1
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Zhao J, Elgeti M, O'Brien ES, Sár CP, Ei Daibani A, Heng J, Sun X, White E, Che T, Hubbell WL, Kobilka BK, Chen C. Ligand efficacy modulates conformational dynamics of the µ-opioid receptor. Nature 2024; 629:474-480. [PMID: 38600384 PMCID: PMC11078757 DOI: 10.1038/s41586-024-07295-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
The µ-opioid receptor (µOR) is an important target for pain management1 and molecular understanding of drug action on µOR will facilitate the development of better therapeutics. Here we show, using double electron-electron resonance and single-molecule fluorescence resonance energy transfer, how ligand-specific conformational changes of µOR translate into a broad range of intrinsic efficacies at the transducer level. We identify several conformations of the cytoplasmic face of the receptor that interconvert on different timescales, including a pre-activated conformation that is capable of G-protein binding, and a fully activated conformation that markedly reduces GDP affinity within the ternary complex. Interaction of β-arrestin-1 with the μOR core binding site appears less specific and occurs with much lower affinity than binding of Gi.
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Affiliation(s)
- Jiawei Zhao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Matthias Elgeti
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Drug Discovery, University of Leipzig Medical Center, Leipzig, Germany.
| | - Evan S O'Brien
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cecília P Sár
- Institute of Organic and Medicinal Chemistry, School of Pharmaceutical Sciences, University of Pécs, Pécs, Hungary
| | - Amal Ei Daibani
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
| | - Jie Heng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaoou Sun
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Elizabeth White
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tao Che
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Chunlai Chen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.
- School of Life Sciences, Tsinghua University, Beijing, China.
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2
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Kish M, Ivory DP, Phillips JJ. Transient Structural Dynamics of Glycogen Phosphorylase from Nonequilibrium Hydrogen/Deuterium-Exchange Mass Spectrometry. J Am Chem Soc 2024; 146:298-307. [PMID: 38158228 PMCID: PMC10786028 DOI: 10.1021/jacs.3c08934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
It remains a major challenge to ascertain the specific structurally dynamic changes that underpin protein functional switching. There is a growing need in molecular biology and drug discovery to complement structural models with the ability to determine the dynamic structural changes that occur as these proteins are regulated and function. The archetypal allosteric enzyme glycogen phosphorylase is a clinical target of great interest to treat type II diabetes and metastatic cancers. Here, we developed a time-resolved nonequilibrium millisecond hydrogen/deuterium-exchange mass spectrometry (HDX-MS) approach capable of precisely locating dynamic structural changes during allosteric activation and inhibition of glycogen phosphorylase. We resolved obligate transient changes in the localized structure that are absent when directly comparing active/inactive states of the enzyme and show that they are common to allosteric activation by AMP and inhibition by caffeine, operating at different sites. This indicates that opposing allosteric regulation by inhibitor and activator ligands is mediated by pathways that intersect with a common structurally dynamic motif. This mass spectrometry approach uniquely stands to discover local transient structural dynamics and could be used broadly to identify features that influence the structural transitions of proteins.
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Affiliation(s)
- Monika Kish
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
| | - Dylan P. Ivory
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
| | - Jonathan J. Phillips
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
- Alan
Turing Institute, British Library, London NW1 2DB, U.K.
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3
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Schafer CT, Pauszek III RF, Gustavsson M, Handel TM, Millar DP. Distinct Activation Mechanisms of CXCR4 and ACKR3 Revealed by Single-Molecule Analysis of their Conformational Landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564925. [PMID: 37961571 PMCID: PMC10635023 DOI: 10.1101/2023.10.31.564925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Canonical chemokine receptor CXCR4 and atypical receptor ACKR3 both respond to CXCL12 but induce different intracellular effector responses to regulate cell migration: CXCR4 couples to G proteins and arrestins, while ACKR3 is arrestin-biased. CXCR4 also signals only in response to CXCL12, whereas ACKR3 recruits β-arrestin in response to CXCL12, CXCL12 variants, and other peptides and proteins. To investigate the role of conformational dynamics in the distinct pharmacological behaviors of CXCR4 and ACKR3, we utilized single-molecule FRET. The data revealed that apo CXCR4 preferentially populates a high-FRET inactive state while apo ACKR3 shows little conformational preference, consistent with its promiscuous ligand recognition and propensity for activation. Markedly different conformational landscapes of the receptors in response to ligands suggest that activation of ACKR3 may be achieved by a broader distribution of conformational states than CXCR4. The dynamic properties of ACKR3 may also underly its inability to couple to G proteins, making it arrestin-biased.
