1
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Kalinichenko L, Kornhuber J, Sinning S, Haase J, Müller CP. Serotonin Signaling through Lipid Membranes. ACS Chem Neurosci 2024; 15:1298-1320. [PMID: 38499042 PMCID: PMC10995955 DOI: 10.1021/acschemneuro.3c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
Serotonin (5-HT) is a vital modulatory neurotransmitter responsible for regulating most behaviors in the brain. An inefficient 5-HT synaptic function is often linked to various mental disorders. Primarily, membrane proteins controlling the expression and activity of 5-HT synthesis, storage, release, receptor activation, and inactivation are critical to 5-HT signaling in synaptic and extra-synaptic sites. Moreover, these signals represent information transmission across membranes. Although the lipid membrane environment is often viewed as fairly stable, emerging research suggests significant functional lipid-protein interactions with many synaptic 5-HT proteins. These protein-lipid interactions extend to almost all the primary lipid classes that form the plasma membrane. Collectively, these lipid classes and lipid-protein interactions affect 5-HT synaptic efficacy at the synapse. The highly dynamic lipid composition of synaptic membranes suggests that these lipids and their interactions with proteins may contribute to the plasticity of the 5-HT synapse. Therefore, this broader protein-lipid model of the 5-HT synapse necessitates a reconsideration of 5-HT's role in various associated mental disorders.
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Affiliation(s)
- Liubov
S. Kalinichenko
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
| | - Johannes Kornhuber
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
| | - Steffen Sinning
- Department
of Forensic Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Jana Haase
- School
of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Christian P. Müller
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
- Institute
of Psychopharmacology, Central Institute of Mental Health, Medical
Faculty Mannheim, Heidelberg University, 69047, Mannheim, Germany
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2
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Davolio AJ, J. Jankowski W, Várnai C, Irwin BWJ, Payne MC, Chau PL. Efficiently Differentiating Agonists and Competitive Antagonists for Weak Allosteric Protein-Ligand Interactions with Linear Response Theory. ACS OMEGA 2023; 8:44537-44544. [PMID: 38046342 PMCID: PMC10688131 DOI: 10.1021/acsomega.3c03503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/05/2023] [Indexed: 12/05/2023]
Abstract
What makes an agonist and a competitive antagonist? In this work, we aim to answer this question by performing parallel tempering Monte Carlo simulations on the serotonin type 3A (5-HT3A) receptor. We use linear response theory to predict conformational changes in the 5-HT3A receptor active site after weak perturbations are applied to its allosteric binding sites. A covariance tensor is built from conformational sampling of its apo state, and a harmonic approximation allows us to substitute the calculation of ligand-induced forces with the binding site's displacement vector. Remarkably, our study demonstrates the feasibility of effectively discerning between agonists and competitive antagonists for multiple ligands, requiring computationally expensive calculations only once per protein.
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Affiliation(s)
- Anthony J. Davolio
- Theory
of Condensed Matter Group, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Wojciech J. Jankowski
- Theory
of Condensed Matter Group, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Csilla Várnai
- Centre
for Computational Biology, University of
Birmingham, Birmingham B15 2TT, U.K.
- Institute
of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, U.K.
| | - Benedict W. J. Irwin
- Theory
of Condensed Matter Group, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Michael C. Payne
- Theory
of Condensed Matter Group, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Pak-Lee Chau
- Bioinformatique
Structurale, Institut Pasteur, CNRS URA
3528, CB3I CNRS USR 3756, 75724 Paris, France
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3
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Li Z, Chan KC, Nickels JD, Cheng X. Molecular Dynamics Refinement of Open State Serotonin 5-HT 3A Receptor Structures. J Chem Inf Model 2023; 63:1196-1207. [PMID: 36757760 DOI: 10.1021/acs.jcim.2c01441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Pentameric ligand-gated ion channels play an important role in mediating fast neurotransmissions. As a member of this receptor family, cation-selective 5-HT3 receptors are a clinical target for treating nausea and vomiting associated with chemotherapy and radiation therapy (Thompson and Lummis, 2006). Multiple cryo-electron microscopy (cryo-EM) structures of 5-HT3 receptors have been determined in distinct functional states (e.g., open, closed, etc.) (Basak et al., 2018; Basak et al., 2018; Polovinkin et al., 2018; Zhang et al., 2015). However, recent work has shown that the transmembrane pores of the open 5-HT3 receptor structures rapidly collapse and become artificially asymmetric in molecular dynamics (MD) simulations. To avoid this hydrophobic collapse, Dämgen and Biggin developed an equilibration protocol that led to a stable open state structure of the glycine receptor in MD simulations (Dämgen and Biggin, 2020). However, the protocol failed to yield open-like structures of the 5-HT3 receptor in our simulations. Here, we present a refined equilibration protocol that involves the rearrangement of the transmembrane helices to achieve stable open state structures of the 5-HT3 receptor that allow both water and ion permeation through the channel. Notably, channel gating is mediated through collective movement of the transmembrane helices, involving not only pore lining M2 helices but also their cross-talk with the adjacent M1 and M3 helices. Thus, the successful application of our refined equilibration protocol underscores the importance of the conformational coupling between the transmembrane helices in stabilizing open-like structures of the 5-HT3 receptor.
