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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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2
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Rodríguez S, Silva ML, Benaím G, Bubis J. Phosphorylation-induced conformational changes of photoactivated rhodopsin probed by fluorescent labeling at Cys 140 and Cys 316. Biochimie 2018; 150:57-69. [PMID: 29730301 DOI: 10.1016/j.biochi.2018.04.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 04/29/2018] [Indexed: 11/28/2022]
Abstract
In order to monitor conformational changes following photoactivation and phosphorylation of bovine rhodopsin, the two reactive sulfhydryl groups at Cys140 and Cys316 were specifically labeled with the monobromobimane (mBBr) fluorophore. Although alterations in conformation after light exposure of rhodopsin were not detected by fluorescence excitation scans (300-450 nm) of the mBBr-labeled protein, the fluorescence signal was reduced ∼ 90% in samples containing photoactivated phosphorhodopsin. Predominant labeling at either Cys140 or Cys316 in light-activated and phosphorylated rhodopsin merely generated a decrease of ∼38% and 28%, respectively, in the fluorescence excitation intensity. Thus, neither mBBr-modified Cys140 nor mBBr-modified Cys316 were involved single-handedly in the remarkable fall seen on the signal following phosphorylation of the protein; rather, the incorporation of phosphate groups on the mBBr-labeled light-activated rhodopsin appeared to affect its fluorescence signal in a cooperative or synergistic manner. These findings demonstrated that the phosphorylation of specific hydroxyl groups at the carboxyl terminal tail of rhodopsin causes definite conformational changes in the three-dimensional fold of the protein. Apparently, amino acid residues that are buried in the interior of the inactive protein become accessible following illumination and phosphorylation of rhodopsin, quenching in turn the fluorescence excitation signal of mBBr-modified rhodopsin.
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Affiliation(s)
- Sheerly Rodríguez
- Departamento de Biología Celular, Universidad Simón Bolívar, Caracas, Venezuela; Escuela de Química, Facultad de Ciencias, Universidad Central de Venezuela, Caracas, Venezuela.
| | - May-Li Silva
- Instituto de Estudios Avanzados IDEA, Caracas, Venezuela.
| | - Gustavo Benaím
- Instituto de Estudios Avanzados IDEA, Caracas, Venezuela; Instituto de Biología Experimental, Facultad de Ciencias, Universidad Central de Venezuela, Caracas, Venezuela.
| | - José Bubis
- Departamento de Biología Celular, Universidad Simón Bolívar, Caracas, Venezuela.
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3
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Plazinska A, Plazinski W, Luchowski R, Wnorowski A, Grudzinski W, Gruszecki WI. Ligand-induced action of the W286 6.48 rotamer toggle switch in the β 2-adrenergic receptor. Phys Chem Chem Phys 2017; 20:581-594. [PMID: 29226293 DOI: 10.1039/c7cp04808d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studies focused on GPCRs, particularly on the β2-adrenergic receptor (β2-AR), have demonstrated the relationship between ligand structure, receptor conformational changes and the corresponding pharmacological outcomes. Herein, we studied the molecular details of the rotameric flip of the W2866.48 sidechain, i.e. a presumed action switch that has not been reported in native β2-AR thus far. It is believed that although both the 'active' and 'inactive' conformers of β2-AR exhibit similar conformations of this switch, it may still play a substantial role in the ligand-induced activation of the receptor. By using both experimental methods (time-resolved fluorescence spectroscopy) and molecular modeling techniques (enhanced-sampling molecular dynamics), we characterized the conformational rearrangements of W2866.48 in relation to the type of ligand present in the binding cavity and to the conformation of the receptor ('active' vs. 'inactive' β2-AR). We found that the conformational behaviour of W2866.48 is correlated with the pharmacological character of the ligand present in the binding cavity but not with the instantaneous conformation of the receptor. Namely, agonists promote the W2866.48 conformations that facilitate the increase of the solvation within the inner receptor channel. In contrast, antagonists and inverse agonists act toward the decrease of the solvation in the inner channel. This creates an opportunity for using computational methodologies in determining the pharmacological properties of various ligands. The combination of the time-resolved fluorescence spectroscopy technique with the enhanced-sampling molecular dynamics simulations is shown to be a powerful tool for studying the ligand-induced conformational rearrangements in GPCRs.
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Affiliation(s)
- Anita Plazinska
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, W. Chodzki Str., 4a, 20-093 Lublin, Poland.
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4
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Purification of Functional CB 1 and Analysis by Site-Directed Fluorescence Labeling Methods. Methods Enzymol 2017; 593:343-370. [PMID: 28750810 DOI: 10.1016/bs.mie.2017.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The human cannabinoid receptor, CB1, has been difficult to purify in a functional form, hampering structural and biophysical studies. Here, we present our approaches for obtaining pure, detergent solubilized, functional CB1. We also discuss our site-directed fluorescence labeling (SDFL) methods for identifying different structural changes that CB1 can undergo upon binding different cannabinoid ligands. To identify optimal CB1 constructs for these studies (those with the best expression levels, solubility in detergent and function), we first screened various CB1-green fluorescent protein chimeras in a mammalian expression system. Once identified, we then tagged the best candidates with the 1D4 epitope (the C-terminus of rhodopsin) and purified them using a single-step immunoaffinity process. The resulting, highly pure proteins retain their ability to activate G-protein, and are ~85% functional, as assessed by radioligand binding studies. The SDFL studies involve introducing single cysteine residues at key places in the receptor, then labeling them with a small fluorophore, bimane. The spectral properties of the bimane probe are then monitored before and after addition of cannabinoid ligands. Changes in fluorescence of the attached probe indicate regions of the receptor undergoing conformational changes upon ligand binding. Together, these approaches set the stage for a deeper understanding of the structure and function of CB1. Access to pure, functional CB1 makes subsequent structural studies possible (such as crystallography and single-particle EM analysis), and the SDFL studies enable a better structural and mechanistic understanding of this key receptor and the dynamic changes it undergoes during activation and attenuation.
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5
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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
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6
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Jones Brunette AM, Sinha A, David L, Farrens DL. Evidence that the Rhodopsin Kinase (GRK1) N-Terminus and the Transducin Gα C-Terminus Interact with the Same "Hydrophobic Patch" on Rhodopsin TM5. Biochemistry 2016; 55:3123-35. [PMID: 27078130 DOI: 10.1021/acs.biochem.6b00328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Phosphorylation of G protein-coupled receptors (GPCRs) terminates their ability to couple with and activate G proteins by increasing their affinity for arrestins. Unfortunately, detailed information regarding how GPCRs interact with the kinases responsible for their phosphorylation is still limited. Here, we purified fully functional GPCR kinase 1 (GRK1) using a rapid method and used it to gain insights into how this important kinase interacts with the GPCR rhodopsin. Specifically, we find that GRK1 uses the same site on rhodopsin as the transducin (Gt) Gtα C-terminal tail and the arrestin "finger loop", a cleft formed in the cytoplasmic face of the receptor upon activation. Our studies also show GRK1 requires two conserved residues located in this cleft (L226 and V230) that have been shown to be required for Gt activation due to their direct interactions with hydrophobic residues on the Gα C-terminal tail. Our data and modeling studies are consistent with the idea that all three proteins (Gt, GRK1, and visual arrestin) bind, at least in part, in the same site on rhodopsin and interact with the receptor through a similar hydrophobic contact-driven mechanism.
