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Seljeset S, Sintsova O, Wang Y, Harb HY, Lynagh T. Constitutive activity of ionotropic glutamate receptors via hydrophobic substitutions in the ligand-binding domain. Structure 2024; 32:966-978.e6. [PMID: 38677289 DOI: 10.1016/j.str.2024.04.001] [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: 08/11/2023] [Revised: 02/11/2024] [Accepted: 04/02/2024] [Indexed: 04/29/2024]
Abstract
Neurotransmitter ligands electrically excite neurons by activating ionotropic glutamate receptor (iGluR) ion channels. Knowledge of the iGluR amino acid residues that dominate ligand-induced activation would enable the prediction of function from sequence. We therefore explored the molecular determinants of activity in rat N-methyl-D-aspartate (NMDA)-type iGluRs (NMDA receptors), complex heteromeric iGluRs comprising two glycine-binding GluN1 and two glutamate-binding GluN2 subunits, using amino acid sequence analysis, mutagenesis, and electrophysiology. We find that a broadly conserved aspartate residue controls both ligand potency and channel activity, to the extent that certain substitutions at this position bypass the need for ligand binding in GluN1 subunits, generating NMDA receptors activated solely by glutamate. Furthermore, we identify a homomeric iGluR from the placozoan Trichoplax adhaerens that has utilized native mutations of this crucial residue to evolve into a leak channel that is inhibited by neurotransmitter binding, pointing to a dominant role of this residue throughout the iGluR superfamily.
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Affiliation(s)
- Sandra Seljeset
- Michael Sars Centre, University of Bergen, 5008 Bergen, Norway
| | - Oksana Sintsova
- Michael Sars Centre, University of Bergen, 5008 Bergen, Norway
| | - Yuhong Wang
- Michael Sars Centre, University of Bergen, 5008 Bergen, Norway
| | - Hassan Y Harb
- Concept Life Sciences Limited, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG High Peak, UK
| | - Timothy Lynagh
- Michael Sars Centre, University of Bergen, 5008 Bergen, Norway.
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2
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Extracellular mutation induces an allosteric effect across the membrane and hampers the activity of MRP1 (ABCC1). Sci Rep 2021; 11:12024. [PMID: 34103599 PMCID: PMC8187718 DOI: 10.1038/s41598-021-91461-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/24/2021] [Indexed: 01/10/2023] Open
Abstract
Dynamic conformational changes play a major role in the function of proteins, including the ATP-Binding Cassette (ABC) transporters. Multidrug Resistance Protein 1 (MRP1) is an ABC exporter that protects cells from toxic molecules. Overexpression of MRP1 has been shown to confer Multidrug Resistance (MDR), a phenomenon in which cancer cells are capable to defend themselves against a broad variety of drugs. In this study, we used varied computational techniques to explore the unique F583A mutation that is known to essentially lock the transporter in a low-affinity solute binding state. We demonstrate how macro-scale conformational changes affect MRP1’s stability and dynamics, and how these changes correspond to micro-scale structural perturbations in helices 10–11 and the nucleotide-binding domains (NBDs) of the protein in regions known to be crucial for its ATPase activity. We demonstrate how a single substitution of an outward-facing aromatic amino acid causes a long-range allosteric effect that propagates across the membrane, ranging from the extracellular ECL5 loop to the cytoplasmic NBD2 over a distance of nearly 75 Å, leaving the protein in a non-functional state, and provide the putative allosteric pathway. The identified allosteric structural pathway is not only in agreement with experimental data but enhances our mechanical understanding of MRP1, thereby facilitating the rational design of chemosensitizers toward the success of chemotherapy treatments.
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3
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Saranya V, Radhika R, Shankar R, Vijayakumar S. In silico studies of the inhibition mechanism of dengue with papain. J Biomol Struct Dyn 2020; 39:1912-1927. [PMID: 32249700 DOI: 10.1080/07391102.2020.1742205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and His159) complexes are analysed by Density Functional Theory (M06-2X/cc-pVDZ) method. Among the E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and Hys159) complexes, E-protein(Glu76)…Papain(Cys25) complex has the highest interaction value of -352.22 kcal/mol. Moreover, the natural bond orbital analysis also supports the above results. The 100 ns Molecular Dynamics simulation reveals that, E-protein(Ala54-Ile129)…Papain(Cys25) complex had the lowest root mean square deviation value of 1 Å compared to the E-protein(Ala54-Ile129)… Papain(Asn175 & His159) complexes. The salt bridge formation between the Asp103 and Lys110 residues are the important stabilizing factor in E-protein(Ala54-Ile129)…Papain(Cys25) complex. This result can extend our knowledge of the functional behaviour of Papain and provides structural insight to target Envelope protein as forthcoming drug targets in Dengue.