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Affiliation(s)
- Zoe Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio 43210, United States
| | - Kevin C Chan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio 43210, United States
| | - Jonathan D Nickels
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio 43210, United States.,Translational Data Analytics Institute (TDAI) at The Ohio State University, Columbus, Ohio 43210, United States
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4
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Recent Insight into Lipid Binding and Lipid Modulation of Pentameric Ligand-Gated Ion Channels. Biomolecules 2022; 12:biom12060814. [PMID: 35740939 PMCID: PMC9221113 DOI: 10.3390/biom12060814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/03/2022] [Accepted: 06/08/2022] [Indexed: 02/04/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) play a leading role in synaptic communication, are implicated in a variety of neurological processes, and are important targets for the treatment of neurological and neuromuscular disorders. Endogenous lipids and lipophilic compounds are potent modulators of pLGIC function and may help shape synaptic communication. Increasing structural and biophysical data reveal sites for lipid binding to pLGICs. Here, we update our evolving understanding of pLGIC–lipid interactions highlighting newly identified modes of lipid binding along with the mechanistic understanding derived from the new structural data.
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5
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Mesoy SM, Bridgland-Taylor M, Lummis SCR. Mutations of the nACh Receptor M4 Helix Reveal Different Phenotypes in Different Expression Systems: Could Lipids be Responsible? Front Physiol 2022; 13:850782. [PMID: 35600303 PMCID: PMC9116227 DOI: 10.3389/fphys.2022.850782] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/31/2022] [Indexed: 11/18/2022] Open
Abstract
The role of the outermost helix (M4) in the pentameric ligand-gated ion channel (pLGIC) family is currently not fully understood. It is known that M4 is important for receptor assembly, possibly via interactions with neighboring M1 and M3 helices. M4 can also transmit information on the lipid content of the membrane to the gating mechanism, and it may form a link to the extracellular domain via the Cys-loop. Our previous study examining the α4β2 nACh receptor M4 helix using HEK cells indicated M4 here is more sensitive to change than those of other pLGIC. Many of these other studies, however, were performed in Xenopus oocytes. Here we examine the nine previously identified nonfunctional α4β2 nACh receptor M4 mutant receptors using this system. The data reveal that seven of these mutant receptors do function when expressed in oocytes, with only 2, the conserved Asp at the intracellular end of M4 and a Phe in the center, having a similar phenotype (nonfunctional) in both HEK cells and oocytes. The oocyte data are more consistent with studies in other pLGIC and demonstrate the importance of the expression system used. Of the many differences between these two expression systems, we suggest that the different lipid content of the plasma membrane is a possible candidate for explaining these discrepancies.