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Affiliation(s)
- Christopher T. Schafer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmacology, University of California San Diego, La Jolla, CA 92037
| | - Raymond F. Pauszek III
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmacology, University of California San Diego, La Jolla, CA 92037
| | - Tracy M. Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmacology, University of California San Diego, La Jolla, CA 92037
| | - David P. Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
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4
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Sadee W. Ligand-Free Signaling of G-Protein-Coupled Receptors: Physiology, Pharmacology, and Genetics. Molecules 2023; 28:6375. [PMID: 37687205 PMCID: PMC10489045 DOI: 10.3390/molecules28176375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are ubiquitous sensors and regulators of cellular functions. Each GPCR exists in complex aggregates with multiple resting and active conformations. Designed to detect weak stimuli, GPCRs can also activate spontaneously, resulting in basal ligand-free signaling. Agonists trigger a cascade of events leading to an activated agonist-receptor G-protein complex with high agonist affinity. However, the ensuing signaling process can further remodel the receptor complex to reduce agonist affinity, causing rapid ligand dissociation. The acutely activated ligand-free receptor can continue signaling, as proposed for rhodopsin and μ opioid receptors, resulting in robust receptor activation at low agonist occupancy with enhanced agonist potency. Continued receptor stimulation can further modify the receptor complex, regulating sustained ligand-free signaling-proposed to play a role in opioid dependence. Basal, acutely agonist-triggered, and sustained elevated ligand-free signaling could each have distinct functions, reflecting multi-state conformations of GPCRs. This review addresses basal and stimulus-activated ligand-free signaling, its regulation, genetic factors, and pharmacological implications, focusing on opioid and serotonin receptors, and the growth hormone secretagogue receptor (GHSR). The hypothesis is proposed that ligand-free signaling of 5-HT2A receptors mediate therapeutic effects of psychedelic drugs. Research avenues are suggested to close the gaps in our knowledge of ligand-free GPCR signaling.
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Affiliation(s)
- Wolfgang Sadee
- Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- Aether Therapeutics Inc., Austin, TX 78756, USA
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5
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Wygas MM, Laugwitz JM, Schmidt P, Elgeti M, Kaiser A. Dynamics of the Second Extracellular Loop Control Transducer Coupling of Peptide-Activated GPCRs. Int J Mol Sci 2023; 24:12197. [PMID: 37569573 PMCID: PMC10419011 DOI: 10.3390/ijms241512197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Many peptide-activated rhodopsin-like GPCRs share a β-hairpin folding motif in the extracellular loop 2 (ECL2), which interacts with the peptide ligand while at the same time being connected to transmembrane helix 3 (TM3) via a highly conserved disulfide bond. Currently, it remains unknown whether the coupling of the specifically shaped ECL2 to TM3 influences the activation of peptide-activated GPCRs. We investigated this possibility in a selection of peptide GPCRs with known structures. Most of the receptors with cysteine to alanine mutations folded like the respective wild-type and resided in the cell membrane, challenging pure folding stabilization by the disulfide bridge. G-protein signaling of the disulfide mutants was retained to a greater extent in secretin-like GPCRs than in rhodopsin-like GPCRs, while recruitment of arrestin was completely abolished in both groups, which may be linked to alterations in ligand residence time. We found a correlation between receptor activity of the neuropeptide Y2 receptor and alterations in ECL2 dynamics using engineered disulfide bridges or site-directed spin labeling and EPR spectroscopy. These data highlight the functional importance of the TM3-ECL2 link for the activation of specific signaling pathways in peptide-activated GPCRs, which might have implications for future drug discovery.
