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Diakogiannaki I, Papadourakis M, Spyridaki V, Cournia Z, Koutselos A. Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators. J Chem Inf Model 2024; 64:5140-5150. [PMID: 38973304 PMCID: PMC11234361 DOI: 10.1021/acs.jcim.3c01195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 07/09/2024]
Abstract
Beta-N-methylamino-l-alanine (BMAA) is a potential neurotoxic nonprotein amino acid, which can reach the human body through the food chain. When BMAA interacts with bicarbonate in the human body, carbamate adducts are produced, which share a high structural similarity with the neurotransmitter glutamate. It is believed that BMAA and its l-carbamate adducts bind in the glutamate binding site of ionotropic glutamate receptor 2 (GluR2). Chronic exposure to BMAA and its adducts could cause neurological illness such as neurodegenerative diseases. However, the mechanism of BMAA action and its carbamate adducts bound to GluR2 has not yet been elucidated. Here, we investigate the binding modes and the affinity of BMAA and its carbamate adducts to GluR2 in comparison to the natural agonist, glutamate, to understand whether these can act as GluR2 modulators. Initially, we perform molecular dynamics simulations of BMAA and its carbamate adducts bound to GluR2 to examine the stability of the ligands in the S1/S2 ligand-binding core of the receptor. In addition, we utilize alchemical free energy calculations to compute the difference in the free energy of binding of the beta-carbamate adduct of BMAA to GluR2 compared to that of glutamate. Our findings indicate that carbamate adducts of BMAA and glutamate remain stable in the binding site of the GluR2 compared to BMAA. Additionally, alchemical free energy results reveal that glutamate and the beta-carbamate adduct of BMAA have comparable binding affinity to the GluR2. These results provide a rationale that BMAA carbamate adducts may be, in fact, the modulators of GluR2 and not BMAA itself.
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Affiliation(s)
- Isidora Diakogiannaki
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, Athens 11527, Greece
- Department
of Chemistry, Physical Chemistry Laboratory, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Michail Papadourakis
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, Athens 11527, Greece
- Department
of Nursing, Faculty of Health Sciences, Hellenic Mediterranean University, Heraklion, Crete 71004, Greece
| | - Vasileia Spyridaki
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, Athens 11527, Greece
- School
of Chemical Engineering, National Technical
University of Athens, Heroon Polytechniou 9, Zografou 15780, Greece
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, Athens 11527, Greece
| | - Andreas Koutselos
- Department
of Chemistry, Physical Chemistry Laboratory, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
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2
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Yelshanskaya MV, Patel DS, Kottke CM, Kurnikova MG, Sobolevsky AI. Opening of glutamate receptor channel to subconductance levels. Nature 2022; 605:172-178. [PMID: 35444281 PMCID: PMC9068512 DOI: 10.1038/s41586-022-04637-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that open their pores in response to binding of the agonist glutamate1-3. An ionic current through a single iGluR channel shows up to four discrete conductance levels (O1-O4)4-6. Higher conductance levels have been associated with an increased number of agonist molecules bound to four individual ligand-binding domains (LBDs)6-10. Here we determine structures of a synaptic complex of AMPA-subtype iGluR and the auxiliary subunit γ2 in non-desensitizing conditions with various occupancy of the LBDs by glutamate. We show that glutamate binds to LBDs of subunits B and D only after it is already bound to at least the same number of LBDs that belong to subunits A and C. Our structures combined with single-channel recordings, molecular dynamics simulations and machine-learning analysis suggest that channel opening requires agonist binding to at least two LBDs. Conversely, agonist binding to all four LBDs does not guarantee maximal channel conductance and favours subconductance states O1 and O2, with O3 and O4 being rare and not captured structurally. The lack of subunit independence and low efficiency coupling of glutamate binding to channel opening underlie the gating of synaptic complexes to submaximal conductance levels, which provide a potential for upregulation of synaptic activity.
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Affiliation(s)
- Maria V Yelshanskaya
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Dhilon S Patel
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | - Maria G Kurnikova
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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3
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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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4
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Yu A, Salazar H, Plested AJR, Lau AY. Neurotransmitter Funneling Optimizes Glutamate Receptor Kinetics. Neuron 2017; 97:139-149.e4. [PMID: 29249286 PMCID: PMC5766834 DOI: 10.1016/j.neuron.2017.11.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/26/2017] [Accepted: 11/15/2017] [Indexed: 12/29/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) mediate neurotransmission at the majority of excitatory synapses in the brain. Little is known, however, about how glutamate reaches the recessed binding pocket in iGluR ligand-binding domains (LBDs). Here we report the process of glutamate binding to a prototypical iGluR, GluA2, in atomistic detail using unbiased molecular simulations. Charged residues on the LBD surface form pathways that facilitate glutamate binding by effectively reducing a three-dimensional diffusion process to a spatially constrained, two-dimensional one. Free energy calculations identify residues that metastably bind glutamate and help guide it into the binding pocket. These simulations also reveal that glutamate can bind in an inverted conformation and also reorient while in its pocket. Electrophysiological recordings demonstrate that eliminating these transient binding sites slows activation and deactivation, consistent with slower glutamate binding and unbinding. These results suggest that binding pathways have evolved to optimize rapid responses of AMPA-type iGluRs at synapses.
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Affiliation(s)
- Alvin Yu
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Héctor Salazar
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Andrew J R Plested
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany.
| | - Albert Y Lau
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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5
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Tseng YH, Chuang PH, Huang YR, Chen CL. Computational Investigation into the Interactions of Traditional Chinese Medicine Molecules of WenQingYin with GluR2. Int J Mol Sci 2017; 18:ijms18071443. [PMID: 28678159 PMCID: PMC5535934 DOI: 10.3390/ijms18071443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/21/2017] [Accepted: 07/01/2017] [Indexed: 01/27/2023] Open
Abstract
Docking and molecular dynamics simulations have been carried out to investigate the interaction of a traditional Chinese medicine, WenQingYin, with the glutamate receptor 2 (GluR2) subunit of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor. Four representative drug components of WenQingYin, namely 2-(3,4-dihydroxyphenyl)-5,6,7-trihydroxy-4H-chromen-4-one (PHF), 4-hydroxy-3-methoxybenzoic acid (HMB), 4-(2,3-dihydroxy-3-methylbutoxy)-7H-furo[3,2-g]chromen-7-one (DHMBP) and methyl 7-formylcyclopenta[c]pyran-4-carboxylate (cerbinal), and their complexes with GluR2 were simulated. Our results show that PHF, HMB, and DHMBP formed a partial hydrogen bond with GluR2 in its ligand-binding domain. However, cerbinal was not stable in the ligand-binding domain of GluR2 and induced a significant change in the structure of GluR2. Three-dimensional plots represent the contact and movement situation of the traditional Chinese medicine molecules in the ligand-binding domain. The combined results of the docking and molecular dynamics simulations provide insight into the interaction between these traditional Chinese medicine molecules and proteins.
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Affiliation(s)
- Yu-Hui Tseng
- Department of Chemistry, National Sun Yat-Sen University, 80424 Kaohsiung, Taiwan.
| | - Po-Hsiang Chuang
- Department of Chemistry, National Sun Yat-Sen University, 80424 Kaohsiung, Taiwan.
| | - Yu-Ren Huang
- Department of Chemistry, National Sun Yat-Sen University, 80424 Kaohsiung, Taiwan.
- Department of Applied Science, R.O.C. Naval Academy, 81345 Kaohsiung, Taiwan.
| | - Cheng-Lung Chen
- Department of Chemistry, National Sun Yat-Sen University, 80424 Kaohsiung, Taiwan.
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6
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Martins ACV, de-Lima-Neto P, Caetano EWS, Freire VN. An improved quantum biochemistry description of the glutamate–GluA2 receptor binding within an inhomogeneous dielectric function framework. NEW J CHEM 2017. [DOI: 10.1039/c6nj03939a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new methodology to define the inhomogeneous dielectric constant of protein residues, to apply to the calculation of protein–ligand properties such as the electrostatic interaction.