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Affiliation(s)
- Susanne M. Mesoy
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Bridgland-Taylor
- Clinical Pharmacology and Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Sarah C. R. Lummis,
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6
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Heusser SA, Borg CB, Colding JM, Pless SA. Conformational decoupling in acid-sensing ion channels uncovers mechanism and stoichiometry of PcTx1-mediated inhibition. eLife 2022; 11:73384. [PMID: 35156612 PMCID: PMC8871370 DOI: 10.7554/elife.73384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/11/2022] [Indexed: 01/10/2023] Open
Abstract
Acid-sensing ion channels (ASICs) are trimeric proton-gated cation channels involved in fast synaptic transmission. Pharmacological inhibition of ASIC1a reduces neurotoxicity and stroke infarct volumes, with the cysteine knot toxin psalmotoxin-1 (PcTx1) being one of the most potent and selective inhibitors. PcTx1 binds at the subunit interface in the extracellular domain (ECD), but the mechanism and conformational consequences of the interaction, as well as the number of toxin molecules required for inhibition, remain unknown. Here, we use voltage-clamp fluorometry and subunit concatenation to decipher the mechanism and stoichiometry of PcTx1 inhibition of ASIC1a. Besides the known inhibitory binding mode, we propose PcTx1 to have at least two additional binding modes that are decoupled from the pore. One of these modes induces a long-lived ECD conformation that reduces the activity of an endogenous neuropeptide. This long-lived conformational state is proton-dependent and can be destabilized by a mutation that decreases PcTx1 sensitivity. Lastly, the use of concatemeric channel constructs reveals that disruption of a single PcTx1 binding site is sufficient to destabilize the toxin-induced conformation, while functional inhibition is not impaired until two or more binding sites are mutated. Together, our work provides insight into the mechanism of PcTx1 inhibition of ASICs and uncovers a prolonged conformational change with possible pharmacological implications.
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Affiliation(s)
- Stephanie A Heusser
- Department of Drug Design and Pharmacology, University of Copenhagen, Copehagen, Denmark
| | - Christian B Borg
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Janne M Colding
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Stephan A Pless
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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7
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Irving H, Turek I, Kettle C, Yaakob N. Tapping into 5-HT 3 Receptors to Modify Metabolic and Immune Responses. Int J Mol Sci 2021; 22:ijms222111910. [PMID: 34769340 PMCID: PMC8584345 DOI: 10.3390/ijms222111910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 02/07/2023] Open
Abstract
5-hydroxytryptamine type 3 (5-HT3) receptors are ligand gated ion channels, which clearly distinguish their mode of action from the other G-protein coupled 5-HT or serotonin receptors. 5-HT3 receptors are well established targets for emesis and gastrointestinal mobility and are used as adjunct targets in treating schizophrenia. However, the distribution of these receptors is wider than the nervous system and there is potential that these additional sites can be targeted to modulate inflammatory and/or metabolic conditions. Recent progress in structural biology and pharmacology of 5-HT3 receptors have provided profound insights into mechanisms of their action. These advances, combined with insights into clinical relevance of mutations in genes encoding 5-HT3 subunits and increasing understanding of their implications in patient's predisposition to diseases and response to the treatment, open new avenues for personalized precision medicine. In this review, we recap on the current status of 5-HT3 receptor-based therapies using a biochemical and physiological perspective. We assess the potential for targeting 5-HT3 receptors in conditions involving metabolic or inflammatory disorders based on recent findings, underscoring the challenges and limitations of this approach.
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Affiliation(s)
- Helen Irving
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC 3550, Australia; (I.T.); (C.K.)
- Correspondence:
| | - Ilona Turek
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC 3550, Australia; (I.T.); (C.K.)
| | - Christine Kettle
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC 3550, Australia; (I.T.); (C.K.)
| | - Nor Yaakob
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Malaysia;
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8
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Bergh C, Heusser SA, Howard R, Lindahl E. Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel. eLife 2021; 10:68369. [PMID: 34652272 PMCID: PMC8635979 DOI: 10.7554/elife.68369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 10/14/2021] [Indexed: 01/03/2023] Open
Abstract
Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels, the details of gating remain unclear, partly due to limited structural data and simulation timescales. Here, we used enhanced sampling to simulate the pH-gated channel GLIC, and construct Markov state models (MSMs) of gating. Consistent with new functional recordings, we report in oocytes, our analysis revealed differential effects of protonation and mutation on free-energy wells. Clustering of closed- versus open-like states enabled estimation of open probabilities and transition rates, while higher-order clustering affirmed conformational trends in gating. Furthermore, our models uncovered state- and protonation-dependent symmetrization. This demonstrates the applicability of MSMs to map energetic and conformational transitions between ion-channel functional states, and how they reproduce shifts upon activation or mutation, with implications for modeling neuronal function and developing state-selective drugs.