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4
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Dämgen MA, Biggin PC. Computational methods to examine conformational changes and ligand-binding properties: Examples in neurobiology. Neurosci Lett 2019. [DOI: 10.1016/j.neulet.2018.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Krieger J, Lee JY, Greger IH, Bahar I. Activation and desensitization of ionotropic glutamate receptors by selectively triggering pre-existing motions. Neurosci Lett 2018; 700:22-29. [PMID: 29481851 PMCID: PMC6107436 DOI: 10.1016/j.neulet.2018.02.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/15/2018] [Accepted: 02/22/2018] [Indexed: 01/03/2023]
Abstract
Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are key players in synaptic transmission and plasticity. They are composed of four subunits, each containing four functional domains, the quaternary packing and collective structural dynamics of which are important determinants of their molecular mechanism of function. With the explosion of structural studies on different members of the family, including the structures of activated open channels, the mechanisms of action of these central signaling machines are now being elucidated. We review the current state of computational studies on two major members of the family, AMPA and NMDA receptors, with focus on molecular simulations and elastic network model analyses that have provided insights into the coupled movements of extracellular and transmembrane domains. We describe the newly emerging mechanisms of activation, allosteric signaling and desensitization, as mainly a selective triggering of pre-existing soft motions, as deduced from computational models and analyses that leverage structural data on intact AMPA and NMDA receptors in different states.
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Affiliation(s)
- James Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, 15260, United States
| | - Ji Young Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, 15260, United States
| | - Ingo H Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA, 15260, United States.
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6
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Haslak ZP, Bozkurt E, Dutagaci B, De Proft F, Aviyente V, De Vleeschouwer F. A DFT approach to discriminate the antagonist and partial agonist activity of ligands binding to the NMDA receptor. Mol Phys 2018. [DOI: 10.1080/00268976.2017.1384579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Zeynep Pinar Haslak
- Department of Chemistry, Bogaziçi University, Bebek, Istanbul, Turkey
- Faculty of Science and Letters, Piri Reis University, Tuzla, Istanbul, Turkey
| | - Esra Bozkurt
- Department of Chemistry, Bogaziçi University, Bebek, Istanbul, Turkey
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bercem Dutagaci
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, MI, USA
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Viktorya Aviyente
- Department of Chemistry, Bogaziçi University, Bebek, Istanbul, Turkey
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7
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Silva RHM, Lima NDFM, Lopes AJO, Vasconcelos CC, de Mesquita JWC, de Mesquita LSS, Lima FCVM, Ribeiro MNDS, Ramos RM, Cartágenes MDSDS, Garcia JBS. Antinociceptive Activity of Borreria verticillata: In vivo and In silico Studies. Front Pharmacol 2017; 8:283. [PMID: 28588488 PMCID: PMC5439013 DOI: 10.3389/fphar.2017.00283] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/04/2017] [Indexed: 01/08/2023] Open
Abstract
Borreria verticillata (L.) G. Mey. known vassourinha has antibacterial, antimalarial, hepatoprotective, antioxidative, analgesic, and anti-inflammatory, however, its antinociceptive action requires further studies. Aim of the study evaluated the antinociceptive activity of B. verticillata hydroalcoholic extract (EHBv) and ethyl acetate fraction (FAc) by in vivo and in silico studies. In vivo assessment included the paw edema test, writhing test, formalin test and tail flick test. Wistar rats and Swiss mice were divided into 6 groups and given the following treatments oral: 0.9% NaCl control group (CTRL), 10 mg/kg memantine (MEM), 10 mg/kg indomethacin (INDO), 500 mg/kg EHBv (EHBv 500), 25 mg/kg FAc (FAc 25) and 50 mg/kg FAc (FAc 50). EHBv, FAc 25 and 50 treatments exhibited anti-edematous and peripheral antinociceptive effects. For in silico assessment, compounds identified in FAc were subjected to molecular docking with COX-2, GluN1a and GluN2B. Ursolic acid (UA) was the compound with best affinity parameters (binding energy and inhibition constant) for COX-2, GluN1a, GluN2B, and was selected for further analysis with molecular dynamics (MD) simulations. In MD simulations, UA exhibited highly frequent interactions with residues Arg120 and Glu524 in the COX-2 active site and NMDA, whereby it might prevent COX-2 and NMDA receptor activation. Treatment with UA 10 mg/Kg showed peripheral and central antinociceptive effect. The antinociceptive effect of B. verticillata might be predominantly attributed to peripheral actions, including the participation of anti-inflammatory components. Ursolic acid is the main active component and seems to be a promising source of COX-2 inhibitors and NMDA receptor antagonists.
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Affiliation(s)
- Rosa H M Silva
- Experimental Study of Pain Laboratory, Department of Physiological Sciences, Federal University of MaranhãoSão Luís, Brazil
| | - Nathália de Fátima M Lima
- Experimental Study of Pain Laboratory, Department of Physiological Sciences, Federal University of MaranhãoSão Luís, Brazil
| | - Alberto J O Lopes
- Experimental Study of Pain Laboratory, Department of Physiological Sciences, Federal University of MaranhãoSão Luís, Brazil
| | - Cleydlenne C Vasconcelos
- Experimental Study of Pain Laboratory, Department of Physiological Sciences, Federal University of MaranhãoSão Luís, Brazil
| | - José W C de Mesquita
- Laboratory of Pharmacognosy, Department of Pharmacy, Federal University of MaranhãoSão Luís, Brazil
| | - Ludmilla S S de Mesquita
- Laboratory of Pharmacognosy, Department of Pharmacy, Federal University of MaranhãoSão Luís, Brazil
| | - Fernando C V M Lima
- Experimental Study of Pain Laboratory, Department of Physiological Sciences, Federal University of MaranhãoSão Luís, Brazil
| | - Maria N de S Ribeiro
- Laboratory of Pharmacognosy, Department of Pharmacy, Federal University of MaranhãoSão Luís, Brazil
| | - Ricardo M Ramos
- Research Laboratory Information Systems, Department of Information, Environment, Health and Food Production, Federal Institute of PiauíTeresina, Brazil
| | | | - João B S Garcia
- Experimental Study of Pain Laboratory, Department of Pain and Palliative Care, Federal University of MaranhãoSão Luís, Brazil
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8
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Swanger SA, Chen W, Wells G, Burger PB, Tankovic A, Bhattacharya S, Strong KL, Hu C, Kusumoto H, Zhang J, Adams DR, Millichap JJ, Petrovski S, Traynelis SF, Yuan H. Mechanistic Insight into NMDA Receptor Dysregulation by Rare Variants in the GluN2A and GluN2B Agonist Binding Domains. Am J Hum Genet 2016; 99:1261-1280. [PMID: 27839871 PMCID: PMC5142120 DOI: 10.1016/j.ajhg.2016.10.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/03/2016] [Indexed: 12/30/2022] Open
Abstract
Epilepsy and intellectual disability are associated with rare variants in the GluN2A and GluN2B (encoded by GRIN2A and GRIN2B) subunits of the N-methyl-D-aspartate receptor (NMDAR), a ligand-gated ion channel with essential roles in brain development and function. By assessing genetic variation across GluN2 domains, we determined that the agonist binding domain, transmembrane domain, and the linker regions between these domains were particularly intolerant to functional variation. Notably, the agonist binding domain of GluN2B exhibited significantly more variation intolerance than that of GluN2A. To understand the ramifications of missense variation in the agonist binding domain, we investigated the mechanisms by which 25 rare variants in the GluN2A and GluN2B agonist binding domains dysregulated NMDAR activity. When introduced into recombinant human NMDARs, these rare variants identified in individuals with neurologic disease had complex, and sometimes opposing, consequences on agonist binding, channel gating, receptor biogenesis, and forward trafficking. Our approach combined quantitative assessments of these effects to estimate the overall impact on synaptic and non-synaptic NMDAR function. Interestingly, similar neurologic diseases were associated with both gain- and loss-of-function variants in the same gene. Most rare variants in GluN2A were associated with epilepsy, whereas GluN2B variants were associated with intellectual disability with or without seizures. Finally, discerning the mechanisms underlying NMDAR dysregulation by these rare variants allowed investigations of pharmacologic strategies to correct NMDAR function.
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Affiliation(s)
- Sharon A Swanger
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Wenjuan Chen
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gordon Wells
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Pieter B Burger
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Anel Tankovic
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Katie L Strong
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Chun Hu
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hirofumi Kusumoto
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jing Zhang
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David R Adams
- Undiagnosed Diseases Network, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - John J Millichap
- Departments of Pediatrics and Neurology, Northwestern University Feinberg School of Medicine and Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Slavé Petrovski
- Department of Medicine, The University of Melbourne, Austin Health and Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Stephen F Traynelis
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA; Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Hongjie Yuan
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA; Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA 30322, USA.
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9
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Abstract
Membrane protein structures are underrepresented in the Protein Data Bank (PDB) due to difficulties associated with expression and crystallization. As such, it is one area where computational studies, particularly Molecular Dynamics (MD) simulations, can provide useful additional information. Recently, there has been substantial progress in the simulation of lipid bilayers and membrane proteins embedded within them. Initial efforts at simulating membrane proteins embedded within a lipid bilayer were relatively slow and interactive processes, but recent advances now mean that the setup and running of membrane protein simulations is somewhat more straightforward, though not without its problems. In this chapter, we outline practical methods for setting up and running MD simulations of a membrane protein embedded within a lipid bilayer and discuss methodologies that are likely to contribute future improvements.
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10
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Conformational analysis of NMDA receptor GluN1, GluN2, and GluN3 ligand-binding domains reveals subtype-specific characteristics. Structure 2013; 21:1788-99. [PMID: 23972471 PMCID: PMC3814224 DOI: 10.1016/j.str.2013.07.011] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 07/11/2013] [Accepted: 07/17/2013] [Indexed: 02/06/2023]
Abstract
The NMDA receptor family of glutamate receptor ion channels is formed by obligate heteromeric assemblies of GluN1, GluN2, and GluN3 subunits. GluN1 and GluN3 bind glycine, whereas GluN2 binds glutamate. Crystal structures of the GluN1 and GluN3A ligand-binding domains (LBDs) in their apo states unexpectedly reveal open- and closed-cleft conformations, respectively, with water molecules filling the binding pockets. Computed conformational free energy landscapes for GluN1, GluN2A, and GluN3A LBDs reveal that the apo-state LBDs sample closed-cleft conformations, suggesting that their agonists bind via a conformational selection mechanism. By contrast, free energy landscapes for the AMPA receptor GluA2 LBD suggest binding of glutamate via an induced-fit mechanism. Principal component analysis reveals a rich spectrum of hinge bending, rocking, twisting, and sweeping motions that are different for the GluN1, GluN2A, GluN3A, and GluA2 LBDs. This variation highlights the structural complexity of signaling by glutamate receptor ion channels.
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Abstract
Glutamate-gated ion channels embedded within the neuronal membrane are the primary mediators of fast excitatory synaptic transmission in the CNS. The ion channel of these glutamate receptors contains a pore-lining transmembrane M3 helix surrounded by peripheral M1 and M4 helices. In the NMDA receptor subtype, opening of the ion channel pore, mediated by displacement of the M3 helices away from the central pore axis, occurs in a highly concerted fashion, but the associated temporal movements of the peripheral helices are unknown. To address the gating dynamics of the peripheral helices, we constrained the relative movements of the linkers that connect these helices to the ligand-binding domain using engineered cross-links, either within (intra-GluN1 or GluN2A) or between subunits. Constraining the peripheral linkers in any manner dramatically curtailed channel opening, highlighting the requirement for rearrangements of these peripheral structural elements for efficient gating to occur. However, the magnitude of this gating effect depended on the specific subunit being constrained, with the most dramatic effects occurring when the constraint was between subunits. Based on kinetic and thermodynamic analysis, our results suggest an asynchrony in the displacement of the peripheral linkers during the conformational and energetic changes leading to pore opening. Initially there are large-scale rearrangements occurring between the four subunits. Subsequently, rearrangements occur within individual subunits, mainly GluN2A, leading up to or in concert with pore opening. Thus, the conformational changes induced by agonist binding in NMDA receptors converge asynchronously to permit pore opening.
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12
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Ng HW, Laughton CA, Doughty SW. Molecular dynamics simulations of the adenosine A2a receptor: structural stability, sampling, and convergence. J Chem Inf Model 2013; 53:1168-78. [PMID: 23514445 DOI: 10.1021/ci300610w] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Molecular dynamics (MD) simulations of membrane-embedded G-protein coupled receptors (GPCRs) have rapidly gained popularity among the molecular simulation community in recent years, a trend which has an obvious link to the tremendous pharmaceutical importance of this group of receptors and the increasing availability of crystal structures. In view of the widespread use of this technique, it is of fundamental importance to ensure the reliability and robustness of the methodologies so they yield valid results and enable sufficiently accurate predictions to be made. In this work, 200 ns simulations of the A2a adenosine receptor (A2a AR) have been produced and evaluated in the light of these requirements. The conformational dynamics of the target protein, as obtained from replicate simulations in both the presence and absence of an inverse agonist ligand (ZM241385), have been investigated and compared using principal component analysis (PCA). Results show that, on this time scale, convergence of the replicates is not readily evident and dependent on the types of the protein motions considered. Thus rates of inter- as opposed to intrahelical relaxation and sampling can be different. When studied individually, we find that helices III and IV have noticeably greater stability than helices I, II, V, VI, and VII in the apo form. The addition of the inverse agonist ligand greatly improves the stability of all helices.