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Affiliation(s)
- Marcel M. Wygas
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Jeannette M. Laugwitz
- Medical Faculty, Institute of Medical Physics and Biophysics, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
| | - Peter Schmidt
- Medical Faculty, Institute of Medical Physics and Biophysics, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
| | - Matthias Elgeti
- Medical Faculty, Institute of Medical Physics and Biophysics, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
- Medical Faculty, Institute for Drug Discovery, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
| | - Anette Kaiser
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
- Medical Faculty, Department of Anesthesiology and Intensive Care, Leipzig University, Liebigstrasse 19, 04103 Leipzig, Germany
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6
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Tessmer MH, Stoll S. chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling. PLoS Comput Biol 2023; 19:e1010834. [PMID: 37000838 PMCID: PMC10096462 DOI: 10.1371/journal.pcbi.1010834] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/12/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular double electron-electron resonance (DEER). It is based on in silico attachment of rotamer ensemble representations of spin labels to protein structures. chiLife enables the development of custom protein analysis and modeling pipelines using SDSL EPR experimental data. It allows the user to add custom spin labels, scoring functions and spin label modeling methods. chiLife is designed with integration into third-party software in mind, to take advantage of the diverse and rapidly expanding set of molecular modeling tools available with a Python interface. This article describes the main design principles of chiLife and presents a series of examples.
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Affiliation(s)
- Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
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7
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Quantitative analysis of sterol-modulated monomer-dimer equilibrium of the β 1-adrenergic receptor by DEER spectroscopy. Proc Natl Acad Sci U S A 2023; 120:e2221036120. [PMID: 36745787 PMCID: PMC9963004 DOI: 10.1073/pnas.2221036120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
G protein-coupled receptors (GPCR) activate numerous intracellular signaling pathways. The oligomerization properties of GPCRs, and hence their cellular functions, may be modulated by various components within the cell membrane (such as the presence of cholesterol). Modulation may occur directly via specific interaction with the GPCR or indirectly by affecting the physical properties of the membrane. Here, we use pulsed Q-band double electron-electron resonance (DEER) spectroscopy to probe distances between R1 nitroxide spin labels attached to Cys163 and Cys344 of the β1-adrenergic receptor (β1AR) in n-dodecyl-β-D-maltoside micelles upon titration with two soluble cholesterol analogs, cholesteryl hemisuccinate (CHS) and sodium cholate. The former, like cholesterol, inserts itself into the lipid membrane, parallel to the phospholipid chains; the latter is aligned parallel to the surface of membranes. Global quantitative analysis of DEER echo curves upon titration of spin-labeled β1AR with CHS and sodium cholate reveal the following: CHS binds specifically to the β1AR monomer at a site close to the Cys163-R1 spin label with an equilibrium dissociation constant [Formula: see text] ~1.4 ± 0.4 mM. While no direct binding of sodium cholate to the β1AR receptor was observed by DEER, sodium cholate induces specific β1AR dimerization ([Formula: see text] ~35 ± 6 mM and a Hill coefficient n ~ 2.5 ± 0.4) with intersubunit contacts between transmembrane helices 1 and 2 and helix 8. Analysis of the DEER data obtained upon the addition of CHS to the β1AR dimer in the presence of excess cholate results in dimer dissociation with species occupancies as predicted from the individual KD values.
