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Tauber M, Ben-Chaim Y. Voltage Sensors Embedded in G Protein-Coupled Receptors. Int J Mol Sci 2024; 25:5295. [PMID: 38791333 PMCID: PMC11120775 DOI: 10.3390/ijms25105295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Some signaling processes mediated by G protein-coupled receptors (GPCRs) are modulated by membrane potential. In recent years, increasing evidence that GPCRs are intrinsically voltage-dependent has accumulated. A recent publication challenged the view that voltage sensors are embedded in muscarinic receptors. Herein, we briefly discuss the evidence that supports the notion that GPCRs themselves are voltage-sensitive proteins and an alternative mechanism that suggests that voltage-gated sodium channels are the voltage-sensing molecules involved in such processes.
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Affiliation(s)
| | - Yair Ben-Chaim
- Department of Natural Sciences, The Open University of Israel, Ra’anana 4353701, Israel
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2
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Girych M, Kulig W, Enkavi G, Vattulainen I. How Neuromembrane Lipids Modulate Membrane Proteins: Insights from G-Protein-Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Cold Spring Harb Perspect Biol 2023; 15:a041419. [PMID: 37487628 PMCID: PMC10547395 DOI: 10.1101/cshperspect.a041419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Lipids play a diverse and critical role in cellular processes in all tissues. The unique lipid composition of nerve membranes is particularly interesting because it contains, among other things, polyunsaturated lipids, such as docosahexaenoic acid, which the body only gets through the diet. The crucial role of lipids in neurological processes, especially in receptor-mediated cell signaling, is emphasized by the fact that in many neuropathological diseases there are significant deviations in the lipid composition of nerve membranes compared to healthy individuals. The lipid composition of neuromembranes can significantly affect the function of receptors by regulating the physical properties of the membrane or by affecting specific interactions between receptors and lipids. In addition, it is worth noting that the ligand-binding pocket of many receptors is located inside the cell membrane, due to which lipids can even modulate the binding of ligands to their receptors. These mechanisms highlight the importance of lipids in the regulation of membrane receptor activation and function. In this article, we focus on two major protein families: G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs) and discuss how lipids affect their function in neuronal membranes, elucidating the basic mechanisms underlying neuronal function and dysfunction.
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Affiliation(s)
- Mykhailo Girych
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
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3
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Kostritskii AY, Machtens JP. Domain- and state-specific shape of the electric field tunes voltage sensing in voltage-gated sodium channels. Biophys J 2023; 122:1807-1821. [PMID: 37077046 PMCID: PMC10209041 DOI: 10.1016/j.bpj.2023.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023] Open
Abstract
The ability to sense transmembrane voltage underlies most physiological roles of voltage-gated sodium (Nav) channels. Whereas the key role of their voltage-sensing domains (VSDs) in channel activation is well established, the molecular underpinnings of voltage coupling remain incompletely understood. Voltage-dependent energetics of the activation process can be described in terms of the gating charge that is defined by coupling of charged residues to the external electric field. The shape of the electric field within VSDs is therefore crucial for the activation of voltage-gated ion channels. Here, we employed molecular dynamics simulations of cardiac Nav1.5 and bacterial NavAb, together with our recently developed tool g_elpot, to gain insights into the voltage-sensing mechanisms of Nav channels via high-resolution quantification of VSD electrostatics. In contrast to earlier low-resolution studies, we found that the electric field within VSDs of Nav channels has a complex isoform- and domain-specific shape, which prominently depends on the activation state of a VSD. Different VSDs vary not only in the length of the region where the electric field is focused but also differ in their overall electrostatics, with possible implications in the diverse ion selectivity of their gating pores. Due to state-dependent field reshaping, not only translocated basic but also relatively immobile acidic residues contribute significantly to the gating charge. In the case of NavAb, we found that the transition between structurally resolved activated and resting states results in a gating charge of 8e, which is noticeably lower than experimental estimates. Based on the analysis of VSD electrostatics in the two activation states, we propose that the VSD likely adopts a deeper resting state upon hyperpolarization. In conclusion, our results provide an atomic-level description of the gating charge, demonstrate diversity in VSD electrostatics, and reveal the importance of electric-field reshaping for voltage sensing in Nav channels.
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Affiliation(s)
- Andrei Y Kostritskii
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany; Institute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany.
| | - Jan-Philipp Machtens
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany; Institute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany.
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4
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Li Z, Liu J, Dong F, Chang N, Huang R, Xia M, Patterson TA, Hong H. Three-Dimensional Structural Insights Have Revealed the Distinct Binding Interactions of Agonists, Partial Agonists, and Antagonists with the µ Opioid Receptor. Int J Mol Sci 2023; 24:ijms24087042. [PMID: 37108204 PMCID: PMC10138646 DOI: 10.3390/ijms24087042] [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] [Received: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
The United States is experiencing the most profound and devastating opioid crisis in history, with the number of deaths involving opioids, including prescription and illegal opioids, continuing to climb over the past two decades. This severe public health issue is difficult to combat as opioids remain a crucial treatment for pain, and at the same time, they are also highly addictive. Opioids act on the opioid receptor, which in turn activates its downstream signaling pathway that eventually leads to an analgesic effect. Among the four types of opioid receptors, the µ subtype is primarily responsible for the analgesic cascade. This review describes available 3D structures of the µ opioid receptor in the protein data bank and provides structural insights for the binding of agonists and antagonists to the receptor. Comparative analysis on the atomic details of the binding site in these structures was conducted and distinct binding interactions for agonists, partial agonists, and antagonists were observed. The findings in this article deepen our understanding of the ligand binding activity and shed some light on the development of novel opioid analgesics which may improve the risk benefit balance of existing opioids.
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Affiliation(s)
- Zoe Li
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Jie Liu
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Fan Dong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Nancy Chang
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tucker A Patterson
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
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5
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Shpakov AO. Allosteric Regulation of G-Protein-Coupled Receptors: From Diversity of Molecular Mechanisms to Multiple Allosteric Sites and Their Ligands. Int J Mol Sci 2023; 24:6187. [PMID: 37047169 PMCID: PMC10094638 DOI: 10.3390/ijms24076187] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Allosteric regulation is critical for the functioning of G protein-coupled receptors (GPCRs) and their signaling pathways. Endogenous allosteric regulators of GPCRs are simple ions, various biomolecules, and protein components of GPCR signaling (G proteins and β-arrestins). The stability and functional activity of GPCR complexes is also due to multicenter allosteric interactions between protomers. The complexity of allosteric effects caused by numerous regulators differing in structure, availability, and mechanisms of action predetermines the multiplicity and different topology of allosteric sites in GPCRs. These sites can be localized in extracellular loops; inside the transmembrane tunnel and in its upper and lower vestibules; in cytoplasmic loops; and on the outer, membrane-contacting surface of the transmembrane domain. They are involved in the regulation of basal and orthosteric agonist-stimulated receptor activity, biased agonism, GPCR-complex formation, and endocytosis. They are targets for a large number of synthetic allosteric regulators and modulators, including those constructed using molecular docking. The review is devoted to the principles and mechanisms of GPCRs allosteric regulation, the multiplicity of allosteric sites and their topology, and the endogenous and synthetic allosteric regulators, including autoantibodies and pepducins. The allosteric regulation of chemokine receptors, proteinase-activated receptors, thyroid-stimulating and luteinizing hormone receptors, and beta-adrenergic receptors are described in more detail.