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Affiliation(s)
- Hui Wen Ng
- School of Pharmacy, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
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13
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Wolter T, Steinbrecher T, Elstner M. Computational study of synthetic agonist ligands of ionotropic glutamate receptors. PLoS One 2013; 8:e58774. [PMID: 23536824 PMCID: PMC3607592 DOI: 10.1371/journal.pone.0058774] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/06/2013] [Indexed: 01/24/2023] Open
Abstract
Neurological glutamate receptors are among the most important and intensely studied protein ligand binding systems in humans. They are crucial for the functioning of the central nervous system and involved in a variety of pathologies. Apart from the neurotransmitter glutamate, several artificial, agonistic and antagonistic ligands are known. Of particular interest here are novel photoswitchable agonists that would open the field of optogenetics to glutamate receptors. The receptor proteins are complex, membrane-bound multidomain oligomers that undergo large scale functional conformational changes, making detailed studies of their atomic structure challenging. Therefore, a thorough understanding of the microscopic details of ligand binding and receptor activation remains elusive in many cases. This topic has been successfully addressed by theoretical studies in the past and in this paper, we present extensive molecular dynamics simulation and free energy calculation results on the binding of AMPA and an AMPA derivative, which is the basis for designing light-sensitive ligands. We provide a two-step model for ligand binding domain activation and predict binding free energies for novel compounds in good agreement to experimental observations.
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Affiliation(s)
- Tino Wolter
- Department of Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Thomas Steinbrecher
- Department of Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcus Elstner
- Department of Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
- * E-mail:
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14
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Ylilauri M, Pentikäinen OT. Structural mechanism of N-methyl-D-aspartate receptor type 1 partial agonism. PLoS One 2012; 7:e47604. [PMID: 23077649 PMCID: PMC3471861 DOI: 10.1371/journal.pone.0047604] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 09/12/2012] [Indexed: 12/02/2022] Open
Abstract
N-methyl-D-aspartate (NMDA) receptors belong to a family of ionotropic glutamate receptors that contribute to the signal transmission in the central nervous system. NMDA receptors are heterotetramers that usually consist of two GluN1 and GluN2 monomers. The extracellular ligand-binding domain (LBD) of a monomer is comprised of discontinuous segments that form the functional domains D1 and D2. While the binding of a full agonist glycine to LBD of GluN1 is linked to cleft closure and subsequent ion-channel opening, partial agonists are known to activate the receptor only sub-maximally. Although the crystal structures of the LBD of related GluA2 receptor explain the mechanism for the partial agonism, structures of GluN1-LBD cannot distinguish the difference between full and partial agonists. It is, however, probable that the partial agonists of GluN1 alter the structure of the LBD in order to result in a different pharmacological response than seen with full agonists. In this study, we used molecular dynamics simulations to reveal an intermediate closure-stage for GluN1, which is unseen in crystal structures. According to our calculations, this intermediate closure is not a transient stage but an energetically stable conformation. Our results demonstrate that the partial agonist cannot exert firm GluN1-LBD closure, especially if there is even a small force that disrupts the LBD closure. Accordingly, this result suggests the importance of forces from the ion channel for the relationship between pharmacological response and the structure of the LBD of members of this receptor family.
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Affiliation(s)
- Mikko Ylilauri
- Computational Bioscience Laboratory, Department of Biological and Environmental Science & Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Olli T. Pentikäinen
- Computational Bioscience Laboratory, Department of Biological and Environmental Science & Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
- * E-mail:
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15
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Kennedy AP, Gross RE, Whitfield N, Drexler KP, Kilts CD. A controlled trial of the adjunct use of D-cycloserine to facilitate cognitive behavioral therapy outcomes in a cocaine-dependent population. Addict Behav 2012; 37:900-7. [PMID: 22578380 DOI: 10.1016/j.addbeh.2012.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 02/13/2012] [Accepted: 03/06/2012] [Indexed: 12/24/2022]
Abstract
Cocaine dependence is a chronically relapsing disorder for which its predominant behavioral therapies are associated with only partial efficacy. The goal of this study was to determine if the N-methyl-d-aspartate (NMDA) glutamate receptor partial agonist and cognitive enhancer, d-cycloserine (DCS), could boost the cocaine abstinence and treatment retention goals of cognitive behavioral therapy (CBT). This study employed a placebo-controlled, randomized double-blind trial design of 44 cocaine-dependent men enrolled in a 4-week outpatient Substance Abuse Treatment Program (SATP) at the Atlanta Veteran's Administration Medical Center. Subjects received 50mg of DCS or placebo prior to four weekly sessions of a condensed version of a manual-based CBT for cocaine dependence. Cocaine abstinence and treatment retention measures represented primary outcome variables. Relative to a 12-step based treatment-as-usual, an under-dosed CBT was associated with significant improvements in drug abstinence and treatment retention at 4-weeks and for maintenance of drug abstinence after four more weeks of follow-up. The robust response to the under-dosed CBT was not enhanced by the adjunct administration of DCS at either the 4- or 8-week endpoints. This controlled clinical trial failed to demonstrate an ability of DCS to boost the relapse prevention or treatment retention goals of CBT.