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Affiliation(s)
- Amber M Jones Brunette
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
| | - Abhinav Sinha
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
| | - Larry David
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
| | - David L Farrens
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
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7
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Chatterjee D, Eckert CE, Slavov C, Saxena K, Fürtig B, Sanders CR, Gurevich VV, Wachtveitl J, Schwalbe H. Influence of Arrestin on the Photodecay of Bovine Rhodopsin. Angew Chem Int Ed Engl 2015; 54:13555-60. [PMID: 26383645 PMCID: PMC4685475 DOI: 10.1002/anie.201505798] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/11/2015] [Indexed: 11/07/2022]
Abstract
Continued activation of the photocycle of the dim-light receptor rhodopsin leads to the accumulation of all-trans-retinal in the rod outer segments (ROS). This accumulation can damage the photoreceptor cell. For retinal homeostasis, deactivation processes are initiated in which the release of retinal is delayed. One of these processes involves the binding of arrestin to rhodopsin. Here, the interaction of pre-activated truncated bovine visual arrestin (Arr(Tr)) with rhodopsin in 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC) micelles is investigated by solution NMR techniques and flash photolysis spectroscopy. Our results show that formation of the rhodopsin-arrestin complex markedly influences partitioning in the decay kinetics of rhodopsin, which involves the simultaneous formation of a meta II and a meta III state from the meta I state. Binding of Arr(Tr) leads to an increase in the population of the meta III state and consequently to an approximately twofold slower release of all-trans-retinal from rhodopsin.
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Affiliation(s)
- Deep Chatterjee
- Institute of Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Carl Elias Eckert
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Krishna Saxena
- Institute of Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Boris Fürtig
- Institute of Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Charles R Sanders
- Department of Biochemistry, Center for Structural Biology, Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 (USA)
| | - Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232 (USA)
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany).
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany).
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8
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Culhane KJ, Liu Y, Cai Y, Yan ECY. Transmembrane signal transduction by peptide hormones via family B G protein-coupled receptors. Front Pharmacol 2015; 6:264. [PMID: 26594176 PMCID: PMC4633518 DOI: 10.3389/fphar.2015.00264] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/23/2015] [Indexed: 01/28/2023] Open
Abstract
Although family B G protein-coupled receptors (GPCRs) contain only 15 members, they play key roles in transmembrane signal transduction of hormones. Family B GPCRs are drug targets for developing therapeutics for diseases ranging from metabolic to neurological disorders. Despite their importance, the molecular mechanism of activation of family B GPCRs remains largely unexplored due to the challenges in expression and purification of functional receptors to the quantity for biophysical characterization. Currently, there is no crystal structure available of a full-length family B GPCR. However, structures of key domains, including the extracellular ligand binding regions and seven-helical transmembrane regions, have been solved by X-ray crystallography and NMR, providing insights into the mechanisms of ligand recognition and selectivity, and helical arrangements within the cell membrane. Moreover, biophysical and biochemical methods have been used to explore functions, key residues for signaling, and the kinetics and dynamics of signaling processes. This review summarizes the current knowledge of the signal transduction mechanism of family B GPCRs at the molecular level and comments on the challenges and outlook for mechanistic studies of family B GPCRs.
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Affiliation(s)
- Kelly J Culhane
- Department of Molecular Biophysics and Biochemistry, Yale University New Haven, CT, USA
| | - Yuting Liu
- Department of Chemistry, Yale University New Haven, CT, USA
| | - Yingying Cai
- Department of Chemistry, Yale University New Haven, CT, USA
| | - Elsa C Y Yan
- Department of Chemistry, Yale University New Haven, CT, USA
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9
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Chatterjee D, Eckert CE, Slavov C, Saxena K, Fürtig B, Sanders CR, Gurevich VV, Wachtveitl J, Schwalbe H. Influence of Arrestin on the Photodecay of Bovine Rhodopsin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Struts AV, Barmasov AV, Brown MF. SPECTRAL METHODS FOR STUDY OF THE G-PROTEIN-COUPLED RECEPTOR RHODOPSIN. I. VIBRATIONAL AND ELECTRONIC SPECTROSCOPY. OPTICS AND SPECTROSCOPY 2015; 118:711-717. [PMID: 28260815 PMCID: PMC5334778 DOI: 10.1134/s0030400x15050240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here we review the application of modern spectral methods for the study of G-protein-coupled receptors (GPCRs) using rhodopsin as a prototype. Because X-ray analysis gives us immobile snapshots of protein conformations, it is imperative to apply spectroscopic methods for elucidating their function: vibrational (Raman, FTIR), electronic (UV-visible absorption, fluorescence) spectroscopies, and magnetic resonance (electron paramagnetic resonance, EPR), and nuclear magnetic resonance, NMR). In the first of the two companion articles, we discuss the application of optical spectroscopy for studying rhodopsin in a membrane environment. Information is obtained regarding the time-ordered sequence of events in rhodopsin activation. Isomerization of the chromophore and deprotonation of the retinal Schiff base leads to a structural change of the protein involving the motion of helices H5 and H6 in a pH-dependent process. Information is obtained that is unavailable from X-ray crystallography, which can be combined with spectroscopic studies to achieve a more complete understanding of GPCR function.
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Affiliation(s)
- A V Struts
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia; University of Arizona, Tucson, AZ 85721 USA
| | - A V Barmasov
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia
| | - M F Brown
- University of Arizona, Tucson, AZ 85721 USA
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Malmerberg E, M Bovee-Geurts PH, Katona G, Deupi X, Arnlund D, Wickstrand C, Johansson LC, Westenhoff S, Nazarenko E, Schertler GFX, Menzel A, de Grip WJ, Neutze R. Conformational activation of visual rhodopsin in native disc membranes. Sci Signal 2015; 8:ra26. [PMID: 25759477 DOI: 10.1126/scisignal.2005646] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Rhodopsin is the G protein-coupled receptor (GPCR) that serves as a dim-light receptor for vision in vertebrates. We probed light-induced conformational changes in rhodopsin in its native membrane environment at room temperature using time-resolved wide-angle x-ray scattering. We observed a rapid conformational transition that is consistent with an outward tilt of the cytoplasmic portion of transmembrane helix 6 concomitant with an inward movement of the cytoplasmic portion of transmembrane helix 5. These movements were considerably larger than those reported from the basis of crystal structures of activated rhodopsin, implying that light activation of rhodopsin involves a more extended conformational change than was previously suggested.
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Affiliation(s)
- Erik Malmerberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Petra H M Bovee-Geurts
- Department of Biochemistry, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Xavier Deupi
- Condensed Matter Theory Group, Paul Scherrer Institute, CH-5232 Villigen, Switzerland. Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Linda C Johansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Elena Nazarenko
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland. Department of Biology, ETH Zürich, Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland
| | - Andreas Menzel
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Willem J de Grip
- Department of Biochemistry, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, Netherlands
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
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12
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Schafer CT, Farrens DL. Conformational selection and equilibrium governs the ability of retinals to bind opsin. J Biol Chem 2014; 290:4304-18. [PMID: 25451936 DOI: 10.1074/jbc.m114.603134] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Despite extensive study, how retinal enters and exits the visual G protein-coupled receptor rhodopsin remains unclear. One clue may lie in two openings between transmembrane helix 1 (TM1) and TM7 and between TM5 and TM6 in the active receptor structure. Recently, retinal has been proposed to enter the inactive apoprotein opsin (ops) through these holes when the receptor transiently adopts the active opsin conformation (ops*). Here, we directly test this "transient activation" hypothesis using a fluorescence-based approach to measure rates of retinal binding to samples containing differing relative fractions of ops and ops*. In contrast to what the transient activation hypothesis model would predict, we found that binding for the inverse agonist, 11-cis-retinal (11CR), slowed when the sample contained more ops* (produced using M257Y, a constitutively activating mutation). Interestingly, the increased presence of ops* allowed for binding of the agonist, all-trans-retinal (ATR), whereas WT opsin showed no binding. Shifting the conformational equilibrium toward even more ops* using a G protein peptide mimic (either free in solution or fused to the receptor) accelerated the rate of ATR binding and slowed 11CR binding. An arrestin peptide mimic showed little effect on 11CR binding; however, it stabilized opsin · ATR complexes. The TM5/TM6 hole is apparently not involved in this conformational selection. Increasing its size by mutagenesis did not enable ATR binding but instead slowed 11CR binding, suggesting that it may play a role in trapping 11CR. In summary, our results indicate that conformational selection dictates stable retinal binding, which we propose involves ATR and 11CR binding to different states, the latter a previously unidentified, open-but-inactive conformation.