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Affiliation(s)
- Cathrine Bergh
- Science for Life Laboratory and Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Stephanie A Heusser
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Rebecca Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Erik Lindahl
- Science for Life Laboratory and Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
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9
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Abstract
Molecular simulations of biological molecules require an accurate description of molecular interactions through a force field (FF). The focus of this Perspective is on all-atom lipid FFs. Recent additions to the CHARMM36 lipid FF continue to expand a researcher's ability to probe membrane structure and function with a wide variety of biologically important lipids. Currently, there is an effort to reduce the assumptions in all-atom lipid FFs. The inclusion of long-range dispersion interaction through particle-mesh Ewald is allowing for more accurate descriptions of lipid bilayer and monolayer properties without additional computational cost. Soon, simulations with lipid FFs will no longer depend on short-range cutoffs and will accurately represent long-range dispersion. This requires efficient FF parametrization with an automated approach due to FF complexity. In addition, polarizable FFs for lipids will be important for the next generation of simulations that accurately represent how molecule interactions respond to a varied environment.
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10
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Crnjar A, Mesoy SM, Lummis SCR, Molteni C. A Single Mutation in the Outer Lipid-Facing Helix of a Pentameric Ligand-Gated Ion Channel Affects Channel Function Through a Radially-Propagating Mechanism. Front Mol Biosci 2021; 8:644720. [PMID: 33996899 PMCID: PMC8119899 DOI: 10.3389/fmolb.2021.644720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate fast synaptic transmission and are crucial drug targets. Their gating mechanism is triggered by ligand binding in the extracellular domain that culminates in the opening of a hydrophobic gate in the transmembrane domain. This domain is made of four α-helices (M1 to M4). Recently the outer lipid-facing helix (M4) has been shown to be key to receptor function, however its role in channel opening is still poorly understood. It could act through its neighboring helices (M1/M3), or via the M4 tip interacting with the pivotal Cys-loop in the extracellular domain. Mutation of a single M4 tyrosine (Y441) to alanine renders one pLGIC-the 5-HT3A receptor-unable to function despite robust ligand binding. Using Y441A as a proxy for M4 function, we here predict likely paths of Y441 action using molecular dynamics, and test these predictions with functional assays of mutant receptors in HEK cells and Xenopus oocytes using fluorescent membrane potential sensitive dye and two-electrode voltage clamp respectively. We show that Y441 does not act via the M4 tip or Cys-loop, but instead connects radially through M1 to a residue near the ion channel hydrophobic gate on the pore-lining helix M2. This demonstrates the active role of the M4 helix in channel opening.
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Affiliation(s)
| | - Susanne M. Mesoy
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Carla Molteni
- Physics Department, King's College London, London, United Kingdom
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11
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Asymmetric opening of the homopentameric 5-HT 3A serotonin receptor in lipid bilayers. Nat Commun 2021; 12:1074. [PMID: 33594077 PMCID: PMC7887223 DOI: 10.1038/s41467-021-21016-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop receptor family are key players in fast signal transduction throughout the nervous system. They have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. We report three structures of the Cys-loop 5-HT3A serotonin receptor (5HT3R) reconstituted into saposin-based lipid bilayer discs: a symmetric and an asymmetric apo state, and an asymmetric agonist-bound state. In comparison to previously published 5HT3R conformations in detergent, the lipid bilayer stabilises the receptor in a more tightly packed, ‘coupled’ state, involving a cluster of highly conserved residues. In consequence, the agonist-bound receptor conformation adopts a wide-open pore capable of conducting sodium ions in unbiased molecular dynamics (MD) simulations. Taken together, we provide a structural basis for the modulation of 5HT3R by the membrane environment, and a model for asymmetric activation of the receptor. Pentameric ligand-gated ion channels (pLGICs) are key players in neurotransmission and have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. Here, the authors report structures of the pLGIC 5-HT3A serotonin receptor reconstituted into lipid bilayer discs and reveal lipid–protein interactions as well as asymmetric activation of the homopentameric receptor.