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16
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Evaluation of natural and nitramine binding energies to 3-D models of the S1S2 domains in the N-methyl-D-aspartate receptor. J Mol Model 2012; 18:1273-84. [DOI: 10.1007/s00894-011-1152-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/10/2011] [Indexed: 10/18/2022]
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17
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Molecular dynamics simulations for glutamate-binding and cleft-closing processes of the ligand-binding domain of GluR2. Biophys Chem 2012; 162:35-44. [DOI: 10.1016/j.bpc.2011.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 12/12/2011] [Accepted: 12/20/2011] [Indexed: 11/22/2022]
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Sahai MA, Biggin PC. Quantifying water-mediated protein-ligand interactions in a glutamate receptor: a DFT study. J Phys Chem B 2011; 115:7085-96. [PMID: 21545106 PMCID: PMC3102440 DOI: 10.1021/jp200776t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 04/16/2011] [Indexed: 11/30/2022]
Abstract
It is becoming increasingly clear that careful treatment of water molecules in ligand-protein interactions is required in many cases if the correct binding pose is to be identified in molecular docking. Water can form complex bridging networks and can play a critical role in dictating the binding mode of ligands. A particularly striking example of this can be found in the ionotropic glutamate receptors. Despite possessing similar chemical moieties, crystal structures of glutamate and α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) in complex with the ligand-binding core of the GluA2 ionotropic glutamate receptor revealed, contrary to all expectation, two distinct modes of binding. The difference appears to be related to the position of water molecules within the binding pocket. However, it is unclear exactly what governs the preference for water molecules to occupy a particular site in any one binding mode. In this work we use density functional theory (DFT) calculations to investigate the interaction energies and polarization effects of the various components of the binding pocket. Our results show (i) the energetics of a key water molecule are more favorable for the site found in the glutamate-bound mode compared to the alternative site observed in the AMPA-bound mode, (ii) polarization effects are important for glutamate but less so for AMPA, (iii) ligand-system interaction energies alone can predict the correct binding mode for glutamate, but for AMPA alternative modes of binding have similar interaction energies, and (iv) the internal energy is a significant factor for AMPA but not for glutamate. We discuss the results within the broader context of rational drug-design.
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Affiliation(s)
- Michelle A. Sahai
- Structural Bioinformatics and Computational Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Philip C. Biggin
- Structural Bioinformatics and Computational Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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Vijayan R, Sahai MA, Czajkowski T, Biggin PC. A comparative analysis of the role of water in the binding pockets of ionotropic glutamate receptors. Phys Chem Chem Phys 2010; 12:14057-66. [PMID: 20856958 DOI: 10.1039/c004336b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding pockets within proteins often contain water molecules. The ligand-binding core of ionotropic glutamate receptors represents an example where the binding pocket has many crystallographically reported waters, but the precise role remains unclear. It is also unclear to what extent the dynamic properties of these waters are conserved across the different receptor subtypes. In order to shed some light on these aspects we have performed multiple molecular dynamics simulations of the ligand binding core of four glutamate bound iGluR structures (GluA2, GluK1, GluK2, and GluN2A) and one apo structure (GluA2). We find that the water positions are reproduced from the simulations, but they also reveal that all but one water molecule in the binding site can be rearranged or replaced with water molecules from the bulk that enter the binding site through transient water channels. This one exception is not reported in the apo crystal structure but within 15 ns of simulation, a water molecule enters the site from the bulk suggesting that it is a favoured position regardless of the state of the protein. Further calculations demonstrate that whilst it is not needed in order to be able to predict the correct binding pose, it does contribute a large favourable interaction energy. We also find that one conserved water has a much stronger interaction with the protein in GluA2, GluK1 and GluK2 compared to the GluN2A receptor. The position of this water molecule is such that it can influence the dynamics of the proposed switch in the GluA2 and GluK1/2 receptors.
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Affiliation(s)
- Ranjit Vijayan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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21
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Traynelis SF, Wollmuth LP, McBain CJ, Menniti FS, Vance KM, Ogden KK, Hansen KB, Yuan H, Myers SJ, Dingledine R. Glutamate receptor ion channels: structure, regulation, and function. Pharmacol Rev 2010; 62:405-96. [PMID: 20716669 PMCID: PMC2964903 DOI: 10.1124/pr.109.002451] [Citation(s) in RCA: 2579] [Impact Index Per Article: 184.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The mammalian ionotropic glutamate receptor family encodes 18 gene products that coassemble to form ligand-gated ion channels containing an agonist recognition site, a transmembrane ion permeation pathway, and gating elements that couple agonist-induced conformational changes to the opening or closing of the permeation pore. Glutamate receptors mediate fast excitatory synaptic transmission in the central nervous system and are localized on neuronal and non-neuronal cells. These receptors regulate a broad spectrum of processes in the brain, spinal cord, retina, and peripheral nervous system. Glutamate receptors are postulated to play important roles in numerous neurological diseases and have attracted intense scrutiny. The description of glutamate receptor structure, including its transmembrane elements, reveals a complex assembly of multiple semiautonomous extracellular domains linked to a pore-forming element with striking resemblance to an inverted potassium channel. In this review we discuss International Union of Basic and Clinical Pharmacology glutamate receptor nomenclature, structure, assembly, accessory subunits, interacting proteins, gene expression and translation, post-translational modifications, agonist and antagonist pharmacology, allosteric modulation, mechanisms of gating and permeation, roles in normal physiological function, as well as the potential therapeutic use of pharmacological agents acting at glutamate receptors.