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Affiliation(s)
- Christopher T Schafer
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098
| | - David L Farrens
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098
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13
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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]
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14
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Kakarala KK, Jamil K, Devaraji V. Structure and putative signaling mechanism of Protease activated receptor 2 (PAR2) - a promising target for breast cancer. J Mol Graph Model 2014; 53:179-199. [PMID: 25173751 DOI: 10.1016/j.jmgm.2014.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/16/2014] [Accepted: 07/21/2014] [Indexed: 12/12/2022]
Abstract
Experimental evidences have observed enhanced expression of protease activated receptor 2 (PAR2) in breast cancer consistently. However, it is not yet recognized as an important therapeutic target for breast cancer as the primary molecular mechanisms of its activation are not yet well-defined. Nevertheless, recent reports on the mechanism of GPCR activation and signaling have given new insights to GPCR functioning. In the light of these details, we attempted to understand PAR2 structure & function using molecular modeling techniques. In this work, we generated averaged representative stable models of PAR2, using protease activated receptor 1 (PAR1) as a template and selected conformation based on their binding affinity with PAR2 specific agonist, GB110. Further, the selected model was used for studying the binding affinity of putative ligands. The selected ligands were based on a recent publication on phylogenetic analysis of Class A rhodopsin family of GPCRs. This study reports putative ligands, their interacting residues, binding affinity and molecular dynamics simulation studies on PAR2-ligand complexes. The results reported from this study would be useful for researchers and academicians to investigate PAR2 function as its physiological role is still hypothetical. Further, this information may provide a novel therapeutic scheme to manage breast cancer.
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Affiliation(s)
- Kavita Kumari Kakarala
- Centre for Biotechnology and Bioinformatics (CBB), School of Life Sciences, Jawaharlal Nehru Institute of Advanced Studies (JNIAS), 6th Floor, Buddha Bhawan, M.G. Road, Secunderabad 500003, Andhra Pradesh, India.
| | - Kaiser Jamil
- Centre for Biotechnology and Bioinformatics (CBB), School of Life Sciences, Jawaharlal Nehru Institute of Advanced Studies (JNIAS), 6th Floor, Buddha Bhawan, M.G. Road, Secunderabad 500003, Andhra Pradesh, India
| | - Vinod Devaraji
- College of Pharmacy, Madras Medical College, E.V.R. Periyar Salai, Chennai 600003, India
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15
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Tian H, Naganathan S, Kazmi MA, Schwartz TW, Sakmar TP, Huber T. Bioorthogonal fluorescent labeling of functional G-protein-coupled receptors. Chembiochem 2014; 15:1820-9. [PMID: 25045132 DOI: 10.1002/cbic.201402193] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Indexed: 11/12/2022]
Abstract
Novel methods are required for site-specific, quantitative fluorescent labeling of G-protein-coupled receptors (GPCRs) and other difficult-to-express membrane proteins. Ideally, fluorescent probes should perturb the native structure and function as little as possible. We evaluated bioorthogonal reactions to label genetically encoded p-acetyl-L-phenylalanine (AcF) or p-azido-L-phenylalanine (azF) residues in receptors heterologously expressed in mammalian cells. We found that keto-selective reagents were not truly bioorthogonal, possibly owing to post-translational protein oxidation reactions. In contrast, the strain-promoted [3+2] azide-alkyne cycloaddition (SpAAC) with dibenzocyclooctyne (DIBO) reagents yielded stoichiometric conjugates with azF-rhodopsin while undergoing negligible background reactions. As one application of this technique, we used Alexa488-rhodopsin to measure the kinetics of ligand uptake and release in membrane-mimetic bicelles using a novel fluorescence-quenching assay.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA)
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16
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Sinha A, Jones Brunette AM, Fay JF, Schafer CT, Farrens DL. Rhodopsin TM6 can interact with two separate and distinct sites on arrestin: evidence for structural plasticity and multiple docking modes in arrestin-rhodopsin binding. Biochemistry 2014; 53:3294-307. [PMID: 24724832 PMCID: PMC4039336 DOI: 10.1021/bi401534y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
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Various studies have implicated the
concave surface of arrestin
in the binding of the cytosolic surface of rhodopsin. However, specific
sites of contact between the two proteins have not previously been
defined in detail. Here, we report that arrestin shares part of the
same binding site on rhodopsin as does the transducin Gα subunit C-terminal tail, suggesting binding of both proteins to
rhodopsin may share some similar underlying mechanisms. We also identify
two areas of contact between the proteins near this region. Both sites
lie in the arrestin N-domain, one in the so-called “finger”
loop (residues 67–79) and the other in the 160 loop (residues
155–165). We mapped these sites using a novel tryptophan-induced
quenching method, in which we introduced Trp residues into arrestin
and measured their ability to quench the fluorescence of bimane probes
attached to cysteine residues on TM6 of rhodopsin (T242C and T243C).
The involvement of finger loop binding to rhodopsin was expected,
but the evidence of the arrestin 160 loop contacting rhodopsin was
not. Remarkably, our data indicate one site on rhodopsin can interact
with multiple structurally separate sites on arrestin that are almost
30 Å apart. Although this observation at first seems paradoxical,
in fact, it provides strong support for recent hypotheses that structural
plasticity and conformational changes are involved in the arrestin–rhodopsin
binding interface and that the two proteins may be able to interact
through multiple docking modes, with arrestin binding to both monomeric
and dimeric rhodopsin.
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Affiliation(s)
- Abhinav Sinha
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
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17
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Yamazaki Y, Nagata T, Terakita A, Kandori H, Shichida Y, Imamoto Y. Intramolecular interactions that induce helical rearrangement upon rhodopsin activation: light-induced structural changes in metarhodopsin IIa probed by cysteine S-H stretching vibrations. J Biol Chem 2014; 289:13792-800. [PMID: 24692562 DOI: 10.1074/jbc.m113.527606] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rhodopsin undergoes rearrangements of its transmembrane helices after photon absorption to transfer a light signal to the G-protein transducin. To investigate the mechanism by which rhodopsin adopts the transducin-activating conformation, the local environmental changes in the transmembrane region were probed using the cysteine S-H group, whose stretching frequency is well isolated from the other protein vibrational modes. The S-H stretching modes of cysteine residues introduced into Helix III, which contains several key residues for the helical movements, and of native cysteine residues were measured by Fourier transform infrared spectroscopy. This method was applied to metarhodopsin IIa, a precursor of the transducin-activating state in which the intramolecular interactions are likely to produce a state ready for helical movements. No environmental change was observed near the ionic lock between Arg-135 in Helix III and Glu-247 in Helix VI that maintains the inactive conformation. Rather, the cysteine residues that showed environmental changes were located around the chromophore, Ala-164, His-211, and Phe-261. These findings imply that the hydrogen bond between Helix III and Helix V involving Glu-122 and His-211 and the hydrophobic packing between Helix III and Helix VI involving Gly-121, Leu-125, Phe-261, and Trp-265 are altered before the helical rearrangement leading toward the active conformation.
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Affiliation(s)
- Yoichi Yamazaki
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, the Graduate School of Materials Science, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| | - Tomoko Nagata
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Akihisa Terakita
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, the Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan, and
| | - Hideki Kandori
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, the Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Yoshinori Shichida
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yasushi Imamoto
- From the Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan,
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18
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Stehle J, Silvers R, Werner K, Chatterjee D, Gande S, Scholz F, Dutta A, Wachtveitl J, Klein-Seetharaman J, Schwalbe H. Characterization of the simultaneous decay kinetics of metarhodopsin states II and III in rhodopsin by solution-state NMR spectroscopy. Angew Chem Int Ed Engl 2014; 53:2078-84. [PMID: 24505031 DOI: 10.1002/anie.201309581] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Indexed: 11/09/2022]
Abstract
The mammalian visual dim-light photoreceptor rhodopsin is considered a prototype G protein-coupled receptor. Here, we characterize the kinetics of its light-activation process. Milligram quantities of α,ε-(15)N-labeled tryptophan rhodopsin were produced in stably transfected HEK293 cells. Assignment of the chemical shifts of the indole signals was achieved by generating the single-point-tryptophan to phenylalanine mutants, and the kinetics of each of the five tryptophan residues were recorded. We find kinetic partitioning in rhodopsin decay, including three half-lives, that reveal two parallel processes subsequent to rhodopsin activation that are related to the photocycle. The meta II and meta III states emerge in parallel with a relative ratio of about 3:1. Transient formation of the meta III state was confirmed by flash photolysis experiments. From analysis of the site-resolved kinetic data we propose the involvement of the E2 -loop in the formation of the meta III state.