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Affiliation(s)
- Alexander O Shpakov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 194223 St. Petersburg, Russia
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6
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Davies A, Tomas A. Appreciating the potential for GPCR crosstalk with ion channels. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 195:101-120. [PMID: 36707150 DOI: 10.1016/bs.pmbts.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
G protein-coupled receptors (GPCRs) are expressed by most tissues in the body and are exploited pharmacologically in a variety of pathological conditions including diabetes, cardiovascular disease, neurological diseases, and cancers. Numerous cell signaling pathways can be regulated by GPCR activation, depending on the specific GPCR, ligand and cell type. Ion channels are among the many effector proteins downstream of these signaling pathways. Saliently, ion channels are also recognized as druggable targets, and there is evidence that their activity may regulate GPCR function via membrane potential and cytoplasmic ion concentration. Overall, there appears to be a large potential for crosstalk between ion channels and GPCRs. This might have implications not only for targeting GPCRs for drug development, but also opens the possibility of co-targeting them with ion channels to achieve improved therapeutic outcomes. In this review, we highlight the large variety of possible GPCR-ion channel crosstalk modes.
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Affiliation(s)
- Amy Davies
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom.
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7
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David D, Bentulila Z, Tauber M, Ben-Chaim Y. G Protein-Coupled Receptors Regulated by Membrane Potential. Int J Mol Sci 2022; 23:ijms232213988. [PMID: 36430466 PMCID: PMC9696401 DOI: 10.3390/ijms232213988] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are involved in a vast majority of signal transduction processes. Although they span the cell membrane, they have not been considered to be regulated by the membrane potential. Numerous studies over the last two decades have demonstrated that several GPCRs, including muscarinic, adrenergic, dopaminergic, and glutamatergic receptors, are voltage regulated. Following these observations, an effort was made to elucidate the molecular basis for this regulatory effect. In this review, we will describe the advances in understanding the voltage dependence of GPCRs, the suggested molecular mechanisms that underlie this phenomenon, and the possible physiological roles that it may play.
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Goldberger E, Tauber M, Ben-Chaim Y. Voltage dependence of the cannabinoid CB1 receptor. Front Pharmacol 2022; 13:1022275. [PMID: 36304142 PMCID: PMC9592857 DOI: 10.3389/fphar.2022.1022275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Cannabinoids produce their characteristic effects mainly by binding to two types of G-protein coupled receptors (GPCRs), the CB1 and CB2 cannabinoid receptors. The CB1 receptor is the main cannabinoid receptor in the central nervous system, and it participates in many brain functions. Recent studies showed that membrane potential may serve as a novel modulatory modality of many GPCRs. Here, we used Xenopus oocytes as an expression system to examine whether membrane potential modulates the activity of the CB1 receptor. We found that the potencies of the endocannabinoid 2-AG and the phytocannabinoid THC in activating the receptor are voltage dependent; depolarization enhanced the potency of these agonists and decreased their dissociation from the receptor. This voltage dependence appears to be agonist dependent as the potency of the endocannabinoid anandamide (AEA) was voltage independent. The finding of this agonist-specific modulatory factor for the CB1 receptor may contribute to our future understanding of various physiological functions mediated by the endocannabinoid system.
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9
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Tauber M, Ben Chaim Y. The activity of the serotonergic 5-HT 1A receptor is modulated by voltage and sodium levels. J Biol Chem 2022; 298:101978. [PMID: 35469922 PMCID: PMC9136116 DOI: 10.1016/j.jbc.2022.101978] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/16/2022] [Accepted: 04/20/2022] [Indexed: 11/28/2022] Open
Abstract
G protein–coupled receptors are known to play a key role in many cellular signal transduction processes, including those mediating serotonergic signaling in the nervous system. Several factors have been shown to regulate the activity of these receptors, including membrane potential and the concentration of sodium ions. Whether voltage and sodium regulate the activity of serotonergic receptors is unknown. Here, we used Xenopus oocytes as an expression system to examine the effects of voltage and of sodium ions on the potency of one subtype of serotonin (5-hydroxytryptamine [5-HT]) receptor, the 5-HT1A receptor. We found that the potency of 5-HT in activating the receptor is voltage dependent and that it is higher at resting potential than under depolarized conditions. Furthermore, we found that removal of extracellular Na+ resulted in a decrease of 5-HT potency toward the 5-HT1A receptor and that a conserved aspartate in transmembrane domain 2 is crucial for this effect. Our results suggest that this allosteric effect of Na+ does not underlie the voltage dependence of this receptor. We propose that the characterization of modulatory factors that regulate this receptor may contribute to our future understanding of various physiological functions mediated by serotonergic transmission.
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Affiliation(s)
- Merav Tauber
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - Yair Ben Chaim
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel.
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10
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Ben Boubaker R, Tiss A, Henrion D, Guissouma H, Chabbert M. Evolutionary information helps understand distinctive features of the angiotensin II receptors AT1 and AT2 in amniota. PLoS Comput Biol 2022; 18:e1009732. [PMID: 35202400 PMCID: PMC8870451 DOI: 10.1371/journal.pcbi.1009732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/08/2021] [Indexed: 11/19/2022] Open
Abstract
In vertebrates, the octopeptide angiotensin II (AngII) is an important in vivo regulator of the cardiovascular system. It acts mainly through two G protein-coupled receptors, AT1 and AT2. To better understand distinctive features of these receptors, we carried out a phylogenetic analysis that revealed a mirror evolution of AT1 and AT2, each one split into two clades, separating fish from terrestrial receptors. It also revealed that hallmark mutations occurred at, or near, the sodium binding site in both AT1 and AT2. Electrostatics computations and molecular dynamics simulations support maintained sodium binding to human AT1 with slow ingress from the extracellular side and an electrostatic component of the binding free energy around -3kT, to be compared to around -2kT for human AT2 and the δ opioid receptor. Comparison of the sodium binding modes in wild type and mutated AT1 and AT2 from humans and eels indicates that the allosteric control by sodium in both AT1 and AT2 evolved during the transition from fish to amniota. The unusual S7.46N mutation in AT1 is mirrored by a L3.36M mutation in AT2. In the presence of sodium, the N7.46 pattern in amniota AT1 stabilizes the inward orientation of N3.35 in the apo receptor, which should contribute to efficient N3.35 driven biased signaling. The M3.36 pattern in amniota AT2 favours the outward orientation of N3.35 and the receptor promiscuity. Both mutations have physiological consequences for the regulation of the renin-angiotensin system. The analysis of protein sequences from different species can reveal interesting trends in the structural and functional evolution of a protein family. Here, we analyze the evolution of two G protein-coupled receptors, AT1 and AT2, which bind the angiotensin II peptide and are important regulators of the cardiovascular system. We show that these receptors underwent a mirror evolution. Specific mutations at, or near, the sodium binding pocket occurred in both AT1 and AT2 during the transition to terrestrial life. We carried out electrostatics computations and molecular dynamics simulations to decipher the details of the sodium binding mode in eel and human receptors, as prototypes of fish and amniota receptors. Our results indicate that sodium binding is kinetically slow but thermodynamically stable. Comparison of the sodium binding modes in eel and human receptors reveals that an unusual mutation in the sodium binding pocket of AT1 is critical for biased signaling of amniota AT1 whereas a mutation in AT2 promotes promiscuity of amniota AT2. In turn, these data indicate that a few mutations at a strategic position (here the sodium binding pocket) are an efficient way to gain functional evolution.