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12
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Rao S, Klesse G, Lynch CI, Tucker SJ, Sansom MSP. Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions. J Phys Chem B 2021; 125:981-994. [PMID: 33439645 PMCID: PMC7869105 DOI: 10.1021/acs.jpcb.0c09285] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/13/2020] [Indexed: 12/30/2022]
Abstract
Ion channels are proteins which form gated nanopores in biological membranes. Many channels exhibit hydrophobic gating, whereby functional closure of a pore occurs by local dewetting. The pentameric ligand gated ion channels (pLGICs) provide a biologically important example of hydrophobic gating. Molecular simulation studies comparing additive vs polarizable models indicate predictions of hydrophobic gating are robust to the model employed. However, polarizable models suggest favorable interactions of hydrophobic pore-lining regions with chloride ions, of relevance to both synthetic carriers and channel proteins. Electrowetting of a closed pLGIC hydrophobic gate requires too high a voltage to occur physiologically but may inform designs for switchable nanopores. Global analysis of ∼200 channels yields a simple heuristic for structure-based prediction of (closed) hydrophobic gates. Simulation-based analysis is shown to provide an aid to interpretation of functional states of new channel structures. These studies indicate the importance of understanding the behavior of water and ions within the nanoconfined environment presented by ion channels.
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Affiliation(s)
- Shanlin Rao
- Department
of Biochemistry, University of Oxford, Oxford, U.K.
| | - Gianni Klesse
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford, U.K.
| | | | - Stephen J. Tucker
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford, U.K.
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13
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Orädd F, Andersson M. Tracking Membrane Protein Dynamics in Real Time. J Membr Biol 2021; 254:51-64. [PMID: 33409541 PMCID: PMC7936944 DOI: 10.1007/s00232-020-00165-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022]
Abstract
Abstract Membrane proteins govern critical cellular processes and are central to human health and associated disease. Understanding of membrane protein function is obscured by the vast ranges of structural dynamics—both in the spatial and time regime—displayed in the protein and surrounding membrane. The membrane lipids have emerged as allosteric modulators of membrane protein function, which further adds to the complexity. In this review, we discuss several examples of membrane dependency. A particular focus is on how molecular dynamics (MD) simulation have aided to map membrane protein dynamics and how enhanced sampling methods can enable observing the otherwise inaccessible biological time scale. Also, time-resolved X-ray scattering in solution is highlighted as a powerful tool to track membrane protein dynamics, in particular when combined with MD simulation to identify transient intermediate states. Finally, we discuss future directions of how to further develop this promising approach to determine structural dynamics of both the protein and the surrounding lipids. Graphic Abstract ![]()
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
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14
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Cholesterol content in the membrane promotes key lipid-protein interactions in a pentameric serotonin-gated ion channel. Biointerphases 2021; 15:061018. [PMID: 33397116 DOI: 10.1116/6.0000561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs), embedded in the lipid membranes of nerve cells, mediate fast synaptic transmission and are major pharmaceutical targets. Because of their complexity and the limited knowledge of their structure, their working mechanisms have still to be fully unraveled at the molecular level. Over the past few years, evidence that the lipid membrane may modulate the function of membrane proteins, including pLGICs, has emerged. Here, we investigate, by means of molecular dynamics simulations, the behavior of the lipid membrane at the interface with the 5-HT3A receptor (5-HT3AR), a representative pLGIC which is the target of nausea-suppressant drugs, in a nonconductive state. Three lipid compositions are studied, spanning different concentrations of the phospholipids, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, and of cholesterol, hence a range of viscosities. A variety of lipid interactions and persistent binding events to different parts of the receptor are revealed in the investigated models, providing snapshots of the dynamical environment at the membrane-receptor interface. Some of these events result in lipid intercalation within the transmembrane domain, and others reach out to protein key sections for signal transmission and receptor activation, such as the Cys-loop and the M2-M3 loop. In particular, phospholipids, with their long hydrophobic tails, play an important role in these interactions, potentially providing a bridge between these two structures. A higher cholesterol content appears to promote lipid persistent binding to the receptor.
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15
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Bochicchio A, Brandner AF, Engberg O, Huster D, Böckmann RA. Spontaneous Membrane Nanodomain Formation in the Absence or Presence of the Neurotransmitter Serotonin. Front Cell Dev Biol 2020; 8:601145. [PMID: 33330494 PMCID: PMC7734319 DOI: 10.3389/fcell.2020.601145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/06/2020] [Indexed: 11/23/2022] Open
Abstract
Detailed knowledge on the formation of biomembrane domains, their structure, composition, and physical characteristics is scarce. Despite its frequently discussed importance in signaling, e.g., in obtaining localized non-homogeneous receptor compositions in the plasma membrane, the nanometer size as well as the dynamic and transient nature of domains impede their experimental characterization. In turn, atomistic molecular dynamics (MD) simulations combine both, high spatial and high temporal resolution. Here, using microsecond atomistic MD simulations, we characterize the spontaneous and unbiased formation of nano-domains in a plasma membrane model containing phosphatidylcholine (POPC), palmitoyl-sphingomyelin (PSM), and cholesterol (Chol) in the presence or absence of the neurotransmitter serotonin at different temperatures. In the ternary mixture, highly ordered and highly disordered domains of similar composition coexist at 303 K. The distinction of domains by lipid acyl chain order gets lost at lower temperatures of 298 and 294 K, suggesting a phase transition at ambient temperature. By comparison of domain ordering and composition, we demonstrate how the domain-specific binding of the neurotransmitter serotonin results in a modified domain lipid composition and a substantial downward shift of the phase transition temperature. Our simulations thus suggest a novel mode of action of neurotransmitters possibly of importance in neuronal signal transmission.
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Affiliation(s)
- Anna Bochicchio
- Computational Biology, Department Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Astrid F Brandner
- Computational Biology, Department Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Oskar Engberg
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany.,Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Rainer A Böckmann
- Computational Biology, Department Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
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16
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Basak S, Kumar A, Ramsey S, Gibbs E, Kapoor A, Filizola M, Chakrapani S. High-resolution structures of multiple 5-HT 3AR-setron complexes reveal a novel mechanism of competitive inhibition. eLife 2020; 9:e57870. [PMID: 33063666 PMCID: PMC7655109 DOI: 10.7554/elife.57870] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Serotonin receptors (5-HT3AR) play a crucial role in regulating gut movement, and are the principal target of setrons, a class of high-affinity competitive antagonists, used in the management of nausea and vomiting associated with radiation and chemotherapies. Structural insights into setron-binding poses and their inhibitory mechanisms are just beginning to emerge. Here, we present high-resolution cryo-EM structures of full-length 5-HT3AR in complex with palonosetron, ondansetron, and alosetron. Molecular dynamic simulations of these structures embedded in a fully-hydrated lipid environment assessed the stability of ligand-binding poses and drug-target interactions over time. Together with simulation results of apo- and serotonin-bound 5-HT3AR, the study reveals a distinct interaction fingerprint between the various setrons and binding-pocket residues that may underlie their diverse affinities. In addition, varying degrees of conformational change in the setron-5-HT3AR structures, throughout the channel and particularly along the channel activation pathway, suggests a novel mechanism of competitive inhibition.
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Affiliation(s)
- Sandip Basak
- Department of Physiology and Biophysics, Case Western Reserve UniversityClevelandUnited States
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve UniversityClevelandUnited States
| | - Arvind Kumar
- Department of Physiology and Biophysics, Case Western Reserve UniversityClevelandUnited States
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve UniversityClevelandUnited States
| | - Steven Ramsey
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Eric Gibbs
- Department of Physiology and Biophysics, Case Western Reserve UniversityClevelandUnited States
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve UniversityClevelandUnited States
| | - Abhijeet Kapoor
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve UniversityClevelandUnited States
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve UniversityClevelandUnited States
- Department of Neuroscience, School of Medicine, Case Western Reserve UniversityClevelandUnited States
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17
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Gupta P, Liang Z, Freed JH. Microsecond dynamics in proteins by two-dimensional ESR: Predictions. J Chem Phys 2020; 152:214112. [PMID: 32505151 PMCID: PMC7863697 DOI: 10.1063/5.0008094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/14/2020] [Indexed: 01/04/2023] Open
Abstract
Two-dimensional electron-electron double resonance (2D-ELDOR) provides extensive insight into molecular motions. Recent developments permitting experiments at higher frequencies (95 GHz) provide molecular orientational resolution, enabling a clearer description of the nature of the motions. In this work, simulations are provided for the example of domain motions within proteins that are themselves slowly tumbling in solution. These show the nature of the exchange cross-peaks that are predicted to develop in real time from such domain motions. However, we find that the existing theoretical methods for computing 2D-ELDOR experiments over a wide motional range begin to fail seriously when applied to very slow motions characteristic of proteins in solution. One reason is the failure to obtain accurate eigenvectors and eigenvalues of the complex symmetric stochastic Liouville matrices describing the experiment when computed by the efficient Lanczos algorithm in the range of very slow motion. Another, perhaps more serious, issue is that these matrices are "non-normal," such that for the very slow motional range even rigorous diagonalization algorithms do not yield the correct eigenvalues and eigenvectors. We have employed algorithms that overcome both these issues and lead to valid 2D-ELDOR predictions even for motions approaching the rigid limit. They are utilized to describe the development of cross-peaks in 2D-ELDOR at 95 GHz for a particular case of domain motion.
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Affiliation(s)
- Pranav Gupta
- Department of Chemistry and Chemical Biology, National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, USA
| | - Zhichun Liang
- Department of Chemistry and Chemical Biology, National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, USA
| | - Jack H. Freed
- Department of Chemistry and Chemical Biology, National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, New York 14853, USA
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18
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Varadarajan V, Desikan R, Ayappa KG. Assessing the extent of the structural and dynamic modulation of membrane lipids due to pore forming toxins: insights from molecular dynamics simulations. SOFT MATTER 2020; 16:4840-4857. [PMID: 32421131 DOI: 10.1039/d0sm00086h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Infections caused by many virulent bacterial strains are triggered by the release of pore forming toxins (PFTs), which form oligomeric transmembrane pore complexes on the target plasma membrane. The spatial extent of the perturbation to the surrounding lipids during pore formation is relatively unexplored. Using all-atom molecular dynamics simulations, we investigate the changes in the structure and dynamics of lipids in a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer in the presence of contrasting PFTs. Cytolysin A (ClyA), an α toxin with its inserted wedge shaped bundle of inserted α helices, induces significant asymmetry across the membrane leaflets in comparison with α hemolysin (AHL), a β toxin. Despite the differences in hydrophobic mismatch and uniquely different topologies of the two oligomers, perturbations to lipid order as reflected in the tilt angle and order parameters and membrane thinning are short ranged, lying within ∼2.5 nm from the periphery of either pore complex, and commensurate with distances typically associated with van der Waals forces. In contrast, the spatial extent of perturbations to the lipid dynamics extends outward to at least 4 nm for both proteins, and the continuous survival probabilities reveal the presence of a tightly bound shell of lipids in this region. Displacement probability distributions show long tails and the distinctly non-Gaussian features reflect the induced dynamic heterogeneity. A detailed profiling of the protein-lipid contacts with tyrosine, tryptophan, lysine and arginine residues shows increased non-polar contacts in the cytoplasmic leaflet for both PFTs, with a higher number of atomic contacts in the case of AHL in the extracellular leaflet due to the mushroom-like topology of the pore complex. The short ranged nature of the perturbations observed in this simple one component membrane suggests inherent plasticity of membrane lipids enabling the recovery of the structure and membrane fluidity even in the presence of these large oligomeric transmembrane protein assemblies. This observation has implications in membrane repair processes such as budding or vesicle fusion events used to mitigate PFT virulence, where the underlying lipid dynamics and fluidity in the vicinity of the pore complex are expected to play an important role.
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Affiliation(s)
- Vadhana Varadarajan
- Department of Chemical Engineering, Indian Institute of Science, Bangalore-560012, India.
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19
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Várnai C, Irwin BWJ, Payne MC, Csányi G, Chau PL. Functional movements of the GABA type A receptor. Phys Chem Chem Phys 2020; 22:16023-16031. [DOI: 10.1039/d0cp01128b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have performed a Monte Carlo simulation of the GABA type A receptor. We have analysed the configurations and developed a correlation tensor method to predict receptor gating.
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Affiliation(s)
- Csilla Várnai
- Centre for Computational Biology
- University of Birmingham
- Birmingham
- UK
| | - B. W. J. Irwin
- Theory of Condensed Matter Group
- Cavendish Laboratory, Department of Physics
- University of Cambridge
- Cambridge CB3 0HE
- UK
| | - M. C. Payne
- Theory of Condensed Matter Group
- Cavendish Laboratory, Department of Physics
- University of Cambridge
- Cambridge CB3 0HE
- UK
| | - Gábor Csányi
- Department of Engineering
- University of Cambridge
- Cambridge CB2 1PZ
- UK
| | - P.-L. Chau
- Bioinformatique Structurale
- Institut Pasteur CNRS URA 3528
- CB3I CNRS USR 3756
- 75724 Paris
- France
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