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Affiliation(s)
- Jochen Stehle
- Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
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19
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Stehle J, Silvers R, Werner K, Chatterjee D, Gande S, Scholz F, Dutta A, Wachtveitl J, Klein-Seetharaman J, Schwalbe H. Characterization of the Simultaneous Decay Kinetics of Metarhodopsin States II and III in Rhodopsin by Solution-State NMR Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309581] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Sridharan R, Zuber J, Connelly SM, Mathew E, Dumont ME. Fluorescent approaches for understanding interactions of ligands with G protein coupled receptors. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1838:15-33. [PMID: 24055822 PMCID: PMC3926105 DOI: 10.1016/j.bbamem.2013.09.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 09/03/2013] [Accepted: 09/08/2013] [Indexed: 11/18/2022]
Abstract
G protein coupled receptors are responsible for a wide variety of signaling responses in diverse cell types. Despite major advances in the determination of structures of this class of receptors, the underlying mechanisms by which binding of different types of ligands specifically elicits particular signaling responses remain unclear. The use of fluorescence spectroscopy can provide important information about the process of ligand binding and ligand dependent conformational changes in receptors, especially kinetic aspects of these processes that can be difficult to extract from X-ray structures. We present an overview of the extensive array of fluorescent ligands that have been used in studies of G protein coupled receptors and describe spectroscopic approaches for assaying binding and probing the environment of receptor-bound ligands with particular attention to examples involving yeast pheromone receptors. In addition, we discuss the use of fluorescence spectroscopy for detecting and characterizing conformational changes in receptors induced by the binding of ligands. Such studies have provided strong evidence for diversity of receptor conformations elicited by different ligands, consistent with the idea that GPCRs are not simple on and off switches. This diversity of states constitutes an underlying mechanistic basis for biased agonism, the observation that different stimuli can produce different responses from a single receptor. It is likely that continued technical advances will allow fluorescence spectroscopy to play an important role in continued probing of structural transitions in G protein coupled receptors. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
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Affiliation(s)
- Rajashri Sridharan
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Jeffrey Zuber
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Sara M. Connelly
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Elizabeth Mathew
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Mark E. Dumont
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
- Department of Pediatrics, P.O. Box 777, University of Rochester Medical Center, Rochester, NY 14642
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21
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Alexiev U, Farrens DL. Fluorescence spectroscopy of rhodopsins: insights and approaches. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:694-709. [PMID: 24183695 DOI: 10.1016/j.bbabio.2013.10.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/11/2013] [Accepted: 10/16/2013] [Indexed: 01/30/2023]
Abstract
Fluorescence spectroscopy has become an established tool at the interface of biology, chemistry and physics because of its exquisite sensitivity and recent technical advancements. However, rhodopsin proteins present the fluorescence spectroscopist with a unique set of challenges and opportunities due to the presence of the light-sensitive retinal chromophore. This review briefly summarizes some approaches that have successfully met these challenges and the novel insights they have yielded about rhodopsin structure and function. We start with a brief overview of fluorescence fundamentals and experimental methodologies, followed by more specific discussions of technical challenges rhodopsin proteins present to fluorescence studies. Finally, we end by discussing some of the unique insights that have been gained specifically about visual rhodopsin and its interactions with affiliate proteins through the use of fluorescence spectroscopy. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Ulrike Alexiev
- Physics Department, Freie Universität Berlin, Berlin, Germany.
| | - David L Farrens
- Departments of Biochemistry and Molecular Biology, Oregon Health Sciences University, USA
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22
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Naganathan S, Grunbeck A, Tian H, Huber T, Sakmar TP. Genetically-encoded molecular probes to study G protein-coupled receptors. J Vis Exp 2013. [PMID: 24056801 DOI: 10.3791/50588] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
To facilitate structural and dynamic studies of G protein-coupled receptor (GPCR) signaling complexes, new approaches are required to introduce informative probes or labels into expressed receptors that do not perturb receptor function. We used amber codon suppression technology to genetically-encode the unnatural amino acid, p-azido-L-phenylalanine (azF) at various targeted positions in GPCRs heterologously expressed in mammalian cells. The versatility of the azido group is illustrated here in different applications to study GPCRs in their native cellular environment or under detergent solubilized conditions. First, we demonstrate a cell-based targeted photocrosslinking technology to identify the residues in the ligand-binding pocket of GPCR where a tritium-labeled small-molecule ligand is crosslinked to a genetically-encoded azido amino acid. We then demonstrate site-specific modification of GPCRs by the bioorthogonal Staudinger-Bertozzi ligation reaction that targets the azido group using phosphine derivatives. We discuss a general strategy for targeted peptide-epitope tagging of expressed membrane proteins in-culture and its detection using a whole-cell-based ELISA approach. Finally, we show that azF-GPCRs can be selectively tagged with fluorescent probes. The methodologies discussed are general, in that they can in principle be applied to any amino acid position in any expressed GPCR to interrogate active signaling complexes.
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Affiliation(s)
- Saranga Naganathan
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University
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23
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Tsukamoto H, Farrens DL. A constitutively activating mutation alters the dynamics and energetics of a key conformational change in a ligand-free G protein-coupled receptor. J Biol Chem 2013; 288:28207-16. [PMID: 23940032 DOI: 10.1074/jbc.m113.472464] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptors (GPCRs) undergo dynamic transitions between active and inactive conformations. Usually, these conversions are triggered when the receptor detects an external signal, but some so-called constitutively activating mutations, or CAMs, induce a GPCR to bind and activate G proteins in the absence of external stimulation, in ways still not fully understood. Here, we investigated how a CAM alters the structure of a GPCR and the dynamics involved as the receptor transitions between different conformations. Our approach used site-directed fluorescence labeling (SDFL) spectroscopy to compare opsin, the ligand-free form of the GPCR rhodopsin, with opsin containing the CAM M257Y, focusing specifically on key movements that occur in the sixth transmembrane helix (TM6) during GPCR activation. The site-directed fluorescence labeling data indicate opsin is constrained to an inactive conformation both in detergent micelles and lipid membranes, but when it contains the M257Y CAM, opsin is more dynamic and can interact with a G protein mimetic. Further study of these receptors using tryptophan-induced quenching (TrIQ) methods indicates that in detergent, the CAM significantly increases the population of receptors in the active state, but not in lipids. Subsequent Arrhenius analysis of the TrIQ data suggests that, both in detergent and lipids, the CAM lowers the energy barrier for TM6 movement, a key transition required for conversion between the inactive and active conformations. Together, these data suggest that the lowered energy barrier is a primary effect of the CAM on the receptor dynamics and energetics.
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Affiliation(s)
- Hisao Tsukamoto
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098
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24
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Zocher M, Bippes CA, Zhang C, Müller DJ. Single-molecule force spectroscopy of G-protein-coupled receptors. Chem Soc Rev 2013; 42:7801-15. [PMID: 23799399 DOI: 10.1039/c3cs60085h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The applicability of single-molecule force spectroscopy (SMFS) to characterize membrane proteins in vitro is developing rapidly and opening a wide range of fascinating possibilities to study how intra- and intermolecular interactions determine their structural stability and functional state. In particular, understanding how molecular interactions contribute to the functional state of G-protein-coupled receptors (GPCRs) is of importance because they mediate most of our physiological responses and act as therapeutic targets for a broad spectrum of diseases. In our review we focus on SMFS to characterize GPCRs embedded in their physiologically relevant membranes and exposed to physiologically relevant conditions. SMFS uses a molecularly sharp stylus to grasp the terminal end of a GPCR and to quickly unfold the receptor while recording interaction forces. The positional accuracy of SMFS localizes these interactions to structural segments of the GPCR whereas the sensitivity of SMFS enables their stabilizing interaction forces to be quantified. To further investigate the kinetic, energetic and mechanical properties of the structural segments, dynamic SMFS (DFS) probes their stability over a wide range of loading rates. These parameters provide insight into the energy landscape that provides information on the structural and functional properties of the GPCRs. Selected highlights exemplify the application of SMFS to characterize inter- and intramolecular interactions, which change the properties of GPCRs in relation to their functional state (e.g., ligand binding), diseased state (e.g., mutation), or lipid environment such as cholesterol.