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Affiliation(s)
- Rym Ben Boubaker
- CNRS UMR 6015 – INSERM U1083, Laboratoire MITOVASC, Université d’Angers, Angers, France
| | - Asma Tiss
- CNRS UMR 6015 – INSERM U1083, Laboratoire MITOVASC, Université d’Angers, Angers, France
- INSAT de Tunis, Université de Carthage, Carthage, Tunisie
| | - Daniel Henrion
- CNRS UMR 6015 – INSERM U1083, Laboratoire MITOVASC, Université d’Angers, Angers, France
| | | | - Marie Chabbert
- CNRS UMR 6015 – INSERM U1083, Laboratoire MITOVASC, Université d’Angers, Angers, France
- * E-mail:
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11
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Dutta S, Selvam B, Shukla D. Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid Receptors. ACS Chem Neurosci 2022; 13:379-389. [PMID: 35019279 DOI: 10.1021/acschemneuro.1c00760] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The therapeutic potential of cannabinoid receptors is not fully explored due to psychoactive side effects and lack of selectivity associated with orthosteric ligands. Allosteric modulators have the potential to become selective therapeutics for cannabinoid receptors. Biochemical experiments have shown the effects of the allosteric Na+ binding on cannabinoid receptor activity. However, the Na+ coordination site and binding pathway are still unknown. Here, we perform molecular dynamic simulations to explore Na+ binding in the cannabinoid receptors, CB1 and CB2. Simulations reveal that Na+ binds to the primary binding site from different extracellular sites for CB1 and CB2. A distinct secondary Na+ coordination site is identified in CB1 that is not present in CB2. Furthermore, simulations also show that intracellular Na+ could bind to the Na+ binding site in CB1. Constructed Markov state models show that the standard free energy of Na+ binding is similar to the previously calculated free energy for other class A GPCRs.
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Affiliation(s)
- Soumajit Dutta
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Balaji Selvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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12
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Conrad M, Söldner CA, Sticht H. Effect of Ions and Sequence Variants on the Antagonist Binding Properties of the Histamine H 1 Receptor. Int J Mol Sci 2022; 23:ijms23031420. [PMID: 35163341 PMCID: PMC8836275 DOI: 10.3390/ijms23031420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022] Open
Abstract
The histamine H1 receptor (H1R) is a G protein-coupled receptor (GPCR) and represents a main target in the treatment of allergic reactions as well as inflammatory reactions and depressions. Although the overall effect of antagonists on H1 function has been extensively investigated, rather little is known about the potential modulatory effect of ions or sequence variants on antagonist binding. We investigated the dynamics of a phosphate ion present in the crystal structure and of a sodium ion, for which we determined the position in the allosteric pocket by metadynamics simulations. Both types of ions exhibit significant dynamics within their binding site; however, some key contacts remain stable over the simulation time, which might be exploited to develop more potent drugs targeting these sites. The dynamics of the ions is almost unaffected by the presence or absence of doxepin, as also reflected in their small effect (less than 1 kcal·mol-1) on doxepin binding affinity. We also examined the effect of four H1R sequence variants observed in the human population on doxepin binding. These variants cause a reduction in doxepin affinity of up to 2.5 kcal·mol-1, indicating that personalized medical treatments that take into account individual mutation patterns could increase precision in the dosage of GPCR-targeting drugs.
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Affiliation(s)
- Marcus Conrad
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (C.A.S.)
| | - Christian A. Söldner
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (C.A.S.)
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (C.A.S.)
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
- Correspondence:
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13
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Ozkan AD, Gettas T, Sogata A, Phaychanpheng W, Zhou M, Lacroix JJ. Mechanical and chemical activation of GPR68 probed with a genetically encoded fluorescent reporter. J Cell Sci 2021; 134:271846. [PMID: 34322699 DOI: 10.1242/jcs.255455] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 07/17/2021] [Indexed: 12/24/2022] Open
Abstract
G-protein-coupled receptor (GPCR) 68 (GPR68, or OGR1) couples extracellular acidifications and mechanical stimuli to G-protein signaling and plays important roles in vascular physiology, neuroplasticity and cancer progression. Inspired by previous GPCR-based reporters, here, we inserted a cyclic permuted fluorescent protein into the third intracellular loop of GPR68 to create a genetically encoded fluorescent reporter of GPR68 activation we call 'iGlow'. iGlow responds to known physiological GPR68 activators such as fluid shear stress and extracellular acidifications. In addition, iGlow responds to Ogerin, a synthetic GPR68-selective agonist, but not to a non-active Ogerin analog, showing the specificity of iGlow-mediated fluorescence signals. Flow-induced iGlow activation is not eliminated by pharmacological modulation of downstream G-protein signaling, disruption of actin filaments or application of GsMTx4, an inhibitor of certain mechanosensitive ion channels activated by membrane stretch. Deletion of the conserved helix 8, proposed to mediate mechanosensitivity in certain GPCRs, does not eliminate flow-induced iGlow activation. iGlow could be useful to investigate the contribution of GPR68-dependent signaling in health and disease.
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Affiliation(s)
- Alper D Ozkan
- Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 E. Second St, Pomona, CA 91766, USA
| | - Tina Gettas
- Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 E. Second St, Pomona, CA 91766, USA
| | - Audrey Sogata
- Chino Hills High School, 16150 Pomona Rincon Rd, Chino Hills, CA 91709, USA
| | - Wynn Phaychanpheng
- Chino Hills High School, 16150 Pomona Rincon Rd, Chino Hills, CA 91709, USA
| | - Miou Zhou
- Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 E. Second St, Pomona, CA 91766, USA
| | - Jérôme J Lacroix
- Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 E. Second St, Pomona, CA 91766, USA
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14
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Bockaert J, Perroy J, Ango F. The Complex Formed by Group I Metabotropic Glutamate Receptor (mGluR) and Homer1a Plays a Central Role in Metaplasticity and Homeostatic Synaptic Scaling. J Neurosci 2021; 41:5567-5578. [PMID: 34193623 PMCID: PMC8244974 DOI: 10.1523/jneurosci.0026-21.2021] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/28/2022] Open
Abstract
G-protein-coupled receptors can be constitutively activated following physical interaction with intracellular proteins. The first example described was the constitutive activation of Group I metabotropic glutamate receptors (mGluR: mGluR1,5) following their interaction with Homer1a, an activity-inducible early-termination variant of the scaffolding protein Homer that lacks dimerization capacity (Ango et al., 2001). Homer1a disrupts the links, maintained by the long form of Homer (cross-linking Homers), between mGluR1,5 and the Shank-GKAP-PSD-95-ionotropic glutamate receptor network. Two characteristics of the constitutive activation of the Group I mGluR-Homer1a complex are particularly interesting: (1) it affects a large number of synapses in which Homer1a is upregulated following enhanced, long-lasting neuronal activity; and (2) it mainly depends on Homer1a protein turnover. The constitutively active Group I mGluR-Homer1a complex is involved in the two main forms of non-Hebbian neuronal plasticity: "metaplasticity" and "homeostatic synaptic scaling," which are implicated in a large series of physiological and pathologic processes. Those include non-Hebbian plasticity observed in visual system, synapses modulated by addictive drugs (rewarded synapses), chronically overactivated synaptic networks, normal sleep, and sleep deprivation.
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Affiliation(s)
- Joël Bockaert
- Institut de Génomique Fonctionnelle, Université Montpellier, Center National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 34094 Montpellier, France
| | - Julie Perroy
- Institut de Génomique Fonctionnelle, Université Montpellier, Center National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 34094 Montpellier, France
| | - Fabrice Ango
- Institut des Neurosciences de Montpellier, Université Montpellier, Center National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 34295 Montpellier, France
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15
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Correlated Motions of Conserved Polar Motifs Lay out a Plausible Mechanism of G Protein-Coupled Receptor Activation. Biomolecules 2021; 11:biom11050670. [PMID: 33946214 PMCID: PMC8146931 DOI: 10.3390/biom11050670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/17/2021] [Accepted: 04/28/2021] [Indexed: 02/01/2023] Open
Abstract
Recent advancements in the field of experimental structural biology have provided high-resolution structures of active and inactive state G protein-coupled receptors (GPCRs), a highly important pharmaceutical target family, but the process of transition between these states is poorly understood. According to the current theory, GPCRs exist in structurally distinct, dynamically interconverting functional states of which populations are shifted upon binding of ligands and intracellular signaling proteins. However, explanation of the activation mechanism, on an entirely structural basis, gets complicated when multiple activation pathways and active receptor states are considered. Our unbiased, atomistic molecular dynamics simulations of the μ opioid receptor (MOP) revealed that transmission of external stimulus to the intracellular surface of the receptor is accompanied by subtle, concerted movements of highly conserved polar amino acid side chains along the 7th transmembrane helix. This may entail the rearrangement of polar species and the shift of macroscopic polarization in the transmembrane domain, triggered by agonist binding. Based on our observations and numerous independent indications, we suggest amending the widely accepted theory that the initiation event of GPCR activation is the shift of macroscopic polarization between the ortho- and allosteric binding pockets and the intracellular G protein-binding interface.
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16
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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17
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Sodium ions allosterically modulate the M2 muscarinic receptor. Sci Rep 2020; 10:11177. [PMID: 32636499 PMCID: PMC7341750 DOI: 10.1038/s41598-020-68133-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/15/2020] [Indexed: 11/08/2022] Open
Abstract
G protein coupled receptors (GPCRs) play a key role in the vast majority of cellular signal transduction processes. Previous experimental evidence has shown that sodium ion (Na+) allosterically modulate several class A GPCRs and theoretical studies suggested that the same also holds true for muscarinic receptors. Here we examined, using Xenopus oocytes as an expression system, the effect of Na+ on a prototypical GPCR, the M2 muscarinic receptor (M2R). We found that removal of extracellular Na+ resulted in a decrease in the potency of ACh toward the M2R and that a conserved aspartate in transmembrane domain 2 is crucial for this effect. We further show that this allosteric effect of Na+ does not underlie the voltage-dependence of this receptor.
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18
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Helix 8 is the essential structural motif of mechanosensitive GPCRs. Nat Commun 2019; 10:5784. [PMID: 31857598 PMCID: PMC6923424 DOI: 10.1038/s41467-019-13722-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 11/19/2019] [Indexed: 12/16/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are versatile cellular sensors for chemical stimuli, but also serve as mechanosensors involved in various (patho)physiological settings like vascular regulation, cardiac hypertrophy and preeclampsia. However, the molecular mechanisms underlying mechanically induced GPCR activation have remained elusive. Here we show that mechanosensitive histamine H1 receptors (H1Rs) are endothelial sensors of fluid shear stress and contribute to flow-induced vasodilation. At the molecular level, we observe that H1Rs undergo stimulus-specific patterns of conformational changes suggesting that mechanical forces and agonists induce distinct active receptor conformations. GPCRs lacking C-terminal helix 8 (H8) are not mechanosensitive, and transfer of H8 to non-responsive GPCRs confers, while removal of H8 precludes, mechanosensitivity. Moreover, disrupting H8 structural integrity by amino acid exchanges impairs mechanosensitivity. Altogether, H8 is the essential structural motif endowing GPCRs with mechanosensitivity. These findings provide a mechanistic basis for a better understanding of the roles of mechanosensitive GPCRs in (patho)physiology. GPCRs are versatile cellular sensors for chemical stimuli but the molecular mechanisms underlying mechanically induced GPCR activation have remained elusive. Here authors identify the C-terminal helix 8 (H8) as the essential structural motif endowing H1R and other GPCRs with mechanosensitivity.
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19
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Wei AD, Ramirez JM. Presynaptic Mechanisms and KCNQ Potassium Channels Modulate Opioid Depression of Respiratory Drive. Front Physiol 2019; 10:1407. [PMID: 31824331 PMCID: PMC6882777 DOI: 10.3389/fphys.2019.01407] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 10/31/2019] [Indexed: 01/02/2023] Open
Abstract
Opioid-induced respiratory depression (OIRD) is the major cause of death associated with opioid analgesics and drugs of abuse, but the underlying cellular and molecular mechanisms remain poorly understood. We investigated opioid action in vivo in unanesthetized mice and in in vitro medullary slices containing the preBötzinger Complex (preBötC), a locus critical for breathing and inspiratory rhythm generation. Although hypothesized as a primary mechanism, we found that mu-opioid receptor (MOR1)-mediated GIRK activation contributed only modestly to OIRD. Instead, mEPSC recordings from genetically identified Dbx1-derived interneurons, essential for rhythmogenesis, revealed a prevalent presynaptic mode of action for OIRD. Consistent with MOR1-mediated suppression of presynaptic release as a major component of OIRD, Cacna1a KO slices lacking P/Q-type Ca2+ channels enhanced OIRD. Furthermore, OIRD was mimicked and reversed by KCNQ potassium channel activators and blockers, respectively. In vivo whole-body plethysmography combined with systemic delivery of GIRK- and KCNQ-specific potassium channel drugs largely recapitulated these in vitro results, and revealed state-dependent modulation of OIRD. We propose that respiratory failure from OIRD results from a general reduction of synaptic efficacy, leading to a state-dependent collapse of rhythmic network activity.
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Affiliation(s)
- Aguan D. Wei
- Seattle Children’s Research Institute, Center for Integrative Brain Research, Seattle, WA, United States
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, United States
| | - Jan-Marino Ramirez
- Seattle Children’s Research Institute, Center for Integrative Brain Research, Seattle, WA, United States
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, United States
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20
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Hu X, Provasi D, Ramsey S, Filizola M. Mechanism of μ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation. Biophys J 2019; 118:909-921. [PMID: 31676132 DOI: 10.1016/j.bpj.2019.10.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/31/2019] [Accepted: 10/08/2019] [Indexed: 01/09/2023] Open
Abstract
In the era of opioid abuse epidemics, there is an increased demand for understanding how opioid receptors can be allosterically modulated to guide the development of more effective and safer opioid therapies. Among the modulators of the μ-opioid (MOP) receptor, which is the pharmacological target for the majority of clinically used opioid drugs, are monovalent and divalent cations. Specifically, the monovalent sodium cation (Na+) has been known for decades to affect MOP receptor signaling by reducing agonist binding, whereas the divalent magnesium cation (Mg2+) has been shown to have the opposite effect, notwithstanding the presence of sodium chloride. Although ultra-high-resolution opioid receptor crystal structures have revealed a specific Na+ binding site and molecular dynamics (MD) simulation studies have supported the idea that this monovalent ion reduces agonist binding by stabilizing the receptor inactive state, the putative binding site of Mg2+ on the MOP receptor, as well as the molecular determinants responsible for its positive allosteric modulation of the receptor, are unknown. In this work, we carried out tens of microseconds of all-atom MD simulations to investigate the simultaneous binding of Mg2+ and Na+ cations to inactive and active crystal structures of the MOP receptor embedded in an explicit lipid-water environment and confirmed adequate sampling of Mg2+ ion binding with a grand canonical Monte Carlo MD method. Analyses of these simulations shed light on 1) the preferred binding sites of Mg2+ on the MOP receptor, 2) details of the competition between Mg2+ and Na+ cations for specific sites, 3) estimates of binding affinities, and 4) testable hypotheses of the molecular mechanism underlying the positive allosteric modulation of the MOP receptor by the Mg2+ cation.
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Affiliation(s)
- Xiaohu Hu
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Steven Ramsey
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
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21
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Zarzycka B, Zaidi SA, Roth BL, Katritch V. Harnessing Ion-Binding Sites for GPCR Pharmacology. Pharmacol Rev 2019; 71:571-595. [PMID: 31551350 PMCID: PMC6782022 DOI: 10.1124/pr.119.017863] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Endogenous ions play important roles in the function and pharmacology of G-protein coupled receptors (GPCRs). Historically the evidence for ionic modulation of GPCR function dates to 1973 with studies of opioid receptors, where it was demonstrated that physiologic concentrations of sodium allosterically attenuated agonist binding. This Na+-selective effect was distinct from effects of other monovalent and divalent cations, with the latter usually counteracting sodium's negative allosteric modulation of binding. Since then, numerous studies documenting the effects of mono- and divalent ions on GPCR function have been published. While ions can act selectively and nonselectively at many sites in different receptors, the discovery of the conserved sodium ion site in class A GPCR structures in 2012 revealed the unique nature of Na+ site, which has emerged as a near-universal site for allosteric modulation of class A GPCR structure and function. In this review, we synthesize and highlight recent advances in the functional, biophysical, and structural characterization of ions bound to GPCRs. Taken together, these findings provide a molecular understanding of the unique roles of Na+ and other ions as GPCR allosteric modulators. We will also discuss how this knowledge can be applied to the redesign of receptors and ligand probes for desired functional and pharmacological profiles. SIGNIFICANCE STATEMENT: The function and pharmacology of GPCRs strongly depend on the presence of mono and divalent ions in experimental assays and in living organisms. Recent insights into the molecular mechanism of this ion-dependent allosterism from structural, biophysical, biochemical, and computational studies provide quantitative understandings of the pharmacological effects of drugs in vitro and in vivo and open new avenues for the rational design of chemical probes and drug candidates with improved properties.
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Affiliation(s)
- Barbara Zarzycka
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Saheem A Zaidi
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Bryan L Roth
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Vsevolod Katritch
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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22
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Aguayo-Ortiz R, Dominguez L. APH-1A Component of γ-Secretase Forms an Internal Water and Ion-Containing Cavity. ACS Chem Neurosci 2019; 10:2931-2938. [PMID: 30979338 DOI: 10.1021/acschemneuro.9b00150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Anterior pharynx-defective 1A (APH-1A) is a seven transmembrane component of γ-secretase (GS), an aspartyl protease enzyme involved in the production of toxic amyloid-β peptides in Alzheimer's disease patients. Cryo-electron microscopy structures of the enzyme complex revealed a central cavity in its APH-1A component, similar to water-containing cavities in G-protein coupled receptors (GPCRs). In this work, we performed molecular dynamics and umbrella sampling simulations to understand the role of the APH-1A cavity in the GS complex. Our results suggest that APH-1A is able to store water molecules in its inner cavity and transport some of them between cell spaces. Additionally, APH-1A allows the influx of extracellular cations into a central hydrophilic cavity but cannot transport them into the intracellular space. Overall, this study seeks to describe an alternative APH-1A function in GS besides its complex stabilization role and provide novel approaches to understand the functioning of the GS enzyme.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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23
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Lamim Ribeiro JM, Filizola M. Allostery in G protein-coupled receptors investigated by molecular dynamics simulations. Curr Opin Struct Biol 2019; 55:121-128. [PMID: 31096158 DOI: 10.1016/j.sbi.2019.03.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 01/14/2023]
Abstract
G-protein-coupled receptors (GPCRs) are allosteric signaling machines that trigger distinct functional responses depending on the particular conformational state they adopt upon binding. This so-called GPCR functional selectivity is prompted by ligands of different efficacy binding at orthosteric or allosteric sites on the receptor, as well as by interactions with intracellular protein partners or other receptor types. Molecular dynamics (MD) simulations can provide important mechanistic, thermodynamic, and kinetic insights into these interactions at a level of molecular detail that is necessary to rightly inform modern drug discovery. Here, we review the most recent MD contributions to understanding GPCR allostery, with an emphasis on their strengths and limitations.
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Affiliation(s)
- João Marcelo Lamim Ribeiro
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, NY, 10029, USA
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, NY, 10029, USA.
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24
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Cong X, Golebiowski J. Allosteric Na +-binding site modulates CXCR4 activation. Phys Chem Chem Phys 2018; 20:24915-24920. [PMID: 30238101 DOI: 10.1039/c8cp04134b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
G protein-coupled receptors (GPCRs) control most cellular communications with the environment and are the largest protein family of drug targets. As strictly regulated molecular machines, profound comprehension of their activation mechanism is expected to significantly facilitate structure-based drug design. This study provides atomistic-level description of the activation dynamics of the C-X-C chemokine receptor type 4 (CXCR4), a class A GPCR and important drug target. Using molecular dynamics and enhanced sampling, we demonstrate how mutations and protonation of conserved residues trigger activation through microswitches at the receptor core, while sodium ion - a known allosteric modulator - inhibits it. The findings point to a conserved mechanism of activation and the allosteric modulation by sodium in the chemokine receptor family. From the technical aspect, the enhanced sampling protocol effectively samples receptor conformational changes toward activation, and differentiates three variants of the receptor by their basal activity. This work provides structural basis and a powerful in silico tool for CXCR4 agonist design.
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Affiliation(s)
- Xiaojing Cong
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, 06108 Nice, France.
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25
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Kasimova MA, Lindahl E, Delemotte L. Determining the molecular basis of voltage sensitivity in membrane proteins. J Gen Physiol 2018; 150:1444-1458. [PMID: 30150239 PMCID: PMC6168238 DOI: 10.1085/jgp.201812086] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/07/2018] [Indexed: 12/31/2022] Open
Abstract
The identification of voltage-sensing elements in membrane proteins is challenging due to the diversity of voltage-sensing mechanisms. Kasimova et al. present a computational approach to predict the elements involved in voltage sensing, which they validate using voltage-gated ion channels. Voltage-sensitive membrane proteins are united by their ability to transform changes in membrane potential into mechanical work. They are responsible for a spectrum of physiological processes in living organisms, including electrical signaling and cell-cycle progression. Although the mechanism of voltage-sensing has been well characterized for some membrane proteins, including voltage-gated ion channels, even the location of the voltage-sensing elements remains unknown for others. Moreover, the detection of these elements by using experimental techniques is challenging because of the diversity of membrane proteins. Here, we provide a computational approach to predict voltage-sensing elements in any membrane protein, independent of its structure or function. It relies on an estimation of the propensity of a protein to respond to changes in membrane potential. We first show that this property correlates well with voltage sensitivity by applying our approach to a set of voltage-sensitive and voltage-insensitive membrane proteins. We further show that it correctly identifies authentic voltage-sensitive residues in the voltage-sensor domain of voltage-gated ion channels. Finally, we investigate six membrane proteins for which the voltage-sensing elements have not yet been characterized and identify residues and ions that might be involved in the response to voltage. The suggested approach is fast and simple and enables a characterization of voltage sensitivity that goes beyond mere identification of charges. We anticipate that its application before mutagenesis experiments will significantly reduce the number of potential voltage-sensitive elements to be tested.
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Affiliation(s)
- Marina A Kasimova
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Erik Lindahl
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Lucie Delemotte
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
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26
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Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M. Evolution of chemokine receptors is driven by mutations in the sodium binding site. PLoS Comput Biol 2018; 14:e1006209. [PMID: 29912865 PMCID: PMC6037435 DOI: 10.1371/journal.pcbi.1006209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 07/09/2018] [Accepted: 05/16/2018] [Indexed: 12/22/2022] Open
Abstract
Chemokines and their receptors (members of the GPCR super-family) are involved in a wide variety of physiological processes and diseases; thus, understanding the specificity of the chemokine receptor family could help develop new receptor specific drugs. Here, we explore the evolutionary mechanisms that led to the emergence of the chemokine receptors. Based on GPCR hierarchical classification, we analyzed nested GPCR sets with an eigen decomposition approach of the sequence covariation matrix and determined three key residues whose mutation was crucial for the emergence of the chemokine receptors and their subsequent divergence into homeostatic and inflammatory receptors. These residues are part of the allosteric sodium binding site. Their structural and functional roles were investigated by molecular dynamics simulations of CXCR4 and CCR5 as prototypes of homeostatic and inflammatory chemokine receptors, respectively. This study indicates that the three mutations crucial for the evolution of the chemokine receptors dramatically altered the sodium binding mode. In CXCR4, the sodium ion is tightly bound by four protein atoms and one water molecule. In CCR5, the sodium ion is mobile within the binding pocket and moves between different sites involving from one to three protein atoms and two to five water molecules. Analysis of chemokine receptor evolution reveals that a highly constrained sodium binding site characterized most ancient receptors, and that the constraints were subsequently loosened during the divergence of this receptor family. We discuss the implications of these findings for the evolution of the chemokine receptor functions and mechanisms of action.
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Affiliation(s)
- Bruck Taddese
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Madeline Deniaud
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Antoine Garnier
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Asma Tiss
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Hajer Guissouma
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Hervé Abdi
- The University of Texas at Dallas, School of Behavioral and Brain Sciences, Dallas, Texas, United States of America
| | - Daniel Henrion
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Marie Chabbert
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
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Abstract
This paper is the thirty-ninth consecutive installment of the annual review of research concerning the endogenous opioid system. It summarizes papers published during 2016 that studied the behavioral effects of molecular, pharmacological and genetic manipulation of opioid peptides, opioid receptors, opioid agonists and opioid antagonists. The particular topics that continue to be covered include the molecular-biochemical effects and neurochemical localization studies of endogenous opioids and their receptors related to behavior, and the roles of these opioid peptides and receptors in pain and analgesia, stress and social status, tolerance and dependence, learning and memory, eating and drinking, drug abuse and alcohol, sexual activity and hormones, pregnancy, development and endocrinology, mental illness and mood, seizures and neurologic disorders, electrical-related activity and neurophysiology, general activity and locomotion, gastrointestinal, renal and hepatic functions, cardiovascular responses, respiration and thermoregulation, and immunological responses.
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Affiliation(s)
- Richard J Bodnar
- Department of Psychology and CUNY Neuroscience Collaborative, Queens College, City University of New York, Flushing, NY 11367, United States.