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8
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Schmidt P, Vogel A, Schwarze B, Seufert F, Licha K, Wycisk V, Kilian W, Hildebrand PW, Mitschang L. Towards Probing Conformational States of Y2 Receptor Using Hyperpolarized 129Xe NMR. Molecules 2023; 28:molecules28031424. [PMID: 36771089 PMCID: PMC9919357 DOI: 10.3390/molecules28031424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
G protein-coupled receptors can adopt many different conformational states, each of them exhibiting different restraints towards downstream signaling pathways. One promising strategy to identify and quantify this conformational landscape is to introduce a cysteine at a receptor site sensitive to different states and label this cysteine with a probe for detection. Here, the application of NMR of hyperpolarized 129Xe for the detection of the conformational states of human neuropeptide Y2 receptor is introduced. The xenon trapping cage molecule cryptophane-A attached to a cysteine in extracellular loop 2 of the receptor facilitates chemical exchange saturation transfer experiments without and in the presence of native ligand neuropeptide Y. High-quality spectra indicative of structural states of the receptor-cage conjugate were obtained. Specifically, five signals could be assigned to the conjugate in the apo form. After the addition of NPY, one additional signal and subtle modifications in the persisting signals could be detected. The correlation of the spectroscopic signals and structural states was achieved with molecular dynamics simulations, suggesting frequent contact between the xenon trapping cage and the receptor surface but a preferred interaction with the bound ligand.
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Affiliation(s)
- Peter Schmidt
- Institute of Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Alexander Vogel
- Institute of Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Benedikt Schwarze
- Institute of Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Florian Seufert
- Institute of Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Kai Licha
- Institute of Chemistry and Biochemistry, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Virginia Wycisk
- Institute of Chemistry and Biochemistry, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Wolfgang Kilian
- Physikalisch-Technische Bundesanstalt Braunschweig und Berlin (PTB), Abbestrasse 2-12, 10587 Berlin, Germany
| | - Peter W. Hildebrand
- Institute of Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
| | - Lorenz Mitschang
- Physikalisch-Technische Bundesanstalt Braunschweig und Berlin (PTB), Abbestrasse 2-12, 10587 Berlin, Germany
- Correspondence:
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9
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Thermodynamic architecture and conformational plasticity of GPCRs. Nat Commun 2023; 14:128. [PMID: 36624096 PMCID: PMC9829892 DOI: 10.1038/s41467-023-35790-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are ubiquitous integral membrane proteins involved in diverse cellular signaling processes. Here, we carry out a large-scale ensemble thermodynamic study of 45 ligand-free GPCRs employing a structure-based statistical mechanical framework. We find that multiple partially structured states co-exist in the GPCR native ensemble, with the TM helices 1, 6 and 7 displaying varied folding status, and shaping the conformational landscape. Strongly coupled residues are anisotropically distributed, accounting for only 13% of the residues, illustrating that a large number of residues are inherently dynamic. Active-state GPCRs are characterized by reduced conformational heterogeneity with altered coupling-patterns distributed throughout the structural scaffold. In silico alanine-scanning mutagenesis reveals that extra- and intra-cellular faces of GPCRs are coupled thermodynamically, highlighting an exquisite structural specialization and the fluid nature of the intramolecular interaction network. The ensemble-based perturbation methodology presented here lays the foundation for understanding allosteric mechanisms and the effects of disease-causing mutations in GCPRs.