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Affiliation(s)
- A. C. V. Martins
- Department of Analytical Chemistry and Physical-Chemistry
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| | - P. de-Lima-Neto
- Department of Analytical Chemistry and Physical-Chemistry
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| | - E. W. S. Caetano
- Federal Institute of Education
- Science and Technology of Ceara
- 60040-531 Fortaleza
- Brazil
| | - V. N. Freire
- Department of Physics
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
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7
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Carreón YJ, Mercado-Uribe H. Dielectric spectroscopy of biomolecules at low frequencies: Evidence of proton wires. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Cooper DR, Dolino DM, Jaurich H, Shuang B, Ramaswamy S, Nurik CE, Chen J, Jayaraman V, Landes CF. Conformational transitions in the glycine-bound GluN1 NMDA receptor LBD via single-molecule FRET. Biophys J 2016; 109:66-75. [PMID: 26153703 PMCID: PMC4572502 DOI: 10.1016/j.bpj.2015.05.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 12/30/2022] Open
Abstract
The N-methyl-D-aspartate receptor (NMDAR) is a member of the glutamate receptor family of proteins and is responsible for excitatory transmission. Activation of the receptor is thought to be controlled by conformational changes in the ligand binding domain (LBD); however, glutamate receptor LBDs can occupy multiple conformations even in the activated form. This work probes equilibrium transitions among NMDAR LBD conformations by monitoring the distance across the glycine-bound LBD cleft using single-molecule Förster resonance energy transfer (smFRET). Recent improvements in photoprotection solutions allowed us to monitor transitions among the multiple conformations. Also, we applied a recently developed model-free algorithm called "step transition and state identification" to identify the number of states, their smFRET efficiencies, and their interstate kinetics. Reversible interstate conversions, corresponding to transitions among a wide range of cleft widths, were identified in the glycine-bound LBD, on much longer timescales compared to channel opening. These transitions were confirmed to be equilibrium in nature by shifting the distribution reversibly via denaturant. We found that the NMDAR LBD proceeds primarily from one adjacent smFRET state to the next under equilibrium conditions, consistent with a cleft-opening/closing mechanism. Overall, by analyzing the state-to-state transition dynamics and distributions, we achieve insight into specifics of long-lived LBD equilibrium structural dynamics, as well as obtain a more general description of equilibrium folding/unfolding in a conformationally dynamic protein. The relationship between such long-lived LBD dynamics and channel function in the full receptor remains an open and interesting question.
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Affiliation(s)
- David R Cooper
- Department of Chemistry, Rice University, Houston, Texas
| | - Drew M Dolino
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas
| | | | - Bo Shuang
- Department of Chemistry, Rice University, Houston, Texas
| | - Swarna Ramaswamy
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas
| | - Caitlin E Nurik
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas
| | - Jixin Chen
- Department of Chemistry, Rice University, Houston, Texas
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, Texas.
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, Texas; Department of Electrical and Computer Engineering, Rice University, Houston, Texas.
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9
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Lima Neto JX, Fulco UL, Albuquerque EL, Corso G, Bezerra EM, Caetano EWS, da Costa RF, Freire VN. A quantum biochemistry investigation of willardiine partial agonism in AMPA receptors. Phys Chem Chem Phys 2015; 17:13092-103. [DOI: 10.1039/c4cp05630b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ quantum biochemistry methods based on the Density Functional Theory (DFT) approach to unveil detailed binding energy features of willardiines co-crystallized with the AMPA receptor.
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Affiliation(s)
- José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | - Gilberto Corso
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Eveline M. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | - Roner F. da Costa
- Departamento de Física
- Universidade Federal Rural do Semi-Árido
- 59780-000 Caraúbas-RN
- Brazil
| | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza-CE
- Brazil
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10
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Paganelli MA, Kussius CL, Popescu GK. Role of cross-cleft contacts in NMDA receptor gating. PLoS One 2013; 8:e80953. [PMID: 24278352 PMCID: PMC3836766 DOI: 10.1371/journal.pone.0080953] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 10/14/2013] [Indexed: 11/23/2022] Open
Abstract
In response to brief glutamate exposure, NMDA receptors produce excitatory currents that have sub-maximal amplitudes and characteristically slow kinetics. The activation sequence starts when glutamate binds to residues located on the upper lobe of extracellularly located ligand-binding domains (LBDs) and then contacts lower lobe residues to bridge the cleft between the two hinged lobes. This event stabilizes a narrow-cleft LBD conformation and may facilitate subsequent inter-lobe contacts that further stabilize the closed cleft. Agonist efficacy has been traced to the degree of agonist-induced cleft-closure and may also depend on the stability of the closed-cleft conformation. To investigate how cross-cleft contacts contribute to the amplitude and kinetics of NMDA receptor response, we examined the activation reaction of GluN1/GluN2A receptors that had single-residue substitutions at the interface between LBD lobes. We found that side-chain truncations at residues of putative contact between lobes increased glutamate efficacy through independent additive mechanisms in GluN1 and GluN2A subunits. In contrast, removing side-chain charge with isosteric substitutions at the same sites decreased glutamate efficacy. These results support the view that in GluN1/GluN2A receptors’ natural interactions between residues on opposing sides of the ligand-binding cleft encode the stability of the glutamate-bound closed-cleft conformations and limit the degree of cleft closure, thus contributing to the sub-maximal response and emblematically slow NMDA receptor deactivation after brief stimulation.