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28
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Selvam B, Shamsi Z, Shukla D. Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors. Angew Chem Int Ed Engl 2018; 57:3048-3053. [DOI: 10.1002/anie.201708889] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/20/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Balaji Selvam
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Zahra Shamsi
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- Department of Plant Biology, Center for Biophysics & Quantitative Biology, National Center for Supercomputing Applications; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
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29
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Selvam B, Shamsi Z, Shukla D. Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201708889] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Balaji Selvam
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Zahra Shamsi
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
- Department of Plant Biology, Center for Biophysics & Quantitative Biology, National Center for Supercomputing Applications; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
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30
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Vickery ON, Carvalheda CA, Zaidi SA, Pisliakov AV, Katritch V, Zachariae U. Intracellular Transfer of Na + in an Active-State G-Protein-Coupled Receptor. Structure 2018; 26:171-180.e2. [PMID: 29249607 PMCID: PMC5805466 DOI: 10.1016/j.str.2017.11.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/13/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023]
Abstract
Playing a central role in cell signaling, G-protein-coupled receptors (GPCRs) are the largest superfamily of membrane proteins and form the majority of drug targets in humans. How extracellular agonist binding triggers the activation of GPCRs and associated intracellular effector proteins remains, however, poorly understood. Structural studies have revealed that inactive class A GPCRs harbor a conserved binding site for Na+ ions in the center of their transmembrane domain, accessible from the extracellular space. Here, we show that the opening of a conserved hydrated channel in the activated state receptors allows the Na+ ion to egress from its binding site into the cytosol. Coupled with protonation changes, this ion movement occurs without significant energy barriers, and can be driven by physiological transmembrane ion and voltage gradients. We propose that Na+ ion exchange with the cytosol is a key step in GPCR activation. Further, we hypothesize that this transition locks receptors in long-lived active-state conformations.
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Affiliation(s)
- Owen N Vickery
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK
| | - Catarina A Carvalheda
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK
| | - Saheem A Zaidi
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrei V Pisliakov
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK
| | - Vsevolod Katritch
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Ulrich Zachariae
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK.
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31
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Point mutation of a conserved aspartate, D69, in the muscarinic M 2 receptor does not modify voltage-sensitive agonist potency. Biochem Biophys Res Commun 2018; 496:101-104. [DOI: 10.1016/j.bbrc.2018.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/01/2018] [Indexed: 12/30/2022]
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32
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Wang S, Wacker D, Levit A, Che T, Betz RM, McCorvy JD, Venkatakrishnan AJ, Huang XP, Dror RO, Shoichet BK, Roth BL. D 4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Science 2017; 358:381-386. [PMID: 29051383 PMCID: PMC5856174 DOI: 10.1126/science.aan5468] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 09/07/2017] [Indexed: 12/25/2022]
Abstract
Dopamine receptors are implicated in the pathogenesis and treatment of nearly every neuropsychiatric disorder. Although thousands of drugs interact with these receptors, our molecular understanding of dopaminergic drug selectivity and design remains clouded. To illuminate dopamine receptor structure, function, and ligand recognition, we determined crystal structures of the D4 dopamine receptor in its inactive state bound to the antipsychotic drug nemonapride, with resolutions up to 1.95 angstroms. These structures suggest a mechanism for the control of constitutive signaling, and their unusually high resolution enabled a structure-based campaign for new agonists of the D4 dopamine receptor. The ability to efficiently exploit structure for specific probe discovery-rapidly moving from elucidating receptor structure to discovering previously unrecognized, selective agonists-testifies to the power of structure-based approaches.
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Affiliation(s)
- Sheng Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA.
| | - Daniel Wacker
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA.
| | - Anat Levit
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158-2280, USA
| | - Tao Che
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA
| | - Robin M Betz
- Department of Computer Science, Stanford University, CA 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - John D McCorvy
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA
| | - A J Venkatakrishnan
- Department of Computer Science, Stanford University, CA 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, CA 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158-2280, USA.
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA.
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360, USA
- National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365, USA
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33
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Chen IS, Furutani K, Kurachi Y. Structural determinants at the M2 muscarinic receptor modulate the RGS4-GIRK response to pilocarpine by impairment of the receptor voltage sensitivity. Sci Rep 2017; 7:6110. [PMID: 28733581 PMCID: PMC5522400 DOI: 10.1038/s41598-017-05128-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/24/2017] [Indexed: 12/23/2022] Open
Abstract
Membrane potential controls the response of the M2 muscarinic receptor to its ligands. Membrane hyperpolarization increases response to the full agonist acetylcholine (ACh) while decreasing response to the partial agonist pilocarpine. We previously have demonstrated that the regulator of G-protein signaling (RGS) 4 protein discriminates between the voltage-dependent responses of ACh and pilocarpine; however, the underlying mechanism remains unclear. Here we show that RGS4 is involved in the voltage-dependent behavior of the M2 muscarinic receptor-mediated signaling in response to pilocarpine. Additionally we revealed structural determinants on the M2 muscarinic receptor underlying the voltage-dependent response. By electrophysiological recording in Xenopus oocytes expressing M2 muscarinic receptor and G-protein-gated inwardly rectifying K+ channels, we quantified voltage-dependent desensitization of pilocarpine-induced current in the presence or absence of RGS4. Hyperpolarization-induced desensitization of the current required for RGS4, also depended on pilocarpine concentration. Mutations of charged residues in the aspartic acid-arginine-tyrosine motif of the M2 muscarinic receptor, but not intracellular loop 3, significantly impaired the voltage-dependence of RGS4 function. Thus, our results demonstrated that voltage-dependence of RGS4 modulation is derived from the M2 muscarinic receptor. These results provide novel insights into how membrane potential impacts G-protein signaling by modulating GPCR communication with downstream effectors.
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Affiliation(s)
- I-Shan Chen
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuharu Furutani
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan. .,Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Yoshihisa Kurachi
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan. .,Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, 565-0871, Japan.
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34
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Krah A, Zachariae U. Insights into the ion-coupling mechanism in the MATE transporter NorM-VC. Phys Biol 2017; 14:045009. [DOI: 10.1088/1478-3975/aa5ee7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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35
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Margolis EB, Fujita W, Devi LA, Fields HL. Two delta opioid receptor subtypes are functional in single ventral tegmental area neurons, and can interact with the mu opioid receptor. Neuropharmacology 2017. [PMID: 28645621 DOI: 10.1016/j.neuropharm.2017.06.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The mu and delta opioid receptors (MOR and DOR) are highly homologous members of the opioid family of GPCRs. There is evidence that MOR and DOR interact, however the extent to which these interactions occur in vivo and affect synaptic function is unknown. There are two stable DOR subtypes: DPDPE sensitive (DOR1) and deltorphin II sensitive (DOR2); both agonists are blocked by DOR selective antagonists. Robust motivational effects are produced by local actions of both MOR and DOR ligands in the ventral tegmental area (VTA). Here we demonstrate that a majority of both dopaminergic and non-dopaminergic VTA neurons express combinations of functional DOR1, DOR2, and/or MOR, and that within a single VTA neuron, DOR1, DOR2, and MOR agonists can differentially couple to downstream signaling pathways. As reported for the MOR agonist DAMGO, DPDPE and deltorphin II produced either a predominant K+ dependent hyperpolarization or a Cav2.1 mediated depolarization in different neurons. In some neurons DPDPE and deltorphin II produced opposite responses. Excitation, inhibition, or no effect by DAMGO did not predict the response to DPDPE or deltorphin II, arguing against a MOR-DOR interaction generating DOR subtypes. However, in a subset of VTA neurons the DOR antagonist TIPP-Ψ augmented DAMGO responses; we also observed DPDPE or deltorphin II responses augmented by the MOR selective antagonist CTAP. These findings directly support the existence of two independent, stable forms of the DOR, and show that MOR and DOR can interact in some neurons to alter downstream signaling.
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Affiliation(s)
- Elyssa B Margolis
- Department of Neurology, The Wheeler Center for the Neurobiology of Addiction, Alcoholism and Addiction Research Group, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Wakako Fujita
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lakshmi A Devi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Howard L Fields
- Department of Neurology, The Wheeler Center for the Neurobiology of Addiction, Alcoholism and Addiction Research Group, University of California San Francisco, San Francisco, CA 94143, USA
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36
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Barchad-Avitzur O, Priest MF, Dekel N, Bezanilla F, Parnas H, Ben-Chaim Y. A Novel Voltage Sensor in the Orthosteric Binding Site of the M2 Muscarinic Receptor. Biophys J 2017; 111:1396-1408. [PMID: 27705763 DOI: 10.1016/j.bpj.2016.08.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 08/28/2016] [Accepted: 08/31/2016] [Indexed: 12/31/2022] Open
Abstract
G protein-coupled receptors (GPCRs) mediate many signal transduction processes in the body. The discovery that these receptors are voltage-sensitive has changed our understanding of their behavior. The M2 muscarinic acetylcholine receptor (M2R) was found to exhibit depolarization-induced charge movement-associated currents, implying that this prototypical GPCR possesses a voltage sensor. However, the typical domain that serves as a voltage sensor in voltage-gated channels is not present in GPCRs, making the search for the voltage sensor in the latter challenging. Here, we examine the M2R and describe a voltage sensor that is comprised of tyrosine residues. This voltage sensor is crucial for the voltage dependence of agonist binding to the receptor. The tyrosine-based voltage sensor discovered here constitutes a noncanonical by which membrane proteins may sense voltage.
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Affiliation(s)
- Ofra Barchad-Avitzur
- Department of Neurobiology, Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Michael F Priest
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Noa Dekel
- Department of Neurobiology, Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Hanna Parnas
- Department of Neurobiology, Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Yair Ben-Chaim
- Natural and Life Sciences, Open University of Israel, Raanana, Israel.
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37
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Machtens JP, Briones R, Alleva C, de Groot BL, Fahlke C. Gating Charge Calculations by Computational Electrophysiology Simulations. Biophys J 2017; 112:1396-1405. [PMID: 28402882 DOI: 10.1016/j.bpj.2017.02.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 01/03/2017] [Accepted: 02/16/2017] [Indexed: 11/15/2022] Open
Abstract
Electrical cell signaling requires adjustment of ion channel, receptor, or transporter function in response to changes in membrane potential. For the majority of such membrane proteins, the molecular details of voltage sensing remain insufficiently understood. Here, we present a molecular dynamics simulation-based method to determine the underlying charge movement across the membrane-the gating charge-by measuring electrical capacitor properties of membrane-embedded proteins. We illustrate the approach by calculating the charge transfer upon membrane insertion of the HIV gp41 fusion peptide, and validate the method on two prototypical voltage-dependent proteins, the Kv1.2 K+ channel and the voltage sensor of the Ciona intestinalis voltage-sensitive phosphatase, against experimental data. We then use the gating charge analysis to study how the T1 domain modifies voltage sensing in Kv1.2 channels and to investigate the voltage dependence of the initial binding of two Na+ ions in Na+-coupled glutamate transporters. Our simulation approach quantifies various mechanisms of voltage sensing, enables direct comparison with experiments, and supports mechanistic interpretation of voltage sensitivity by fractional amino acid contributions.
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Affiliation(s)
- Jan-Philipp Machtens
- Institute of Complex Systems, Zelluläre Biophysik (ICS-4) and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany.
| | - Rodolfo Briones
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Claudia Alleva
- Institute of Complex Systems, Zelluläre Biophysik (ICS-4) and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christoph Fahlke
- Institute of Complex Systems, Zelluläre Biophysik (ICS-4) and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany
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38
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Marino KA, Shang Y, Filizola M. Insights into the function of opioid receptors from molecular dynamics simulations of available crystal structures. Br J Pharmacol 2017; 175:2834-2845. [PMID: 28266020 DOI: 10.1111/bph.13774] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/23/2017] [Accepted: 02/28/2017] [Indexed: 01/12/2023] Open
Abstract
The opioid receptors are key targets in the treatment of acute and chronic pain, and the development of novel analgesics with reduced side effects is crucial in the search for more effective medications. The crystal structures of opioid receptors have provided a wealth of knowledge on many aspects of opioid receptor pharmacology and function, including ligand binding poses, location of the sodium allosteric binding site, conformational changes associated with activation and putative dimeric interfaces. These crystal structures also offer a starting point for molecular dynamics (MD) simulations to capture one aspect of drug design that static structures cannot resolve, namely protein dynamics. With the increase in computing power, MD simulations of crystal structures have become an influential tool in understanding the function of GPCRs in general. Here, we discuss lessons learned from MD simulations of opioid receptor crystal structures with reference to (i) the binding pathway of sodium to its crystallographic allosteric site, (ii) the dynamics of ligand-receptor and receptor-receptor interactions, both at the ligand- and G protein-binding sites, (iii) the binding pathway and binding pose of novel ligands, and (iv) opioid receptor oligomerization. LINKED ARTICLES This article is part of a themed section on Emerging Areas of Opioid Pharmacology. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.14/issuetoc.
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Affiliation(s)
- Kristen A Marino
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yi Shang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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39
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Vickery ON, Machtens JP, Zachariae U. Membrane potentials regulating GPCRs: insights from experiments and molecular dynamics simulations. Curr Opin Pharmacol 2016; 30:44-50. [PMID: 27474871 PMCID: PMC5080454 DOI: 10.1016/j.coph.2016.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 01/27/2023]
Abstract
G-protein coupled receptors (GPCRs) form the largest class of membrane proteins in humans and the targets of most present drugs. Membrane potential is one of the defining characteristics of living cells. Recent work has shown that the membrane voltage, and changes thereof, modulates signal transduction and ligand binding in GPCRs. As it may allow differential signalling patterns depending on tissue, cell type, and the excitation status of excitable cells, GPCR voltage sensitivity could have important implications for their pharmacology. This review summarises recent experimental insights on GPCR voltage regulation and the role of molecular dynamics simulations in identifying the structural basis of GPCR voltage-sensing. We discuss the potential significance for drug design on GPCR targets from excitable and non-excitable cells.
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Affiliation(s)
- Owen N Vickery
- Physics, School of Science and Engineering, University of Dundee, Nethergate Dundee DD1 4NH, UK; Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jan-Philipp Machtens
- Institute of Complex Systems, Zelluläre Biophysik (ICS-4), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Ulrich Zachariae
- Physics, School of Science and Engineering, University of Dundee, Nethergate Dundee DD1 4NH, UK; Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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