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10
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Insights into the Promising Prospect of G Protein and GPCR-Mediated Signaling in Neuropathophysiology and Its Therapeutic Regulation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8425640. [PMID: 36187336 PMCID: PMC9519337 DOI: 10.1155/2022/8425640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/23/2022] [Indexed: 11/18/2022]
Abstract
G protein-coupled receptors (GPCRs) are intricately involved in the conversion of extracellular feedback to intracellular responses. These specialized receptors possess a crucial role in neurological and psychiatric disorders. Most nonsensory GPCRs are active in almost 90% of complex brain functions. At the time of receptor phosphorylation, a GPCR pathway is essentially activated through a G protein signaling mechanism via a G protein-coupled receptor kinase (GRK). Dopamine, an important neurotransmitter, is primarily involved in the pathophysiology of several CNS disorders; for instance, bipolar disorder, schizophrenia, Parkinson's disease, and ADHD. Since dopamine, acetylcholine, and glutamate are potent neuropharmacological targets, dopamine itself has potential therapeutic effects in several CNS disorders. GPCRs essentially regulate brain functions by modulating downstream signaling pathways. GPR6, GPR52, and GPR8 are termed orphan GPCRs because they colocalize with dopamine D1 and D2 receptors in neurons of the basal ganglia, either alone or with both receptors. Among the orphan GPCRs, the GPR52 is recognized for being an effective psychiatric receptor. Various antipsychotics like aripiprazole and quetiapine mainly target GPCRs to exert their actions. One of the most important parts of signal transduction is the regulation of G protein signaling (RGS). These substances inhibit the activation of the G protein that initiates GPCR signaling. Developing a combination of RGS inhibitors with GPCR agonists may prove to have promising therapeutic potential. Indeed, several recent studies have suggested that GPCRs represent potentially valuable therapeutic targets for various psychiatric disorders. Molecular biology and genetically modified animal model studies recommend that these enriched GPCRs may also act as potential therapeutic psychoreceptors. Neurotransmitter and neuropeptide GPCR malfunction in the frontal cortex and limbic-related regions, including the hippocampus, hypothalamus, and brainstem, is likely responsible for the complex clinical picture that includes cognitive, perceptual, emotional, and motor symptoms. G protein and GPCR-mediated signaling play a critical role in developing new treatment options for mental health issues, and this study is aimed at offering a thorough picture of that involvement. For patients who are resistant to current therapies, the development of new drugs that target GPCR signaling cascades remains an interesting possibility. These discoveries might serve as a fresh foundation for the creation of creative methods for pharmacologically useful modulation of GPCR function.
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11
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Tessmer MH, Canarie ER, Stoll S. Comparative evaluation of spin-label modeling methods for protein structural studies. Biophys J 2022; 121:3508-3519. [PMID: 35957530 PMCID: PMC9515001 DOI: 10.1016/j.bpj.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Site-directed spin-labeling electron paramagnetic resonance spectroscopy is a powerful technique for the investigation of protein structure and dynamics. Accurate spin-label modeling methods are essential to make full quantitative use of site-directed spin-labeling electron paramagnetic resonance data for protein modeling and model validation. Using a set of double electron-electron resonance data from seven different site pairs on maltodextrin/maltose-binding protein under two different conditions using five different spin labels, we compare the ability of two widely used spin-label modeling methods, based on accessible volume sampling and rotamer libraries, to predict experimental distance distributions. We present a spin-label modeling approach inspired by canonical side-chain modeling methods and compare modeling accuracy with the established methods.
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Affiliation(s)
- Maxx H Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington
| | | | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington.
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12
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Seyedabadi M, Gharghabi M, Gurevich EV, Gurevich VV. Structural basis of GPCR coupling to distinct signal transducers: implications for biased signaling. Trends Biochem Sci 2022; 47:570-581. [PMID: 35396120 DOI: 10.1016/j.tibs.2022.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/10/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
Three classes of G-protein-coupled receptor (GPCR) partners - G proteins, GPCR kinases, and arrestins - preferentially bind active GPCRs. Our analysis suggests that the structures of GPCRs bound to these interaction partners available today do not reveal a clear conformational basis for signaling bias, which would have enabled the rational design of biased GRCR ligands. In view of this, three possibilities are conceivable: (i) there are no generalizable GPCR conformations conducive to binding a particular type of partner; (ii) subtle differences in the orientation of individual residues and/or their interactions not easily detectable in the receptor-transducer structures determine partner preference; or (iii) the dynamics of GPCR binding to different types of partners rather than the structures of the final complexes might underlie transducer bias.