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Affiliation(s)
- Meaghan A. Paganelli
- Neuroscience Program, University at Buffalo, Buffalo, New York, United States of America
| | - Cassandra L. Kussius
- Department of Biochemistry, University at Buffalo, Buffalo, New York, United States of America
| | - Gabriela K. Popescu
- Neuroscience Program, University at Buffalo, Buffalo, New York, United States of America
- Department of Biochemistry, University at Buffalo, Buffalo, New York, United States of America
- * E-mail:
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11
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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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12
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Martins ACV, de Lima-Neto P, Barroso-Neto IL, Cavada BS, Freire VN, Caetano EWS. An ab initio explanation of the activation and antagonism strength of an AMPA-sensitive glutamate receptor. RSC Adv 2013. [DOI: 10.1039/c3ra42149j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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13
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Yonkunas M, Kurnikova M. Characterizing the energetic states of the GluR2 ligand binding domain core-dimer. Biophys J 2011; 100:L5-7. [PMID: 21244821 DOI: 10.1016/j.bpj.2010.10.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 10/08/2010] [Accepted: 10/19/2010] [Indexed: 11/17/2022] Open
Abstract
Tetrameric ligand binding domains of the family of ionotropic glutamate receptors assemble as dimers-of-dimers. Crystallographic studies of several glutamate receptor subtype isolated core-dimers suggest a single stable dimeric conformation. A binding domain dimer has not been captured in other conformations without the aid of biochemical methods to disrupt a critical dimer interface. Molecular dynamics simulations and continuum electrostatics calculations reveal that the active glutamate bound form of the ligand-binding domain found in typical crystal structures is the preferred energetic state of the isolated core-dimer in the presence of agonist glutamate. A desensitized conformational state is a higher energy ligand-bound state of the core-dimer. The resting apo conformational state is comparatively the least energetically favored conformation and does not contain a single state but a set of energetically equivalent conformational core-dimer states. We hypothesize the energetic balance of an open versus closed transmembrane region must be included to characterize the absolute energetic states of the full receptor, which in the presence of the ligand is believed to be a desensitized state.
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14
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Serafimoska Z, N. Johansen T, Frydenvang K, Suturkova L. Ionotropic Glutamate Receptors (iGluRs): Overview of iGluR2 ligand binding domain in complex with agonists and antagonists. MAKEDONSKO FARMACEVTSKI BILTEN 2011. [DOI: 10.33320/maced.pharm.bull.2011.57.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ionotropic glutamate receptors (iGluRs) constitute a family of ligand gated ion channels subdivided in three classes, NMDA, AMPA (iGluA1-4) and KA (1-5) according to the agonists that selectively activate them. iGluRs are tetrameric assemblies of highly homologous
receptor subunits. They are critically important for normal brain function and are considered to be involved on neurological disorders and degenerative diseases such as schizophrenia, Alzheimer’s disease, brain damage following stroke and epilepsy. Since the first publication of the structure of recombinant soluble protein of ligand binding domain of GluA2 extensive studies on this group of receptors were performed and many crystal structures as complexes of GluA2-LBD with agonists, partial agonists and antagonists were obtained. The structural information in combination with functional data makes good platform for consecutive investigation and design of new selective drugs
which will be used in treatment of neurodegerative diseases.
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15
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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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16
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Essiz SG, Coalson RD. Dynamic Linear Response Theory for Conformational Relaxation of Proteins. J Phys Chem B 2009; 113:10859-69. [DOI: 10.1021/jp900745u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sebnem G. Essiz
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Rob D. Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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Selectivity and cooperativity of modulatory ions in a neurotransmitter receptor. Biophys J 2009; 96:1751-60. [PMID: 19254535 DOI: 10.1016/j.bpj.2008.11.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 11/13/2008] [Indexed: 02/02/2023] Open
Abstract
Ions play a modulatory role in many proteins. Kainate receptors, members of the ionotropic glutamate receptor family, require both monovalent anions and cations in the extracellular milieu for normal channel activity. Molecular dynamics simulations and extensive relative binding free energy calculations using thermodynamic integration were performed to elucidate the rank order of binding of monovalent cations, using x-ray crystal structures of the GluR5 kainate receptor dimers with bound cations from the alkali metal family. The simulations show good agreement with experiments and reveal that the underlying backbone structure of the binding site is one of the most rigid regions of the protein. A simplified model where the partial charge of coordinating oxygens was varied suggests that selectivity arises from the presence of two carboxylate groups. Furthermore, using a potential of mean force derived from umbrella sampling, we show that the presence of cations lower the energy barrier for anion approach and binding in the buried anion binding cavity.
