skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel

Abstract

Desensitization in pentameric ligand-gated ion channels plays an important role in regulating neuronal excitability. Here, we show that docosahexaenoic acid (DHA), a key ω-3 polyunsaturated fatty acid in synaptic membranes, enhances the agonist-induced transition to the desensitized state in the prokaryotic channel GLIC. We determined a 3.25 Å crystal structure of the GLIC-DHA complex in a potentially desensitized conformation. The DHA molecule is bound at the channel-periphery near the M4 helix and exerts a long-range allosteric effect on the pore across domain-interfaces. In this previously unobserved conformation, the extracellular-half of the pore-lining M2 is splayed open, reminiscent of the open conformation, while the intracellular-half is constricted, leading to a loss of both water and permeant ions. These findings, in combination with spin-labeling/EPR spectroscopic measurements in reconstituted-membranes, provide novel mechanistic details of desensitization in pentameric channels.

Authors:
ORCiD logo [1];  [2]; ORCiD logo [1]; ORCiD logo [1]
  1. Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, United States
  2. Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, United States
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
AHANIGMS
OSTI Identifier:
1390872
Resource Type:
Journal Article
Journal Name:
eLife
Additional Journal Information:
Journal Volume: 6; Journal Issue: 03, 2017; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Basak, Sandip, Schmandt, Nicolaus, Gicheru, Yvonne, and Chakrapani, Sudha. Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel. United States: N. p., 2017. Web. doi:10.7554/eLife.23886.
Basak, Sandip, Schmandt, Nicolaus, Gicheru, Yvonne, & Chakrapani, Sudha. Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel. United States. doi:10.7554/eLife.23886.
Basak, Sandip, Schmandt, Nicolaus, Gicheru, Yvonne, and Chakrapani, Sudha. Mon . "Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel". United States. doi:10.7554/eLife.23886.
@article{osti_1390872,
title = {Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel},
author = {Basak, Sandip and Schmandt, Nicolaus and Gicheru, Yvonne and Chakrapani, Sudha},
abstractNote = {Desensitization in pentameric ligand-gated ion channels plays an important role in regulating neuronal excitability. Here, we show that docosahexaenoic acid (DHA), a key ω-3 polyunsaturated fatty acid in synaptic membranes, enhances the agonist-induced transition to the desensitized state in the prokaryotic channel GLIC. We determined a 3.25 Å crystal structure of the GLIC-DHA complex in a potentially desensitized conformation. The DHA molecule is bound at the channel-periphery near the M4 helix and exerts a long-range allosteric effect on the pore across domain-interfaces. In this previously unobserved conformation, the extracellular-half of the pore-lining M2 is splayed open, reminiscent of the open conformation, while the intracellular-half is constricted, leading to a loss of both water and permeant ions. These findings, in combination with spin-labeling/EPR spectroscopic measurements in reconstituted-membranes, provide novel mechanistic details of desensitization in pentameric channels.},
doi = {10.7554/eLife.23886},
journal = {eLife},
issn = {2050-084X},
number = 03, 2017,
volume = 6,
place = {United States},
year = {2017},
month = {3}
}

Works referenced in this record:

Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography
journal, October 2013

  • Gonzalez-Gutierrez, G.; Cuello, L. G.; Nair, S. K.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 46
  • DOI: 10.1073/pnas.1313156110

Solving structures of protein complexes by molecular replacement with Phaser
journal, December 2006

  • McCoy, Airlie J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 1
  • DOI: 10.1107/S0907444906045975

Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997

  • Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
  • DOI: 10.1107/S0907444996012255

Motion of Spin-Labeled Side Chains in T4 Lysozyme. Correlation with Protein Structure and Dynamics
journal, January 1996

  • Mchaourab, Hassane S.; Lietzow, Michael A.; Hideg, Kalman
  • Biochemistry, Vol. 35, Issue 24
  • DOI: 10.1021/bi960482k

Crystal structure of a human GABAA receptor
journal, June 2014


MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels
journal, November 2007


Conformational Transitions Underlying Pore Opening and Desensitization in Membrane-embedded Gloeobacter violaceus Ligand-gated Ion Channel (GLIC)
journal, September 2012

  • Velisetty, Phanindra; Chalamalasetti, Sreevatsa V.; Chakrapani, Sudha
  • Journal of Biological Chemistry, Vol. 287, Issue 44
  • DOI: 10.1074/jbc.M112.401067

The desensitization gate of inhibitory Cys-loop receptors
journal, April 2015

  • Gielen, Marc; Thomas, Philip; Smart, Trevor G.
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms7829

The CCP4 suite programs for protein crystallography
journal, September 1994


The atypical cation-conduction and gating properties of ELIC underscore the marked functional versatility of the pentameric ligand-gated ion-channel fold
journal, June 2015

  • Gonzalez-Gutierrez, Giovanni; Grosman, Claudio
  • The Journal of General Physiology, Vol. 146, Issue 1
  • DOI: 10.1085/jgp.201411333

Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation
journal, December 2013

  • Sauguet, L.; Shahsavar, A.; Poitevin, F.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 3
  • DOI: 10.1073/pnas.1314997111

An outline of desensitization in pentameric ligand-gated ion channel receptors
journal, August 2012


Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel
journal, November 2008


X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation
journal, November 2008

  • Bocquet, Nicolas; Nury, Hugues; Baaden, Marc
  • Nature, Vol. 457, Issue 7225
  • DOI: 10.1038/nature07462

DeerAnalysis2006—a comprehensive software package for analyzing pulsed ELDOR data
journal, June 2006

  • Jeschke, G.; Chechik, V.; Ionita, P.
  • Applied Magnetic Resonance, Vol. 30, Issue 3-4
  • DOI: 10.1007/BF03166213

X-ray structures of GluCl in apo states reveal a gating mechanism of Cys-loop receptors
journal, August 2014

  • Althoff, Thorsten; Hibbs, Ryan E.; Banerjee, Surajit
  • Nature, Vol. 512, Issue 7514
  • DOI: 10.1038/nature13669

HOLE: A program for the analysis of the pore dimensions of ion channel structural models
journal, December 1996


MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Dead-Time Free Measurement of Dipole–Dipole Interactions between Electron Spins
journal, February 2000

  • Pannier, M.; