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Stuebler AG, Jansen M. Mobility of Lower MA-Helices for Ion Conduction through Lateral Portals in 5-HT 3A Receptors. Biophys J 2020; 119:2593-2603. [PMID: 33157122 PMCID: PMC7822733 DOI: 10.1016/j.bpj.2020.10.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/19/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
The intracellular domain of the serotonin type 3A receptor, a pentameric ligand-gated ion channel, is crucial for regulating conductance. Ion permeation through the extracellular vestibule and the transmembrane channel is well understood, whereas the specific ion conduction pathway through the intracellular domain is less clear. The intracellular domain starts with a short loop after the third transmembrane segment, followed by a short α-helical segment, a large unstructured loop, and finally, the membrane-associated MA-helix that continues into the last transmembrane segment. The MA-helices from all five subunits form the extension of the transmembrane ion channel and shape what has been described as a “closed vestibule,” with their lateral portals obstructed by loops and their cytosolic ends forming a tight hydrophobic constriction. The question remains whether the lateral portals or cytosolic constriction conduct ions upon channel opening. In our study, we used disulfide bond formation between pairs of engineered cysteines to probe the proximity and mobility of segments of the MA-helices most distal to the membrane bilayer. Our results indicate that the proximity and orientation for cysteine pairs at I409C/R410C, in close proximity to the lateral windows, and L402C/L403C, at the cytosolic ends of the MA-helices, are conducive for disulfide bond formation. Although conformational changes associated with gating promote cross-linking for I409C/R410C, which in turn decreases channel currents, cross-linking of L402C/L403C is functionally silent in macroscopic currents. These results support the hypothesis that concerted conformational changes open the lateral portals for ion conduction, rendering ion conduction through the vertical portal unlikely.
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Affiliation(s)
- Antonia G Stuebler
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas.
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Pandhare A, Pirayesh E, Stuebler AG, Jansen M. Triple arginines as molecular determinants for pentameric assembly of the intracellular domain of 5-HT 3A receptors. J Gen Physiol 2019; 151:1135-1145. [PMID: 31409663 PMCID: PMC6719409 DOI: 10.1085/jgp.201912421] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/15/2019] [Indexed: 11/20/2022] Open
Abstract
Serotonin type 3A receptors are homopentameric ligand-gated ion channels that are thought to assemble via interactions involving the subunits’ extracellular and transmembrane domains. Pandhare et al. reveal that channel assembly is also determined by three arginine residues in the receptor’s intracellular domain. Serotonin type 3 receptors (5-HT3Rs) are cation-conducting pentameric ligand-gated ion channels and members of the Cys-loop superfamily in eukaryotes. 5-HT3Rs are found in the peripheral and central nervous system, and they are targets for drugs used to treat anxiety, drug dependence, and schizophrenia, as well as chemotherapy-induced and postoperative nausea and emesis. Decades of research of Cys-loop receptors have identified motifs in both the extracellular and transmembrane domains that mediate pentameric assembly. Those efforts have largely ignored the most diverse domain of these channels, the intracellular domain (ICD). Here we identify molecular determinants within the ICD of serotonin type 3A (5-HT3A) subunits for pentameric assembly by first identifying the segments contributing to pentamerization using deletion constructs of, and finally by making defined amino acid substitutions within, an isolated soluble ICD. Our work provides direct experimental evidence for the contribution of three intracellular arginines, previously implicated in governing the low conductance of 5-HT3ARs, in structural features such as pentameric assembly.
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Affiliation(s)
- Akash Pandhare
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Elham Pirayesh
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Antonia G Stuebler
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
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3
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Frameworking memory and serotonergic markers. Rev Neurosci 2017; 28:455-497. [DOI: 10.1515/revneuro-2016-0079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/16/2017] [Indexed: 12/29/2022]
Abstract
Abstract:The evidence for neural markers and memory is continuously being revised, and as evidence continues to accumulate, herein, we frame earlier and new evidence. Hence, in this work, the aim is to provide an appropriate conceptual framework of serotonergic markers associated with neural activity and memory. Serotonin (5-hydroxytryptamine [5-HT]) has multiple pharmacological tools, well-characterized downstream signaling in mammals’ species, and established 5-HT neural markers showing new insights about memory functions and dysfunctions, including receptors (5-HT1A/1B/1D, 5-HT2A/2B/2C, and 5-HT3-7), transporter (serotonin transporter [SERT]) and volume transmission present in brain areas involved in memory. Bidirectional influence occurs between 5-HT markers and memory/amnesia. A growing number of researchers report that memory, amnesia, or forgetting modifies neural markers. Diverse approaches support the translatability of using neural markers and cerebral functions/dysfunctions, including memory formation and amnesia. At least, 5-HT1A, 5-HT4, 5-HT6, and 5-HT7receptors and SERT seem to be useful neural markers and therapeutic targets. Hence, several mechanisms cooperate to achieve synaptic plasticity or memory, including changes in the expression of neurotransmitter receptors and transporters.
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Fokas AS, Cole DJ, Hine NDM, Wells SA, Payne MC, Chin AW. Evidence of Correlated Static Disorder in the Fenna-Matthews-Olson Complex. J Phys Chem Lett 2017; 8:2350-2356. [PMID: 28485971 DOI: 10.1021/acs.jpclett.7b00669] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Observation of excitonic quantum beats in photosynthetic antennae has prompted wide debate regarding the function of excitonic coherence in pigment-protein complexes. Much of this work focuses on the interactions of excitons with the femto-to-picosecond dynamical fluctuations of their environment. However, in experiments these effects can be masked by static disorder of the excited-state energies across ensembles, whose microscopic origins are challenging to predict. Here the excited-state properties of ∼2000 atom clusters of the Fenna-Matthews-Olson complex are simulated using a unique combination of linear-scaling density functional theory and constrained geometric dynamics. While slow, large amplitude protein motion leads to large variations in the Qy transitions of two pigments, we identify pigment-protein correlations that greatly reduce variations in the energy gap across the ensemble, which is consistent with experimental observations of suppressed inhomogeneous dephasing of quantum beats.
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Affiliation(s)
- Alexander S Fokas
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J Cole
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
- School of Chemistry, Newcastle University , Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Nicholas D M Hine
- Department of Physics, University of Warwick , Coventry CV4 7AL, United Kingdom
| | - Stephen A Wells
- Department of Chemistry, University of Bath , Claverton Down BA2 7AY, United Kingdom
| | - Michael C Payne
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Alex W Chin
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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Hermans SM, Pfleger C, Nutschel C, Hanke CA, Gohlke H. Rigidity theory for biomolecules: concepts, software, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Susanne M.A. Hermans
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christina Nutschel
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christian A. Hanke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
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Powell AD, Grafton G, Roberts A, Larkin S, O'Neill N, Palandri J, Otvos R, Cooper AJ, Ulens C, Barnes NM. Novel mechanism of modulation at a ligand-gated ion channel; action of 5-Cl-indole at the 5-HT 3 A receptor. Br J Pharmacol 2016; 173:3467-3479. [PMID: 27677804 DOI: 10.1111/bph.13638] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 09/09/2016] [Accepted: 09/16/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND AND PURPOSE The 5-HT3 receptor is a prototypical member of the Cys-loop ligand-gated ion channel (LGIC) superfamily and an established therapeutic target. In addition to activation via the orthosteric site, receptor function can be modulated by allosteric ligands. We have investigated the pharmacological action of Cl-indole upon the 5-HT3 A receptor and identified that this positive allosteric modulator possesses a novel mechanism of action for LGICs. EXPERIMENTAL APPROACH The impact of Cl-indole upon the 5-HT3 receptor was assessed using single cell electrophysiological recordings and [3 H]-granisetron binding in HEK293 cells stably expressing the 5-HT3 receptor. KEY RESULTS Cl-indole failed to evoke 5-HT3 A receptor-mediated responses (up to 30 μM) or display affinity for the [3 H]-granisetron binding site. However, in the presence of Cl-indole, termination of 5-HT application revealed tail currents mediated via the 5-HT3 A receptor that were independent of the preceding 5-HT concentration but were antagonized by the 5-HT3 receptor antagonist, ondansetron. These tail currents were absent in the 5-HT3 AB receptor. Furthermore, the presence of 5-HT revealed a concentration-dependent increase in the affinity of Cl-indole for the orthosteric binding site of the human 5-HT3 A receptor. CONCLUSIONS AND IMPLICATIONS Cl-indole acts as both an orthosteric agonist and an allosteric modulator, but the presence of an orthosteric agonist (e.g. 5-HT) is a prerequisite to reveal both actions. Precedent for ago-allosteric action is available, yet the essential additional presence of an orthosteric agonist is now reported for the first time. This widening of the pharmacological mechanisms to modulate LGICs may offer further therapeutic opportunities.
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Affiliation(s)
- Andrew D Powell
- Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,School of Nursing Midwifery and Social Work, Birmingham City University, Edgbaston, UK
| | - Gillian Grafton
- Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Alexander Roberts
- Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Shannon Larkin
- Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nathanael O'Neill
- Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Josephine Palandri
- Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Reka Otvos
- Department of Molecular and Cellular Neurobiology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Alison J Cooper
- Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Chris Ulens
- Laboratory of Structural Neurobiology, KU Leuven, Leuven, Belgium
| | - Nicholas M Barnes
- Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
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Fokas AS, Cole DJ, Ahnert SE, Chin AW. Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis. Sci Rep 2016; 6:33213. [PMID: 27623708 PMCID: PMC5021933 DOI: 10.1038/srep33213] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/12/2016] [Indexed: 01/23/2023] Open
Abstract
Amino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can provide insight into protein function. Herein, we describe a novel AAN construction technique that employs the rigidity analysis tool, FIRST, to build the AAN, which we refer to as the residue geometry network (RGN). We show that this new construction can be combined with network theory methods to include the effects of allowed conformal motions and local chemical environments. Importantly, this is done without costly molecular dynamics simulations required by other AAN-related methods, which allows us to analyse large proteins and/or data sets. We have calculated the centrality of the residues belonging to 795 proteins. The results display a strong, negative correlation between residue centrality and the evolutionary rate. Furthermore, among residues with high closeness, those with low degree were particularly strongly conserved. Random walk simulations using the RGN were also successful in identifying allosteric residues in proteins involved in GPCR signalling. The dynamic function of these residues largely remain hidden in the traditional distance-cutoff construction technique. Despite being constructed from only the crystal structure, the results in this paper suggests that the RGN can identify residues that fulfil a dynamical function.
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Affiliation(s)
- Alexander S. Fokas
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Daniel J. Cole
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Sebastian E. Ahnert
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Alex W. Chin
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
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Di Maio D, Chandramouli B, Brancato G. Pathways and Barriers for Ion Translocation through the 5-HT3A Receptor Channel. PLoS One 2015; 10:e0140258. [PMID: 26465896 PMCID: PMC4605793 DOI: 10.1371/journal.pone.0140258] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 09/12/2015] [Indexed: 11/29/2022] Open
Abstract
Pentameric ligand gated ion channels (pLGICs) are ionotropic receptors that mediate fast intercellular communications at synaptic level and include either cation selective (e.g., nAChR and 5-HT3) or anion selective (e.g., GlyR, GABAA and GluCl) membrane channels. Among others, 5-HT3 is one of the most studied members, since its first cloning back in 1991, and a large number of studies have successfully pinpointed protein residues critical for its activation and channel gating. In addition, 5-HT3 is also the target of a few pharmacological treatments due to the demonstrated benefits of its modulation in clinical trials. Nonetheless, a detailed molecular analysis of important protein features, such as the origin of its ion selectivity and the rather low conductance as compared to other channel homologues, has been unfeasible until the recent crystallization of the mouse 5-HT3A receptor. Here, we present extended molecular dynamics simulations and free energy calculations of the whole 5-HT3A protein with the aim of better understanding its ion transport properties, such as the pathways for ion permeation into the receptor body and the complex nature of the selectivity filter. Our investigation unravels previously unpredicted structural features of the 5-HT3A receptor, such as the existence of alternative intersubunit pathways for ion translocation at the interface between the extracellular and the transmembrane domains, in addition to the one along the channel main axis. Moreover, our study offers a molecular interpretation of the role played by an arginine triplet located in the intracellular domain on determining the characteristic low conductance of the 5-HT3A receptor, as evidenced in previous experiments. In view of these results, possible implications on other members of the superfamily are suggested.
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Affiliation(s)
- Danilo Di Maio
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | | | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
- * E-mail:
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Abstract
Diverse neuropsychiatric disorders present dysfunctional memory and no effective treatment exits for them; likely as result of the absence of neural markers associated to memory. Neurotransmitter systems and signaling pathways have been implicated in memory and dysfunctional memory; however, their role is poorly understood. Hence, neural markers and cerebral functions and dysfunctions are revised. To our knowledge no previous systematic works have been published addressing these issues. The interactions among behavioral tasks, control groups and molecular changes and/or pharmacological effects are mentioned. Neurotransmitter receptors and signaling pathways, during normal and abnormally functioning memory with an emphasis on the behavioral aspects of memory are revised. With focus on serotonin, since as it is a well characterized neurotransmitter, with multiple pharmacological tools, and well characterized downstream signaling in mammals' species. 5-HT1A, 5-HT4, 5-HT5, 5-HT6, and 5-HT7 receptors as well as SERT (serotonin transporter) seem to be useful neural markers and/or therapeutic targets. Certainly, if the mentioned evidence is replicated, then the translatability from preclinical and clinical studies to neural changes might be confirmed. Hypothesis and theories might provide appropriate limits and perspectives of evidence.
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Affiliation(s)
- Alfredo Meneses
- Departamento de Farmacobiología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Mexico City, Mexico
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10
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Fokas AS, Cole DJ, Chin AW. Constrained geometric dynamics of the Fenna-Matthews-Olson complex: the role of correlated motion in reducing uncertainty in excitation energy transfer. PHOTOSYNTHESIS RESEARCH 2014; 122:275-292. [PMID: 25034014 DOI: 10.1007/s11120-014-0027-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
The trimeric Fenna-Mathews-Olson (FMO) complex of green sulphur bacteria is a well-studied example of a photosynthetic pigment-protein complex, in which the electronic properties of the pigments are modified by the protein environment to promote efficient excitonic energy transfer from antenna complexes to the reaction centres. By a range of simulation methods, many of the electronic properties of the FMO complex can be extracted from knowledge of the static crystal structure. However, the recent observation and analysis of long-lasting quantum dynamics in the FMO complex point to protein dynamics as a key factor in protecting and generating quantum coherence under laboratory conditions. While fast inter- and intra-molecular vibrations have been investigated extensively, the slow, conformational dynamics which effectively determine the optical inhomogeneous broadening of experimental ensembles has received less attention. The following study employs constrained geometric dynamics to study the flexibility in the protein network by efficiently generating the accessible conformational states from the published crystal structure. Statistical and principle component analyses reveal highly correlated low frequency motions between functionally relevant elements, including strong correlations between pigments that are excitonically coupled. Our analysis reveals a hierarchy of structural interactions which enforce these correlated motions, from the level of monomer-monomer interfaces right down to the α-helices, β-sheets and pigments. In addition to inducing strong spatial correlations across the conformational ensemble, we find that the overall rigidity of the FMO complex is exceptionally high. We suggest that these observations support the idea of highly correlated inhomogeneous disorder of the electronic excited states, which is further supported by the remarkably low variance (typically <5%) of the excitonic couplings of the conformational ensemble.
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Affiliation(s)
- Alexander S Fokas
- The Theory of Condensed Matter Group Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge, CB3 0HE, UK,
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Vardy E, Kenakin T. The tail wags the dog: possible mechanism for reverse allosteric control of ligand-activated channels. Br J Pharmacol 2014; 171:1614-6. [PMID: 24328812 DOI: 10.1111/bph.12550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 11/12/2013] [Indexed: 10/25/2022] Open
Abstract
In this issue of the British Journal of Pharmacology, a new article by Kozuska et al. discusses the multiple salt bridges in the intracellular domain of the 5HT3A receptor. These interactions increase the overall rigidity of the receptor, stabilize its low conducting state and affect the ligand cooperativity. The authors suggest that the allosteric effects of these regions on the receptor may be involved in a possible 'reverse' allosteric modulation of 5HT3 receptors.
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Affiliation(s)
- E Vardy
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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12
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X-ray structure of the mouse serotonin 5-HT3 receptor. Nature 2014; 512:276-81. [PMID: 25119048 DOI: 10.1038/nature13552] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 06/02/2014] [Indexed: 01/03/2023]
Abstract
Neurotransmitter-gated ion channels of the Cys-loop receptor family mediate fast neurotransmission throughout the nervous system. The molecular processes of neurotransmitter binding, subsequent opening of the ion channel and ion permeation remain poorly understood. Here we present the X-ray structure of a mammalian Cys-loop receptor, the mouse serotonin 5-HT3 receptor, at 3.5 Å resolution. The structure of the proteolysed receptor, made up of two fragments and comprising part of the intracellular domain, was determined in complex with stabilizing nanobodies. The extracellular domain reveals the detailed anatomy of the neurotransmitter binding site capped by a nanobody. The membrane domain delimits an aqueous pore with a 4.6 Å constriction. In the intracellular domain, a bundle of five intracellular helices creates a closed vestibule where lateral portals are obstructed by loops. This 5-HT3 receptor structure, revealing part of the intracellular domain, expands the structural basis for understanding the operating mechanism of mammalian Cys-loop receptors.
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13
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Belfield WJ, Cole DJ, Martin IL, Payne MC, Chau PL. Constrained geometric simulation of the nicotinic acetylcholine receptor. J Mol Graph Model 2014; 52:1-10. [PMID: 24955489 DOI: 10.1016/j.jmgm.2014.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 05/01/2014] [Accepted: 05/02/2014] [Indexed: 10/25/2022]
Abstract
Constrained geometric simulations have been performed for the recently published closed-channel state of the nicotinic acetylcholine receptor. These simulations support the theory that correlated motion in the flexible β-sheet structure of the extracellular domain helps to communicate a "conformational wave", spreading from the acetylcholine binding pocket. Furthermore, we have identified key residues that act at the interface between subunits and between domains that could potentially facilitate rapid communication between the binding site and the transmembrane gate.
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Affiliation(s)
- William J Belfield
- Theory of Condensed Matter Group, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Daniel J Cole
- Theory of Condensed Matter Group, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom; Department of Chemistry, Yale University, New Haven, CT 06520-8107, United States
| | - Ian L Martin
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Mike C Payne
- Theory of Condensed Matter Group, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - P-L Chau
- Bioinformatique Structurale, CNRS UMR 3528, Institut Pasteur, 75724 Paris, France.
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