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Affiliation(s)
- Mohammad Seyedabadi
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran; Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mehdi Gharghabi
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
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13
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Walke G, Aupič J, Kashoua H, Janoš P, Meron S, Shenberger Y, Qasem Z, Gevorkyan-Airapetov L, Magistrato A, Ruthstein S. Dynamical interplay between the human high-affinity copper transporter hCtr1 and its cognate metal ion. Biophys J 2022; 121:1194-1204. [PMID: 35202609 PMCID: PMC9034245 DOI: 10.1016/j.bpj.2022.02.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/12/2021] [Accepted: 02/17/2022] [Indexed: 11/02/2022] Open
Abstract
Abnormal cellular copper levels have been clearly implicated in genetic diseases, cancer, and neurodegeneration. Ctr1, a high affinity copper transporter, is an homotrimeric integral membrane protein that provides the main route for cellular copper uptake. Together with a sophisticated copper transport system, Ctr1 regulates Cu(I) metabolism in eukaryotes. Despite its pivotal role in normal cell function, the molecular mechanism of copper uptake and transport via Ctr1 remains elusive. In this study, electron paramagnetic resonance (EPR), UV-visible spectroscopy, and all-atom simulations were employed to explore Cu(I) binding to full-length human Ctr1 (hCtr1), thereby elucidating how metal binding at multiple distinct sites affects the hCtr1 conformational dynamics. We demonstrate that each hCtr1 monomer binds up to 5 Cu(I) ions and that progressive Cu(I) binding triggers a marked structural rearrangement in the hCtr1 C-terminal region. The observed Cu(I)-induced conformational remodelling suggests that the C-terminal region may play a dual role, serving both as a channel gate and as a shuttle mediating the delivery of Cu ions from the extracellular hCtr1 selectivity filter to intracellular metallochaperones. Our findings thus contribute to a more complete understanding of the mechanism of hCtr1-mediated Cu(I) uptake and provide a conceptual basis for developing mechanism-based therapeutics for treating pathological conditions linked to de-regulated copper metabolism.
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Affiliation(s)
- Gulshan Walke
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Jana Aupič
- Department National Research Council of Italy (CNR) - Institute of Material (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Hadeel Kashoua
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Pavel Janoš
- Department National Research Council of Italy (CNR) - Institute of Material (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Shelly Meron
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Yulia Shenberger
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Zena Qasem
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Alessandra Magistrato
- Department National Research Council of Italy (CNR) - Institute of Material (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy.
| | - Sharon Ruthstein
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002.
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Salas-Estrada L, Fiorillo B, Filizola M. Metadynamics simulations leveraged by statistical analyses and artificial intelligence-based tools to inform the discovery of G protein-coupled receptor ligands. Front Endocrinol (Lausanne) 2022; 13:1099715. [PMID: 36619585 PMCID: PMC9816996 DOI: 10.3389/fendo.2022.1099715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 12/25/2022] Open
Abstract
G Protein-Coupled Receptors (GPCRs) are a large family of membrane proteins with pluridimensional signaling profiles. They undergo ligand-specific conformational changes, which in turn lead to the differential activation of intracellular signaling proteins and the consequent triggering of a variety of biological responses. This conformational plasticity directly impacts our understanding of GPCR signaling and therapeutic implications, as do ligand-specific kinetic differences in GPCR-induced transducer activation/coupling or GPCR-transducer complex stability. High-resolution experimental structures of ligand-bound GPCRs in the presence or absence of interacting transducers provide important, yet limited, insights into the highly dynamic process of ligand-induced activation or inhibition of these receptors. We and others have complemented these studies with computational strategies aimed at characterizing increasingly accurate metastable conformations of GPCRs using a combination of metadynamics simulations, state-of-the-art algorithms for statistical analyses of simulation data, and artificial intelligence-based tools. This minireview provides an overview of these approaches as well as lessons learned from them towards the identification of conformational states that may be difficult or even impossible to characterize experimentally and yet important to discover new GPCR ligands.