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Mamonova T, Yonkunas MJ, Kurnikova MG. Energetics of the cleft closing transition and the role of electrostatic interactions in conformational rearrangements of the glutamate receptor ligand binding domain. Biochemistry 2008; 47:11077-85. [PMID: 18823129 DOI: 10.1021/bi801367d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ionotropic glutamate receptors are localized in the pre- and postsynaptic membrane of neurons in the brain. Activation by the principal excitatory neurotransmitter glutamate allows the ligand binding domain to change conformation, communicating opening of the channel for ion conduction. The free energy of the GluR2 S1S2 ligand binding domain (S1S2) closure transition was computed using a combination of thermodynamic integration and umbrella sampling modeling methods. A path that involves lowering the charge on E705 was chosen to clarify the role of this binding site residue. A continuum electrostatics approach in S1S2 is used to show E705, located in the ligand binding cleft, stabilizes the closed conformation of S1S2 via direct interactions with other protein residues, not through the ligand. In the closed conformation, in the absence of a ligand, S1S2 is somewhat more closed than what has been reported in X-ray structures. A semiopen conformation has been identified which is characterized by disruption of a single cross-cleft interaction and differs only slightly in energy from the fully closed S1S2. The fully open S1S2 conformation exhibits a wide energy well and shares structural similarity with the apo S1S2 crystal structure. Hybrid continuum electrostatics/MD calculations along the chosen closure transition pathway reveal solvation energies, and electrostatic interaction energies between two lobes of the protein increase the relative energetic difference between the open and closed conformational states. By analyzing the role of several cross-cleft contacts as well as other binding site residues, we demonstrate how S1S2 interactions facilitate formation of the closed conformation of the GluR2 ligand binding domain.
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Affiliation(s)
- Tatyana Mamonova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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19
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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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20
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Mamonova T, Speranskiy K, Kurnikova M. Interplay between structural rigidity and electrostatic interactions in the ligand binding domain of GluR2. Proteins 2008; 73:656-71. [DOI: 10.1002/prot.22090] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Lau AY, Roux B. The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain. Structure 2007; 15:1203-14. [PMID: 17937910 DOI: 10.1016/j.str.2007.07.015] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 07/27/2007] [Accepted: 07/31/2007] [Indexed: 11/29/2022]
Abstract
Ionotropic glutamate receptors are ligand-gated transmembrane ion channels activated by the binding of glutamate. The free energy landscapes governing the opening/closing of the GluR2 S1S2 ligand-binding domain in the apo, DNQX-, and glutamate-bound forms are computed by using all-atom molecular dynamics simulations with explicit solvent, in conjunction with an umbrella sampling strategy. The apo S1S2 easily accesses low-energy conformations that are more open than observed in X-ray crystal structures. A free energy of 9-12 kcal/mol becomes available upon glutamate binding for driving conformational changes in S1S2 associated with receptor activation. Small-angle X-ray scattering profiles calculated from computed ensemble averages agree better with experimental results than profiles calculated from static X-ray crystal structures. Water molecules in the cleft may contribute to stabilizing the apo S1S2 in open conformations. Free energy landscapes were also computed for the glutamate-bound T686A and T686S S1S2 mutants, and the results elaborate on findings from experimental functional studies.
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Affiliation(s)
- Albert Y Lau
- Institute for Molecular Pediatric Sciences, Department of Biochemistry and Molecular Biology, Ellen and Melvin Gordon Center for Integrative Science, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
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22
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Madden DR. New light on an open-and-shut case. Nat Chem Biol 2006; 1:317-9. [PMID: 16408066 DOI: 10.1038/nchembio1105-317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Mamonova T, Hespenheide B, Straub R, Thorpe MF, Kurnikova M. Protein flexibility using constraints from molecular dynamics simulations. Phys Biol 2005; 2:S137-47. [PMID: 16280619 DOI: 10.1088/1478-3975/2/4/s08] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteins are held together in the native state by hydrophobic interactions, hydrogen bonds and interactions with the surrounding water, whose strength as well as spatial and temporal distribution affects protein flexibility and hence function. We study these effects using 10 ns molecular dynamics simulations of pure water and of two proteins, the glutamate receptor ligand binding domain and barnase. We find that most of the noncovalent interactions flicker on and off over typically nanoseconds, and so we can obtain good statistics from the molecular dynamics simulations. Based on this information, a topological network of rigid bonds corresponding to a protein structure with covalent and noncovalent bonds is constructed, with account being taken of the influence of the flickering hydrogen bonds. We define the duty cycle for the noncovalent interactions as the percentage of time a given interaction is present, which we use as an input to investigate flexibility/rigidity patterns, in the algorithm FIRST which constructs and analyses topological networks.
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Affiliation(s)
- Tatyana Mamonova
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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