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Affiliation(s)
- Stephen F Traynelis
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, 1510 Clifton Road, Atlanta, GA 30322-3090, USA.
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22
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Abstract
We have studied relative efficacies of NR1 agonists glycine and d-cycloserine (DCS), and found efficacy to be dependent on the NR2 subunit. DCS shows partial agonism at NR1/NR2B but has higher relative efficacy than glycine at NR1/NR2C receptor. Molecular dynamics (MD) simulations of the NR1/NR2B and NR1/NR2C agonist binding domain dimer suggest only subtle differences in the interactions of DCS with NR1 binding site residues relative to glycine. The most pronounced differences were observed in the NR1/NR2C simulation between the orientation of helices F and G of the NR1 subunit. Interestingly, Helix F was previously proposed to influence receptor gating and to adopt an orientation depending on agonist efficacy. MD simulations and site-directed mutagenesis further suggest a role for residues at the agonist binding domain dimer interface in regulating DCS efficacy. To relate the structural rearrangements to receptor gating, we recorded single-channel currents from outside-out patches containing a single active NR1/NR2C receptor. DCS increased the mean open time and open probability of NR1/NR2C receptors compared with glycine. Maximum likelihood fitting of a gating model for NR1/NR2C receptor activation to the single-channel data suggests that DCS specifically accelerates the rate constant governing a fast gating step and reduces the closing rate. These changes appear to reflect a decreased activation energy for a pregating step and increased stability of the open states. We suggest that the higher efficacy of DCS at NR1/NR2C receptors involves structural rearrangements at the dimer interface and an effect on NR1/NR2C receptor pregating conformational changes.
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Krueger BA, Weil T, Schneider G. Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists. J Comput Aided Mol Des 2009; 23:869-81. [PMID: 19890609 DOI: 10.1007/s10822-009-9304-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 10/01/2009] [Indexed: 10/20/2022]
Abstract
Identification of novel compound classes for a drug target is a challenging task for cheminformatics and drug design when considerable research has already been undertaken and many potent lead structures have been identified, which leaves limited unclaimed chemical space for innovation. We validated and successfully applied different state-of-the-art techniques for virtual screening (Bayesian machine learning, automated molecular docking, pharmacophore search, pharmacophore QSAR and shape analysis) of 4.6 million unique and readily available chemical structures to identify promising new and competitive antagonists of the strychnine-insensitive Glycine binding site (Glycine(B) site) of the NMDA receptor. The novelty of the identified virtual hits was assessed by scaffold analysis, putting a strong emphasis on novelty detection. The resulting hits were tested in vitro and several novel, active compounds were identified. While the majority of the computational methods tested were able to partially discriminate actives from structurally similar decoy molecules, the methods differed substantially in their prospective applicability in terms of novelty detection. The results demonstrate that although there is no single best computational method, it is most worthwhile to follow this concept of focused compound library design and screening, as there still can new bioactive compounds be found that possess hitherto unexplored scaffolds and interesting variations of known chemotypes.
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Affiliation(s)
- Bjoern A Krueger
- Institute of Organic Chemistry und Chemical Biology, Johann Wolfgang Goethe-University, 60323 Frankfurt, Germany.