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Affiliation(s)
- Michael Zocher
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
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25
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Rathmann D, Pedragosa-Badia X, Beck-Sickinger AG. In vitro modification of substituted cysteines as tool to study receptor functionality and structure-activity relationships. Anal Biochem 2013; 439:173-83. [PMID: 23624320 DOI: 10.1016/j.ab.2013.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 04/11/2013] [Accepted: 04/16/2013] [Indexed: 12/11/2022]
Abstract
Mutagenic investigations of expressed membrane proteins are routine, but the variety of modifications is limited by the twenty canonical amino acids. We describe an easy and effective cysteine substitution mutagenesis method to modify and investigate distinct amino acids in vitro. The approach combines the substituted cysteine accessibility method (SCAM) with a functional signal transduction readout system using different thiol-specific reagents. We applied this approach to the prolactin-releasing peptide receptor (PrRPR) to facilitate biochemical structure-activity relationship studies of eight crucial positions. Especially for D(6.59)C, the treatment with the positively charged methanethiosulfonate (MTS) ethylammonium led to an induced basal activity, whereas the coupling of the negatively charged MTS ethylsulfonate nearly reconstituted full activity, obviously by mimicking the wild-type charged side chain. At E(5.26)C, W(5.28)C, Y(5.38)C, and Q(7.35)C, accessibility was observed but hindered transfer into the active receptor conformation. Accordingly, the combination of SCAM and signaling assay is feasible and can be adapted to other G-protein-coupled receptors (GPCRs). This method circumvents the laborious way of inserting non-proteinogenic amino acids to investigate activity and ligand binding, with rising numbers of MTS reagents allowing selective side chain modification. This method pinpoints to residues being accessible but also presents potential molecular positions to investigate the global conformation.
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Affiliation(s)
- Daniel Rathmann
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, D-04103 Leipzig, Germany
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26
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Naganathan S, Ye S, Sakmar TP, Huber T. Site-specific epitope tagging of G protein-coupled receptors by bioorthogonal modification of a genetically encoded unnatural amino acid. Biochemistry 2013; 52:1028-36. [PMID: 23317030 DOI: 10.1021/bi301292h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We developed a general strategy for labeling expressed membrane proteins with a peptide epitope tag and detecting the tagged proteins in native cellular membranes. First, we genetically encoded the unnatural amino acid p-azido-L-phenylalanine (azF) at various specific sites in a G protein-coupled receptor (GPCR), C-C chemokine receptor 5 (CCR5). The reactive azido moiety facilitates Staudinger ligation to a triarylphosphine-conjugated FLAG peptide. We then developed a whole-cell-based enzyme-linked immunosorbent assay approach to detect the modified azF-CCR5 using anti-FLAG mAb. We optimized conditions to achieve labeling and detection of low-abundance GPCRs in live cells. We also performed an accessibility screen to identify azF positions on CCR5 amenable to labeling. Finally, we demonstrate a preparative strategy for obtaining pure bioorthogonally modified GPCRs suitable for single-molecule detection fluorescence experiments. This peptide epitope tagging strategy, which employs genetic encoding and bioorthogonal labeling of azF in live cells, should be useful for studying biogenesis of polytopic membrane proteins and GPCR signaling mechanisms.
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Affiliation(s)
- Saranga Naganathan
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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27
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Activation biosensor for G protein-coupled receptors: a FRET-based m1 muscarinic activation sensor that regulates G(q). PLoS One 2012; 7:e45651. [PMID: 23029161 PMCID: PMC3447775 DOI: 10.1371/journal.pone.0045651] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/20/2012] [Indexed: 01/07/2023] Open
Abstract
We describe the design, construction and validation of a fluorescence sensor to measure activation by agonist of the m1 muscarinic cholinergic receptor, a prototypical class I Gq-coupled receptor. The sensor uses an established general design in which Förster resonance energy transfer (FRET) from a circularly permuted CFP mutant to FlAsH, a selectively reactive fluorescein, is decreased 15–20% upon binding of a full agonist. Notably, the sensor displays essentially wild-type capacity to catalyze activation of Gαq, and the purified and reconstituted sensor displays appropriate regulation of affinity for agonists by Gq. We describe the strategies used to increase the agonist-driven change in FRET while simultaneously maintaining regulatory interactions with Gαq, in the context of the known structures of Class I G protein-coupled receptors. The approach should be generally applicable to other Class I receptors which include numerous important drug targets.
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28
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Fay JF, Farrens DL. A key agonist-induced conformational change in the cannabinoid receptor CB1 is blocked by the allosteric ligand Org 27569. J Biol Chem 2012; 287:33873-82. [PMID: 22846992 DOI: 10.1074/jbc.m112.352328] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Allosteric ligands that modulate how G protein-coupled receptors respond to traditional orthosteric drugs are an exciting and rapidly expanding field of pharmacology. An allosteric ligand for the cannabinoid receptor CB1, Org 27569, exhibits an intriguing effect; it increases agonist binding, yet blocks agonist-induced CB1 signaling. Here we explored the mechanism behind this behavior, using a site-directed fluorescence labeling approach. Our results show that Org 27569 blocks conformational changes in CB1 that accompany G protein binding and/or activation, and thus inhibit formation of a fully active CB1 structure. The underlying mechanism behind this behavior is that simultaneous binding of Org 27569 produces a unique agonist-bound conformation, one that may resemble an intermediate structure formed on the pathway to full receptor activation.
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Affiliation(s)
- Jonathan F Fay
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098, USA
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29
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Lohse MJ, Nuber S, Hoffmann C. Fluorescence/bioluminescence resonance energy transfer techniques to study G-protein-coupled receptor activation and signaling. Pharmacol Rev 2012; 64:299-336. [PMID: 22407612 DOI: 10.1124/pr.110.004309] [Citation(s) in RCA: 251] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Fluorescence and bioluminescence resonance energy transfer (FRET and BRET) techniques allow the sensitive monitoring of distances between two labels at the nanometer scale. Depending on the placement of the labels, this permits the analysis of conformational changes within a single protein (for example of a receptor) or the monitoring of protein-protein interactions (for example, between receptors and G-protein subunits). Over the past decade, numerous such techniques have been developed to monitor the activation and signaling of G-protein-coupled receptors (GPCRs) in both the purified, reconstituted state and in intact cells. These techniques span the entire spectrum from ligand binding to the receptors down to intracellular second messengers. They allow the determination and the visualization of signaling processes with high temporal and spatial resolution. With these techniques, it has been demonstrated that GPCR signals may show spatial and temporal patterning. In particular, evidence has been provided for spatial compartmentalization of GPCRs and their signals in intact cells and for distinct physiological consequences of such spatial patterning. We review here the FRET and BRET technologies that have been developed for G-protein-coupled receptors and their signaling proteins (G-proteins, effectors) and the concepts that result from such experiments.
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Affiliation(s)
- Martin J Lohse
- Institute of Pharmacology and Toxicology, Versbacher Str. 9, 97078 Würzburg, Germany.
