, Gemmecker G, Cordes T. Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series*. Chemphyschem 2021; 22:1566-1583. [PMID: 34185946 PMCID: PMC8457111 DOI: 10.1002/cphc.202000935] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 06/01/2021] [Indexed: 12/23/2022]
Abstract
The use of fluorescence techniques has an enormous impact on various research fields including imaging, biochemical assays, DNA-sequencing and medical technologies. This has been facilitated by the development of numerous commercial dyes with optimized photophysical and chemical properties. Often, however, information about the chemical structures of dyes and the attached linkers used for bioconjugation remain a well-kept secret. This can lead to problems for research applications where knowledge of the dye structure is necessary to predict or understand (unwanted) dye-target interactions, or to establish structural models of the dye-target complex. Using a combination of optical spectroscopy, mass spectrometry, NMR spectroscopy and molecular dynamics simulations, we here investigate the molecular structures and spectroscopic properties of dyes from the Alexa Fluor (Alexa Fluor 555 and 647) and AF series (AF555, AF647, AFD647). Based on available data and published structures of the AF and Cy dyes, we propose a structure for Alexa Fluor 555 and refine that of AF555. We also resolve conflicting reports on the linker composition of Alexa Fluor 647 maleimide. We also conducted a comprehensive comparison between Alexa Fluor and AF dyes by continuous-wave absorption and emission spectroscopy, quantum yield determination, fluorescence lifetime and anisotropy spectroscopy of free and protein-attached dyes. All these data support the idea that Alexa Fluor and AF dyes have a cyanine core and are a derivative of Cy3 and Cy5. In addition, we compared Alexa Fluor 555 and Alexa Fluor 647 to their structural homologs AF555 and AF(D)647 in single-molecule FRET applications. Both pairs showed excellent performance in solution-based smFRET experiments using alternating laser excitation. Minor differences in apparent dye-protein interactions were investigated by molecular dynamics simulations. Our findings clearly demonstrate that the AF-fluorophores are an attractive alternative to Alexa- and Cy-dyes in smFRET studies or other fluorescence applications.
Collapse
Affiliation(s)
- Christian Gebhardt
- Physical and Synthetic Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
| | - Martin Lehmann
- Plant Molecular Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
| | - Maria M. Reif
- Theoretical Biophysics (T38), Physics DepartmentTechnical University of MunichCenter for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 885748GarchingGermany
| | - Martin Zacharias
- Theoretical Biophysics (T38), Physics DepartmentTechnical University of MunichCenter for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 885748GarchingGermany
| | - Gerd Gemmecker
- Bavarian NMR Center (B NMRZ), Department of ChemistryTechnical University of MunichLichtenbergstr. 485748GarchingGermany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
| |
Collapse
|
2
|
Rico CA, Berchiche YA, Horioka M, Peeler JC, Lorenzen E, Tian H, Kazmi MA, Fürstenberg A, Gaertner H, Hartley O, Sakmar TP, Huber T. High-Affinity Binding of Chemokine Analogs that Display Ligand Bias at the HIV-1 Coreceptor CCR5. Biophys J 2019; 117:903-919. [PMID: 31421836 DOI: 10.1016/j.bpj.2019.07.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/01/2019] [Accepted: 07/22/2019] [Indexed: 11/30/2022] Open
Abstract
The chemokine receptor CCR5 is a drug target to prevent transmission of HIV/AIDS. We studied four analogs of the native chemokine regulated, on activation, normal T-cell-expressed, and secreted (RANTES) (CCL5) that have anti-HIV potencies of around 25 pM, which is more than four orders of magnitude higher than that of RANTES itself. It has been hypothesized that the ultrahigh potency of the analogs is due to their ability to bind populations of receptors not accessible to native chemokines. To test this hypothesis, we developed a homogeneous dual-color fluorescence cross-correlation spectroscopy assay for saturation- and competition-binding experiments. The fluorescence cross-correlation spectroscopy assay has the advantage that it does not rely on competition with radioactively labeled native chemokines used in conventional assays. We prepared site-specifically labeled fluorescent analogs using native chemical ligation of synthetic peptides, followed by bioorthogonal fluorescent labeling. We engineered a mammalian cell expression construct to provide fluorescently labeled CCR5, which was purified using a tandem immunoaffinity and size-exclusion chromatography approach to obtain monomeric fluorescent CCR5 in detergent solution. We found subnanomolar binding affinities for the two analogs 5P12-RANTES and 5P14-RANTES and about 20-fold reduced affinities for PSC-RANTES and 6P4-RANTES. Using homologous and heterologous competition experiments with unlabeled chemokine analogs, we conclude that the analogs all bind at the same binding site, whereas the native chemokines (RANTES and MIP-1α) fail to displace bound fluorescent analogs even at tens of micromolar concentrations. Our results can be rationalized with de novo structural models of the N-terminal tails of the synthetic chemokines that adopt a different binding mode as compared to the parent compound.