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VanDongen A, Blanke M. Activation Mechanisms of the NMDA Receptor. BIOLOGY OF THE NMDA RECEPTOR 2008. [DOI: 10.1201/9781420044157.ch13] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Bjerrum EJ, Biggin PC. Rigid body essential X-ray crystallography: distinguishing the bend and twist of glutamate receptor ligand binding domains. Proteins 2008; 72:434-46. [PMID: 18214958 DOI: 10.1002/prot.21941] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The ligand-binding domain (LBD) from the ionotropic glutamate receptor subtype 2 (GluR2) has been shown to adopt a range of ligand-dependent conformational states. These states have been described in terms of the rotation required to fit subdomain (lobe) 2 following superposition of subdomain (lobe) 1. The LBD has a closed-cleft conformation for full agonists, but partial agonists induce a range of closure, which in turn controls the open probability of discrete subconductance states in the full-length receptor. Although this description is useful, it may not account for all physiologically important motions that the receptor undergoes. We have used an approach that combines the methods of essential dynamics and rigid-body dynamics to analyze 124 monomer domains from 55 crystal structures of the GluR2 LBD. We are able to show that partial agonists also induce a significant amount of twist that would not be anticipated using one rotational descriptor between apo and full-agonist-bound states. Furthermore, one of the crystal structures (chain B from 1P1U, the GluR2 L650T-AMPA complex), which has been suggested to represent an agonist-bound inactive form of the receptor, lies at the extreme of this twist motion. We suggest that partial agonists not only prevent full closure but also move the receptor closer to this inactive state. We demonstrate additionally how the method can be used to compare the results of molecular dynamics simulations with the crystallographic data and the extent to which the conformational space explored by both overlaps.
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Affiliation(s)
- Esben J Bjerrum
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
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Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors. EMBO J 2008; 27:2158-70. [PMID: 18636091 DOI: 10.1038/emboj.2008.140] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Accepted: 06/26/2008] [Indexed: 11/09/2022] Open
Abstract
NR3 subtype glutamate receptors have a unique developmental expression profile, but are the least well-characterized members of the NMDA receptor gene family, which have key roles in synaptic plasticity and brain development. Using ligand binding assays, crystallographic analysis, and all atom MD simulations, we investigate mechanisms underlying the binding by NR3A and NR3B of glycine and D-serine, which are candidate neurotransmitters for NMDA receptors containing NR3 subunits. The ligand binding domains of both NR3 subunits adopt a similar extent of domain closure as found in the corresponding NR1 complexes, but have a unique loop 1 structure distinct from that in all other glutamate receptor ion channels. Within their ligand binding pockets, NR3A and NR3B have strikingly different hydrogen bonding networks and solvent structures from those found in NR1, and fail to undergo a conformational rearrangement observed in NR1 upon binding the partial agonist ACPC. MD simulations revealed numerous interdomain contacts, which stabilize the agonist-bound closed-cleft conformation, and a novel twisting motion for the loop 1 helix that is unique in NR3 subunits.
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Abstract
Membrane protein structures are underrepresented in the Protein Data Bank (PDB) because of difficulties associated with expression and crystallization. As such, it is one area in which computational studies, particularly molecular dynamics (MD), can provide useful additional information. Recently, there has been substantial progress in the simulation of lipid bilayers and membrane proteins embedded within them. Initial efforts at simulating membrane proteins embedded within a lipid bilayer were relatively slow and interactive processes, but recent advances now mean that the setup and running of membrane protein simulations is somewhat more straightforward, although not without its problems. In this chapter, we outline practical methods for setting up and running MD simulations of a membrane protein embedded within a lipid bilayer and discuss methodologies that are likely to contribute future improvements.
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Affiliation(s)
- Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, UK
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Blanke ML, VanDongen AMJ. Constitutive activation of the N-methyl-D-aspartate receptor via cleft-spanning disulfide bonds. J Biol Chem 2008; 283:21519-29. [PMID: 18450751 DOI: 10.1074/jbc.m709190200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the N-methyl-D-aspartate (NMDA) receptor plays a critical role in the central nervous system, many questions remain regarding the relationship between its structure and functional properties. In particular, the involvement of ligand-binding domain closure in determining agonist efficacy, which has been reported in other glutamate receptor subtypes, remains unresolved. To address this question, we designed dual cysteine point mutations spanning the NR1 and NR2 ligand-binding clefts, aiming to stabilize these domains in closed cleft conformations. Two mutants, E522C/I691C in NR1 (EI) and K487C/N687C in NR2 (KN) were found to exhibit significant glycine- and glutamate-independent activation, respectively, and co-expression of the two subunits produced a constitutively active channel. However, both individual mutants could be activated above constitutive levels in a concentration-dependent manner, indicating that cleft closure does not completely prevent agonist association. Interestingly, whereas the NR2 KN disulfide was found to potentiate channel gating and M3 accessibility, NR1 EI exhibited the opposite phenotype, suggesting that the EI disulfide may trap the NR1 ligand-binding domain in a lower efficacy conformation. Furthermore, both mutants affected agonist sensitivity at the opposing subunit, suggesting that closed cleft stabilization may contribute to coupling between the subunits. These results support a correlation between cleft stability and receptor activation, providing compelling evidence for the Venus flytrap mechanism of glutamate receptor domain closure.
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Affiliation(s)
- Marie L Blanke
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
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Affiliation(s)
- Alasdair J Gibb
- Department of Pharmacology, University College London, Gower Street, London WC1E 6BT, UK.
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