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30
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Ghosh A, Sonavane U, Andhirka SK, Aradhyam GK, Joshi R. Structural insights into human GPCR protein OA1: a computational perspective. J Mol Model 2011; 18:2117-33. [DOI: 10.1007/s00894-011-1228-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 08/18/2011] [Indexed: 11/24/2022]
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31
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Malmerberg E, Omran Z, Hub JS, Li X, Katona G, Westenhoff S, Johansson LC, Andersson M, Cammarata M, Wulff M, van der Spoel D, Davidsson J, Specht A, Neutze R. Time-resolved WAXS reveals accelerated conformational changes in iodoretinal-substituted proteorhodopsin. Biophys J 2011; 101:1345-53. [PMID: 21943415 DOI: 10.1016/j.bpj.2011.07.050] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 06/15/2011] [Accepted: 07/15/2011] [Indexed: 12/20/2022] Open
Abstract
Time-resolved wide-angle x-ray scattering (TR-WAXS) is an emerging biophysical method which probes protein conformational changes with time. Here we present a comparative TR-WAXS study of native green-absorbing proteorhodopsin (pR) from SAR86 and a halogenated derivative for which the retinal chromophore has been replaced with 13-desmethyl-13-iodoretinal (13-I-pR). Transient absorption spectroscopy differences show that the 13-I-pR photocycle is both accelerated and displays more complex kinetics than native pR. TR-WAXS difference data also reveal that protein structural changes rise and decay an order-of-magnitude more rapidly for 13-I-pR than native pR. Despite these differences, the amplitude and nature of the observed helical motions are not significantly affected by the substitution of the retinal's C-20 methyl group with an iodine atom. Molecular dynamics simulations indicate that a significant increase in free energy is associated with the 13-cis conformation of 13-I-pR, consistent with our observation that the transient 13-I-pR conformational state is reached more rapidly. We conclude that although the conformational trajectory is accelerated, the major transient conformation of pR is unaffected by the substitution of an iodinated retinal chromophore.
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Affiliation(s)
- Erik Malmerberg
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, Gothenburg, Sweden
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32
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Kim TY, Schlieter T, Haase S, Alexiev U. Activation and molecular recognition of the GPCR rhodopsin--insights from time-resolved fluorescence depolarisation and single molecule experiments. Eur J Cell Biol 2011; 91:300-10. [PMID: 21803442 DOI: 10.1016/j.ejcb.2011.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/29/2011] [Accepted: 03/29/2011] [Indexed: 10/18/2022] Open
Abstract
The cytoplasmic surface of the G-protein coupled receptor (GPCR) rhodopsin is a key element in membrane receptor activation, molecular recognition by signalling molecules, and receptor deactivation. Understanding of the coupling between conformational changes in the intramembrane domain and the membrane-exposed surface of the photoreceptor rhodopsin is crucial for the elucidation of the molecular mechanism in GPCR activation. As little is known about protein dynamics, particularly the conformational dynamics of the cytoplasmic surface elements on the nanoseconds timescale, we utilised time-resolved fluorescence anisotropy experiments and site-directed fluorescence labelling to provide information on both, conformational space and motion. We summarise our recent advances in understanding rhodopsin dynamics and function using time-resolved fluorescence depolarisation and single molecule fluorescence experiments, with particular focus on the amphipathic helix 8, lying parallel to the cytoplasmic membrane surface and connecting transmembrane helix 7 with the long C-terminal tail.
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Affiliation(s)
- Tai-Yang Kim
- Physics Department, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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33
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Shim JY. Understanding functional residues of the cannabinoid CB1. Curr Top Med Chem 2011; 10:779-98. [PMID: 20370713 DOI: 10.2174/156802610791164210] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 10/27/2009] [Indexed: 02/07/2023]
Abstract
The brain cannabinoid (CB(1)) receptor that mediates numerous physiological processes in response to marijuana and other psychoactive compounds is a G protein coupled receptor (GPCR) and shares common structural features with many rhodopsin class GPCRs. For the rational development of therapeutic agents targeting the CB(1) receptor, understanding of the ligand-specific CB(1) receptor interactions responsible for unique G protein signals is crucial. For a more than a decade, a combination of mutagenesis and computational modeling approaches has been successfully employed to study the ligand-specific CB(1) receptor interactions. In this review, after a brief discussion about recent advances in understanding of some structural and functional features of GPCRs commonly applicable to the CB(1) receptor, the CB(1) receptor functional residues reported from mutational studies are divided into three different types, ligand binding (B), receptor stabilization (S) and receptor activation (A) residues, to delineate the nature of the binding pockets of anandamide, CP55940, WIN55212-2 and SR141716A and to describe the molecular events of the ligand-specific CB(1) receptor activation from ligand binding to G protein signaling. Taken these CB(1) receptor functional residues, some of which are unique to the CB(1) receptor, together with the biophysical knowledge accumulated for the GPCR active state, it is possible to propose the early stages of the CB(1) receptor activation process that not only provide some insights into understanding molecular mechanisms of receptor activation but also are applicable for identifying new therapeutic agents by applying the validated structure-based approaches, such as virtual high throughput screening (HTS) and fragment-based approach (FBA).
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Affiliation(s)
- Joong-Youn Shim
- J.L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA.
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34
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Diaz C, Leplatois P, Angelloz-Nicoud P, Lecomte M, Josse A, Delpech M, Pecceu F, Loison G, Shire D, Pascal M, Ferrara P, Ferran E. Differential Virtual Screening (DVS) with Active and Inactive Molecular Models for Finding and Profiling GPCR Modulators: Case of the CCK1 Receptor. Mol Inform 2011; 30:345-58. [DOI: 10.1002/minf.201000180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 02/23/2011] [Indexed: 11/10/2022]
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35
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Bosch-Presegué L, Iarriccio L, Aguilà M, Toledo D, Ramon E, Cordomí A, Garriga P. Hydrophobic amino acids at the cytoplasmic ends of helices 3 and 6 of rhodopsin conjointly modulate transducin activation. Arch Biochem Biophys 2011; 506:142-9. [DOI: 10.1016/j.abb.2010.11.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Revised: 11/22/2010] [Accepted: 11/22/2010] [Indexed: 11/26/2022]
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36
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Multiscale computational methods for mapping conformational ensembles of G-protein-coupled receptors. COMPUTATIONAL CHEMISTRY METHODS IN STRUCTURAL BIOLOGY 2011; 85:253-80. [DOI: 10.1016/b978-0-12-386485-7.00007-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Abstract
G protein-coupled receptors (GPCRs) comprise a large class of transmembrane proteins that play critical roles in both normal physiology and pathophysiology. These critical roles offer targets for therapeutic intervention, as exemplified by the substantial fraction of current pharmaceutical agents that target members of this family. Tremendous contributions to our understanding of GPCR structure and dynamics have come from both indirect and direct structural characterization techniques. Key features of GPCR conformations derived from both types of characterization techniques are reviewed.
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Affiliation(s)
- Abby L. Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN 38152, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-901-678-2638; Fax: +1-901-678-3447
| | - Debra L. Bautista
- Christian Brothers High School, 5900 Walnut Grove Road, Memphis, TN 38120, USA; E-Mail: (D.L.B.)
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Farrens DL. What site-directed labeling studies tell us about the mechanism of rhodopsin activation and G-protein binding. Photochem Photobiol Sci 2010; 9:1466-74. [PMID: 20967340 DOI: 10.1039/c0pp00283f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rhodopsin is the photoreceptor protein responsible for dim-light vision in mammals. Due to extensive biophysical, structural and computational analysis of this membrane protein, it is presently the best understood G-protein coupled receptor (GPCR). Here I briefly review one approach that has been extensively used to identify dynamic and structural changes in rhodopsin--the use of site-directed labeling methods (SDL) coupled with electron paramagnetic resonance (EPR) and fluorescence spectroscopy. These SDL studies involve introducing individual cysteine residues into the receptor, then labeling them with cysteine-reactive probes for subsequent analysis by the appropriate spectroscopy. I will give a brief overview of how SDL methods are carried out and how the data is analyzed. Then, I will discuss how SDL studies were carried out on rhodopsin, and how they were used to identify a key structural change that occurs in rhodopsin upon activation--movement of transmembrane helix 6 (TM6). I will also briefly discuss how the SDL studies of rhodopsin compare with SDL studies of other GPCRs, and compare the SDL data with early and recent crystal structures of rhodopsin. Finally, I will discuss why the TM6 movement is required for rhodopsin to couple with the G-protein transducin, and speculate how this mechanism might be a universal method used by all GPCRs to bind G-proteins and perhaps other proteins involved in visual signal transduction, such as arrestin and rhodopsin kinase.