Collapse
Affiliation(s)
- Carlos A Rico
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York; Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, New York
| | - Yamina A Berchiche
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York; B Cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland
| | - Mizuho Horioka
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York; Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, New York
| | - Jennifer C Peeler
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York; Deparment of Chemistry, Boston College, Chestnut Hill, Massachusetts
| | - Emily Lorenzen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York
| | - He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York
| | - Manija A Kazmi
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York; Department of Inorganic and Analytical Chemistry, Geneva, Switzerland
| | - Hubert Gaertner
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Oliver Hartley
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York.
| |
Collapse
|
3
|
Tian H, Sakmar TP, Huber T. The Energetics of Chromophore Binding in the Visual Photoreceptor Rhodopsin. Biophys J 2017; 113:60-72. [PMID: 28700926 DOI: 10.1016/j.bpj.2017.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 01/06/2023] Open
Abstract
The visual photoreceptor rhodopsin is a prototypical G-protein-coupled receptor (GPCR) that stabilizes its inverse agonist ligand, 11-cis-retinal (11CR), by a covalent, protonated Schiff base linkage. In the visual dark adaptation, the fundamental molecular event after photobleaching of rhodopsin is the recombination reaction between its apoprotein opsin and 11CR. Here we present a detailed analysis of the kinetics and thermodynamics of this reaction, also known as the "regeneration reaction". We compared the regeneration of purified rhodopsin reconstituted into phospholipid/detergent bicelles with rhodopsin reconstituted into detergent micelles. We found that the lipid bilayer of bicelles stabilized the chromophore-free opsin over the long timescale required for the regeneration experiments, and also facilitated the ligand reuptake binding reaction. We utilized genetic code expansion and site-specific bioorthogonal labeling of rhodopsin with Alexa488 to enable, to our knowledge, a novel fluorescence resonance energy transfer-based measurement of the binding kinetics between opsin and 11CR. Based on these results, we report a complete energy diagram for the regeneration reaction of rhodopsin. We show that the dissociation reaction of rhodopsin to 11CR and opsin has a 25-pM equilibrium dissociation constant, which corresponds to only 0.3 kcal/mol stabilization compared to the noncovalent, tightly bound antagonist-GPCR complex of iodopindolol and β-adrenergic receptor. However, 11CR dissociates four orders-of-magnitude slower than iodopindolol, which corresponds to a 6-kcal/mol higher dissociation free energy barrier. We further used isothermal titration calorimetry to show that ligand binding in rhodopsin is enthalpy driven with -22 kcal/mol, which is 12 kcal/mol more stable than the antagonist-GPCR complex. Our data provide insights into the ligand-receptor binding reaction for rhodopsin in particular, and for GPCRs more broadly.
Collapse
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden.
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York.
| |
Collapse
|
4
|
Periole X. Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations. Chem Rev 2016; 117:156-185. [PMID: 28073248 DOI: 10.1021/acs.chemrev.6b00344] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
G protein-coupled receptors (GPCRs) are central to many fundamental cellular signaling pathways. They transduce signals from the outside to the inside of cells in physiological processes ranging from vision to immune response. It is extremely challenging to look at them individually using conventional experimental techniques. Recently, a pseudo atomistic molecular model has emerged as a valuable tool to access information on GPCRs, more specifically on their interactions with their environment in their native cell membrane and the consequences on their supramolecular organization. This approach uses the Martini coarse grain (CG) model to describe the receptors, lipids, and solvent in molecular dynamics (MD) simulations and in enough detail to allow conserving the chemical specificity of the different molecules. The elimination of unnecessary degrees of freedom has opened up large-scale simulations of the lipid-mediated supramolecular organization of GPCRs. Here, after introducing the Martini CGMD method, we review these studies carried out on various members of the GPCR family, including rhodopsin (visual receptor), opioid receptors, adrenergic receptors, adenosine receptors, dopamine receptor, and sphingosine 1-phosphate receptor. These studies have brought to light an interesting set of novel biophysical principles. The insights range from revealing localized and heterogeneous deformations of the membrane bilayer at the surface of the protein, specific interactions of lipid molecules with individual GPCRs, to the effect of the membrane matrix on global GPCR self-assembly. The review ends with an overview of the lessons learned from the use of the CGMD method, the biophysical-chemical findings on lipid-protein interplay.