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Abrol R, Serrano E, Santiago LJ. Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:325-359. [PMID: 35034722 DOI: 10.1016/bs.apcsb.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
G protein-coupled receptors (GPCRs) make up the largest superfamily of integral membrane proteins and play critical signal transduction roles in many physiological processes. Developments in molecular biology, biophysical, biochemical, pharmacological, and computational techniques aimed at these important therapeutic targets are beginning to provide unprecedented details on the structural as well as functional basis of their pleiotropic signaling mediated by G proteins, β arrestins, and other transducers. This pleiotropy presents a pharmacological challenge as the same ligand-receptor interaction can cause a therapeutic effect as well as an undesirable on-target side-effect through different downstream pathways. GPCRs don't function as simple binary on-off switches but as finely tuned shape-shifting machines described by conformational ensembles, where unique subsets of conformations may be responsible for specific signaling cascades. X-ray crystallography and more recently cryo-electron microscopy are providing snapshots of some of these functionally-important receptor conformations bound to ligands and/or transducers, which are being utilized by computational methods to describe the dynamic conformational energy landscape of GPCRs. In this chapter, we review the progress in computational conformational sampling methods based on molecular dynamics and discrete sampling approaches that have been successful in complementing biophysical and biochemical studies on these receptors in terms of their activation mechanisms, allosteric effects, actions of biased ligands, and effects of pathological mutations. Some of the sampled simulation time scales are beginning to approach receptor activation time scales. The list of conformational sampling methods and example uses discussed is not exhaustive but includes representative examples that have pushed the limits of classical molecular dynamics and discrete sampling methods to describe the activation energy landscape of GPCRs.
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Affiliation(s)
- Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States.
| | - Erik Serrano
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States
| | - Luis Jaimes Santiago
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States
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Hustedt EJ, Stein RA, Mchaourab HS. Protein functional dynamics from the rigorous global analysis of DEER data: Conditions, components, and conformations. J Gen Physiol 2021; 153:212643. [PMID: 34529007 PMCID: PMC8449309 DOI: 10.1085/jgp.201711954] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 08/30/2021] [Indexed: 01/03/2023] Open
Abstract
The potential of spin labeling to reveal the dynamic dimension of macromolecules has been recognized since the dawn of the methodology in the 1960s. However, it was the development of pulsed electron paramagnetic resonance spectroscopy to detect dipolar coupling between spin labels and the availability of turnkey instrumentation in the 21st century that realized the full promise of spin labeling. Double electron-electron resonance (DEER) spectroscopy has seen widespread applications to channels, transporters, and receptors. In these studies, distance distributions between pairs of spin labels obtained under different biochemical conditions report the conformational states of macromolecules, illuminating the key movements underlying biological function. These experimental studies have spurred the development of methods for the rigorous analysis of DEER spectroscopic data along with methods for integrating these distributions into structural models. In this tutorial, we describe a model-based approach to obtaining a minimum set of components of the distance distribution that correspond to functionally relevant protein conformations with a set of fractional amplitudes that define the equilibrium between these conformations. Importantly, we review and elaborate on the error analysis reflecting the uncertainty in the various parameters, a critical step in rigorous structural interpretation of the spectroscopic data.
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Affiliation(s)
- Eric J Hustedt
- Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Richard A Stein
- Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Hassane S Mchaourab
- Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
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Electron paramagnetic resonance spectroscopy on G-protein-coupled receptors: Adopting strategies from related model systems. Curr Opin Struct Biol 2021; 69:177-186. [PMID: 34304006 DOI: 10.1016/j.sbi.2021.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/23/2022]
Abstract
Membrane proteins, including ion channels, transporters and G-protein-coupled receptors (GPCRs), play a significant role in various physiological processes. Many of these proteins are difficult to express in large quantities, imposing crucial experimental restrictions. Nevertheless, there is now a wide variety of studies available utilizing electron paramagnetic resonance (EPR) spectroscopic techniques that expand experimental accessibility by using relatively small quantities of protein. Here, we give an overview starting from basic strategies in EPR on membrane proteins with a focus on GPCRs, while emphasizing several applications from recent years. We highlight how the arsenal of EPR-based techniques may provide significant further contributions to understanding the complex molecular machinery and energetic phenomena responsible for seamless workflow in essential biological processes.
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