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Affiliation(s)
- David L Farrens
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, Oregon 97239, USA
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39
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Structural characteristics of the hydrophobic patch of azurin and its interaction with p53: a site-directed spin labeling study. SCIENCE CHINA-LIFE SCIENCES 2010; 53:1181-8. [PMID: 20953940 DOI: 10.1007/s11427-010-4069-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 05/25/2010] [Indexed: 10/18/2022]
Abstract
Site-directed spin labeling (SDSL) is a powerful tool for monitoring protein structure, dynamics and conformational changes. In this study, the domain-specific properties of azurin and its interaction with p53 were studied using this technique. Mutations of six residues, that are located in the hydrophobic patch of azurin, were prepared and spin labeled. Spectra of the six azurin mutants in solution showed that spin labeled residues 45 and 63 are in a very restricted environment, residues 59 and 65 are in a spacious environment and have free movement, and residues 49 and 51 are located in a relatively closed pocket. Polarity experiments confirmed these results. The changes observed in the spectra of spin labeled azurin upon interaction with p53 indicate that the hydrophobic patch is involved in this interaction. Our results provide valuable insight into the topographic structure of the hydrophobic domain of azurin, as well as direct evidence of its interaction with p53 in solution via the hydrophobic patch. Cytotoxicity studies of azurin mutants showed that residues along the hydrophobic patch are important for its cytotoxicity.
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40
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Tsukamoto H, Terakita A. Diversity and functional properties of bistable pigments. Photochem Photobiol Sci 2010; 9:1435-43. [PMID: 20852774 DOI: 10.1039/c0pp00168f] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Rhodopsin and related opsin-based pigments, which are photosensitive membrane proteins, have been extensively studied using a wide variety of techniques, with rhodopsin being the most understood G protein-coupled receptor (GPCR). Animals use various opsin-based pigments for vision and a wide variety of non-visual functions. Many functionally varied pigments are roughly divided into two kinds, based on their photoreaction: bistable and monostable pigments. Bistable pigments are thermally stable before and after photo-activation, but monostable pigments are stable only before activation. Here, we review the diversity of bistable pigments and their molecular characteristics. We also discuss the mechanisms underlying different molecular characteristics of bistable and monostable pigments. In addition, the potential of bistable pigments as a GPCR model is proposed.
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Affiliation(s)
- Hisao Tsukamoto
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Osaka, Osaka 558-8585, Japan
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41
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Goncalves JA, Ahuja S, Erfani S, Eilers M, Smith SO. Structure and function of G protein-coupled receptors using NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:159-80. [PMID: 20633362 PMCID: PMC2907352 DOI: 10.1016/j.pnmrs.2010.04.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 04/08/2010] [Indexed: 05/15/2023]
Affiliation(s)
- Joseph A Goncalves
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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42
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Straßer A, Wittmann HJ. In silico analysis of the histaprodifen induced activation pathway of the guinea-pig histamine H1-receptor. J Comput Aided Mol Des 2010; 24:759-69. [DOI: 10.1007/s10822-010-9372-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 06/28/2010] [Indexed: 10/19/2022]
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43
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Lu M, Li XF, Le XC, Weinfeld M, Wang H. Identification and characterization of cysteinyl exposure in proteins by selective mercury labeling and nano-electrospray ionization quadrupole time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:1523-1532. [PMID: 20486248 DOI: 10.1002/rcm.4550] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We describe a method for probing surface-exposed cysteines in proteins by selective labeling with p-hydroxymercuribenzoate (PMB) combined with nano-electrospray ionization mass spectrometric analysis (nanoESI-MS). The rapid, stoichiometric, and specific labeling by PMB of surface-exposed cysteines allows for characterization of the accessibility of the cysteines using a single MS analysis. Moreover, by taking advantage of the large mass shift of 321 Da, unique isotopic pattern, and enhanced MS signal of PMB-labeled cysteine-containing peptide fragments, the surface-exposed cysteines in proteins can be accurately identified by peptide mapping. The number and sites of reactive cysteines on the surface of human and rat hemoglobins (hHb and rHb) were identified as examples. Collision-induced dissociation tandem mass spectrometric (MS/MS) analysis of specific peptides further confirmed the selective labeling of PMB in hHb. The subtle difference between the different cysteine residues in rHb was also evaluated by multiple PMB titrations. The difference between the two cysteines in their environment may partially explain their reaction specificity. Cysteine 125 in the beta unit of rHb is exposed on the surface, explaining its reactivity with glutathione. Cysteine 13 in the alpha subunit of rHb is much less exposed, and is located in a hydrophobic pocket, a conclusion that is consistent with the previous observation of its selective binding with dimethylarsinous acid, a reactive arsenic metabolite. The method is potentially useful for probing cysteines in other biologically important proteins and for studying proteins that are associated with conformational or structural changes induced by denaturing processes, protein modifications, protein-protein interactions and protein assemblies.
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Affiliation(s)
- Meiling Lu
- State Key Laboratory for Environmental Chemistry and Ecotoxicology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Haidian District, Beijing 100085, PR China.
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44
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Tikhonova IG, Costanzi S. Unraveling the structure and function of G protein-coupled receptors through NMR spectroscopy. Curr Pharm Des 2010; 15:4003-16. [PMID: 20028318 DOI: 10.2174/138161209789824803] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
G protein-coupled receptors (GPCRs) are a large superfamily of signaling proteins expressed on the plasma membrane. They are involved in a wide range of physiological processes and, therefore, are exploited as drug targets in a multitude of therapeutic areas. In this extent, knowledge of structural and functional properties of GPCRs may greatly facilitate rational design of modulator compounds. Solution and solid-state nuclear magnetic resonance (NMR) spectroscopy represents a powerful method to gather atomistic insights into protein structure and dynamics. In spite of the difficulties inherent the solution of the structure of membrane proteins through NMR, these methods have been successfully applied, sometimes in combination with molecular modeling, to the determination of the structure of GPCR fragments, the mapping of receptor-ligand interactions, and the study of the conformational changes associated with the activation of the receptors. In this review, we provide a summary of the NMR contributions to the study of the structure and function of GPCRs, also in light of the published crystal structures.
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Affiliation(s)
- Irina G Tikhonova
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
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45
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Yan L, Holleran BJ, Lavigne P, Escher E, Guillemette G, Leduc R. Analysis of transmembrane domains 1 and 4 of the human angiotensin II AT1 receptor by cysteine-scanning mutagenesis. J Biol Chem 2009; 285:2284-93. [PMID: 19940150 DOI: 10.1074/jbc.m109.077180] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The octapeptide hormone angiotensin II (AngII) exerts a wide variety of cardiovascular effects through the activation of the AT(1) receptor, which belongs to the G protein-coupled receptor superfamily. Like other G protein-coupled receptors, the AT(1) receptor possesses seven transmembrane domains that provide structural support for the formation of the ligand-binding pocket. Here, we investigated the role of the first and fourth transmembrane domains (TMDs) in the formation of the binding pocket of the human AT(1) receptor using the substituted-cysteine accessibility method. Each residue within the Phe-28((1.32))-Ile-53((1.57)) fragment of TMD1 and Leu-143((4.40))-Phe-170((4.67)) fragment of TMD4 was mutated, one at a time, to a cysteine. The resulting mutant receptors were expressed in COS-7 cells, which were subsequently treated with the charged sulfhydryl-specific alkylating agent methanethiosulfonate ethylammonium (MTSEA). This treatment led to a significant reduction in the binding affinity of TMD1 mutants M30C((1.34))-AT(1) and T33C((1.37))-AT(1) and TMD4 mutant V169C((4.66))-AT(1). Although this reduction in binding of the TMD1 mutants was maintained when examined in a constitutively active receptor (N111G-AT(1)) background, we found that V169C((4.66))-AT(1) remained unaffected when treated with MTSEA compared with untreated in this context. Moreover, the complete loss of binding observed for R167C((4.64))-AT(1) was restored upon treatment with MTSEA. Our results suggest that the extracellular portion of TMD1, particularly residues Met-30((1.34)) and Thr-33((1.37)), as well as residues Arg-167((4.64)) and Val-169((4.66)) at the junction of TMD4 and the second extracellular loop, are important binding determinants within the AT(1) receptor binding pocket but that these TMDs undergo very little movement, if at all, during the activation process.