Collapse
Affiliation(s)
- Xavier Periole
- Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747AG Groningen, The Netherlands
| |
Collapse
|
5
|
Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| |
Collapse
|
6
|
Tian H, Sakmar TP, Huber T. Micelle-Enhanced Bioorthogonal Labeling of Genetically Encoded Azido Groups on the Lipid-Embedded Surface of a GPCR. Chembiochem 2015; 16:1314-22. [PMID: 25962668 PMCID: PMC5287413 DOI: 10.1002/cbic.201500030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Indexed: 12/21/2022]
Abstract
Genetically encoded p-azido-phenylalanine (azF) residues in G protein-coupled receptors (GPCRs) can be targeted with dibenzocyclooctyne-modified (DIBO-modified) fluorescent probes by means of strain-promoted [3+2] azide-alkyne cycloaddition (SpAAC). Here we show that azF residues situated on the transmembrane surfaces of detergent-solubilized receptors exhibit up to 1000-fold rate enhancement relative to azF residues on water-exposed surfaces. We show that the amphipathic moment of the labeling reagent, consisting of hydrophobic DIBO coupled to hydrophilic Alexa dye, results in strong partitioning of the DIBO group into the hydrocarbon core of the detergent micelle and consequently high local reactant concentrations. The observed rate constant for the micelleenhanced SpAAC is comparable with those of the fastest bioorthogonal labeling reactions known. Targeting hydrophobic regions of membrane proteins by use of micelle-enhanced SpAAC should expand the utility of bioorthogonal labeling strategies.
Collapse
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA)
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA).
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Alfred Nobels Allé 23, 141 57 Huddinge (Sweden).
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA).
| |
Collapse
|
7
|
Naganathan S, Ray-Saha S, Park M, Tian H, Sakmar TP, Huber T. Multiplex detection of functional G protein-coupled receptors harboring site-specifically modified unnatural amino acids. Biochemistry 2015; 54:776-86. [PMID: 25524496 PMCID: PMC4310623 DOI: 10.1021/bi501267x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
We developed a strategy for identifying
positions in G protein-coupled
receptors that are amenable to bioorthogonal modification with a peptide
epitope tag under cell culturing conditions. We introduced the unnatural
amino acid p-azido-l-phenylalanine (azF)
into human CC chemokine receptor 5 (CCR5) at site-specific amber codon
mutations. We then used strain-promoted azide–alkyne [3+2]
cycloaddition to label the azF-CCR5 variants with a FLAG peptide epitope-conjugated
aza-dibenzocyclooctyne (DBCO) reagent. A microtiter plate-based sandwich
fluorophore-linked immunosorbent assay was used to probe simultaneously
the FLAG epitope and the receptor using infrared dye-conjugated antibodies
so that the extent of DBCO incorporation, corresponding nominally
to labeling efficiency, could be quantified ratiometrically. The extent
of incorporation of DBCO at the various sites was evaluated in the
context of a recent crystal structure of maraviroc-bound CCR5. We
observed that labeling efficiency varied dramatically depending on
the topological location of the azF in CCR5. Interestingly, position
109 in transmembrane helix 3, located in a hydrophobic cavity on the
extracellular side of the receptor, was labeled most efficiently.
Because the bioorthogonal labeling and detection strategy described
might be used to introduce a variety of different peptide epitopes
or fluorophores into engineered expressed receptors, it might prove
to be useful for a wide range of applications, including single-molecule
detection studies of receptor trafficking and signaling mechanism.
Collapse
Affiliation(s)
- Saranga Naganathan
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University , New York, New York 10065, United States
| | | | | | | | | | | |
Collapse
|
8
|
Park M, Tian H, Naganathan S, Sakmar TP, Huber T. Quantitative Multi-color Detection Strategies for Bioorthogonally Labeled GPCRs. Methods Mol Biol 2015; 1335:67-93. [PMID: 26260595 DOI: 10.1007/978-1-4939-2914-6_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe multiple bioorthogonal approaches to label G protein-coupled receptors (GPCRs) heterologously expressed in mammalian cells. The use of genetically encoded unnatural amino acids as bioorthogonal tags results in receptors that are expressed at lower levels than even their low abundance wild-type counterparts. Therefore, reproducible and sensitive quantification of the labeled GPCRs is extremely important and conventional methods are simply not sufficiently accurate and precise. Silver stains lack reproducibility, spectroscopic methods using fluorescent ligands are limited to quantifying only functional receptor molecules, and immunoassays using epitope tags derived from rhodopsin are particularly variable for low-abundance GPCRs. To avoid these shortcomings, we employ near infrared (NIR) imaging-based methods that enable simultaneous multi-color detection of two different antigens, thus facilitating the ratiometric analysis of bioorthogonally modified GPCRs. We anticipate that these multi-color detection strategies will provide new tools for quantitatively assessing stoichiometrically labeled GPCRs for studies of signalosomes and for structure-function relationships at a single molecule level.
Collapse
Affiliation(s)
- Minyoung Park
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University, New York, NY, 10065, USA
| | | | | | | | | |
Collapse
|
9
|
Huber T, Sakmar T. Chemical Biology Methods for Investigating G Protein-Coupled Receptor Signaling. ACTA ACUST UNITED AC 2014; 21:1224-37. [DOI: 10.1016/j.chembiol.2014.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/21/2014] [Accepted: 08/20/2014] [Indexed: 11/26/2022]
|