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Affiliation(s)
- Liping Yan
- Department of Pharmacology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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46
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Miller D, Charalambous K, Rotem D, Schuldiner S, Curnow P, Booth PJ. In vitro Unfolding and Refolding of the Small Multidrug Transporter EmrE. J Mol Biol 2009; 393:815-32. [DOI: 10.1016/j.jmb.2009.08.039] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 08/12/2009] [Accepted: 08/14/2009] [Indexed: 11/28/2022]
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47
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Fluman N, Cohen-Karni D, Weiss T, Bibi E. A promiscuous conformational switch in the secondary multidrug transporter MdfA. J Biol Chem 2009; 284:32296-304. [PMID: 19808670 DOI: 10.1074/jbc.m109.050658] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Multidrug (Mdr) transporters are membrane proteins that actively export structurally dissimilar drugs from the cell, thereby rendering the cell resistant to toxic compounds. Similar to substrate-specific transporters, Mdr transporters also undergo substrate-induced conformational changes. However, the mechanism by which a variety of dissimilar substrates are able to induce similar transport-compatible conformational responses in a single transporter remains unclear. To address this major aspect of Mdr transport, we studied the conformational behavior of the Escherichia coli Mdr transporter MdfA. Our results show that indeed, different substrates induce similar conformational changes in the transporter. Intriguingly, in addition, we observed that compounds other than substrates are able to confer similar conformational changes when covalently attached at the putative Mdr recognition pocket of MdfA. Taken together, the results suggest that the Mdr-binding pocket of MdfA is conformationally sensitive. We speculate that the same conformational switch that usually drives active transport is triggered promiscuously by merely occupying the Mdr-binding site.
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Affiliation(s)
- Nir Fluman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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48
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Floquet N, M'Kadmi C, Perahia D, Gagne D, Bergé G, Marie J, Banères JL, Galleyrand JC, Fehrentz JA, Martinez J. Activation of the ghrelin receptor is described by a privileged collective motion: a model for constitutive and agonist-induced activation of a sub-class A G-protein coupled receptor (GPCR). J Mol Biol 2009; 395:769-84. [PMID: 19782690 DOI: 10.1016/j.jmb.2009.09.051] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 09/18/2009] [Accepted: 09/20/2009] [Indexed: 10/20/2022]
Abstract
Three homology models of the human ghrelin receptor (GHS-R1a) have been generated from the available X-ray structures of rhodopsin (RHO model), opsin (OPS model) and beta-2 adrenergic receptor (B2 model). The latter was used as a starting point for combined molecular dynamics simulation (MDS) and full atom normal modes analysis (NMA). A low-frequency normal mode (mode 16) perfectly reproduced the intracellular motions observed between B2 and RHO models; in the opposite direction along the same mode, the generated structures are closer to the OPS model, suggesting a direct link with GHS-R1a activation. This was in agreement with motions of the seven transmembranous segments, increase of the solvent accessibility of the 140-ERY-142 sequence, and flip of the Trp276 (C WLP) residue, some features related to GPCRs activation. According to our model, His280 was proposed to stabilize Trp276 in the active state; this was verified by site-directed mutagenesis and biochemical characterization of the resulting H280A and H280S mutants, which were fully functional but sharing an important decrease of their basal activities. Docking performed with short ghrelin derivatives Gly-Ser-Ser ([octa])-Phe-NH (2) and Gly-Ser-Ser ([octa])-Phe-Leu-NH (2) allowed the identification of a robust position of these peptides in the active site of the receptor. This model was refined by MDS and validated by docking experiments performed on a set of 55 ghrelin receptor ligands based on the 1,2,4- triazole scaffold. Finally, NMA performed on the obtained peptide-receptor complex suggested stabilization of the Trp276 residue and of the whole receptor in the active state, preventing the motion observed along mode 16 computed for the unbound receptor. Our results show that NMA offers a powerful approach to study the conformational diversity and the activation mechanism of GPCRs.
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Affiliation(s)
- Nicolas Floquet
- Institut des Biomolécules Max Mousseron (I.B.M.M.), CNRS UMR5247 - Université Montpellier 1 - Université Montpellier 2, Faculté de Pharmacie, 15 avenue Charles Flahault, B.P. 14 491, 34093 Montpellier Cedex 5, France.
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49
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Domazet I, Martin SS, Holleran BJ, Morin ME, Lacasse P, Lavigne P, Escher E, Leduc R, Guillemette G. The fifth transmembrane domain of angiotensin II Type 1 receptor participates in the formation of the ligand-binding pocket and undergoes a counterclockwise rotation upon receptor activation. J Biol Chem 2009; 284:31953-61. [PMID: 19773549 DOI: 10.1074/jbc.m109.051839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The octapeptide hormone angiotensin II exerts a wide variety of cardiovascular effects through the activation of the angiotensin II Type 1 (AT(1)) receptor, which belongs to the G protein-coupled receptor superfamily. Like other G protein- coupled receptors, the AT(1) receptor possesses seven transmembrane domains that provide structural support for the formation of the ligand-binding pocket. The role of the fifth transmembrane domain (TMD5) was investigated using the substituted cysteine accessibility method. All of the residues within Thr-190 to Leu-217 region were mutated one at a time to cysteine, and after expression in COS-7 cells, the mutant receptors were treated with the sulfhydryl-specific alkylating agent methanethiosulfonate-ethylammonium (MTSEA). MTSEA reacts selectively with water-accessible, free sulfhydryl groups of endogenous or introduced point mutation cysteines. If a cysteine is found in the binding pocket, the covalent modification will affect the binding kinetics of the ligand. MTSEA substantially decreased the binding affinity of L197C-AT(1), N200C-AT(1), I201C-AT(1), G203C-AT(1), and F204C-AT(1) mutant receptors, which suggests that these residues orient themselves within the water-accessible binding pocket of the AT(1) receptor. Interestingly, this pattern of acquired MTSEA sensitivity was altered for TMD5 reporter cysteines engineered in a constitutively active N111G-AT(1) receptor background. Indeed, mutant I201C-N111G-AT(1) became more sensitive to MTSEA, whereas mutant G203C-N111G-AT(1) lost some sensitivity. Our results suggest that constitutive activation of AT(1) receptor causes an apparent counterclockwise rotation of TMD5 as viewed from the extracellular side.
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Affiliation(s)
- Ivana Domazet
- Department of Pharmacology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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50
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Clément M, Cabana J, Holleran BJ, Leduc R, Guillemette G, Lavigne P, Escher E. Activation induces structural changes in the liganded angiotensin II type 1 receptor. J Biol Chem 2009; 284:26603-12. [PMID: 19635801 DOI: 10.1074/jbc.m109.012922] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The octapeptide hormone angiotensin II (AngII) binds to and activates the human angiotensin II type 1 receptor (hAT(1)) of the G protein-coupled receptor class A family. Several activation mechanisms have been proposed for this family, but they have not yet been experimentally validated. We previously used the methionine proximity assay to show that 11 residues in transmembrane domain (TMD) III, VI, and VII of the hAT(1) receptor reside in close proximity to the C-terminal residue of AngII. With the exception of a single change in TMD VI, the same contacts are present on N111G-hAT(1), a constitutively active mutant; this N111G-hAT(1) is a model for the active form of the receptor. In this study, two series of 53 individual methionine mutations were constructed in TMD I, II, IV, and V on both receptor forms. The mutants were photolabeled with a neutral antagonist, (125)I-[Sar(1),p-benzoyl-L-Phe(8)]AngII, and the resulting complexes were digested with cyanogen bromide. Although no new contacts were found for the hAT(1) mutants, two were found in the constitutively active mutants, Phe-77 in TMD II and Asn-200 in TMD V. To our knowledge, this is the first time that a direct ligand contact with TMD II and TMD V has been reported. These contact point differences were used to identify the structural changes between the WT-hAT(1) and N111G-hAT(1) complexes through homology-based modeling and restrained molecular dynamics. The model generated revealed an important structural rearrangement of several TMDs from the basal to the activated form in the WT-hAT(1) receptor.
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Affiliation(s)
- Martin Clément
- Department of Pharmacology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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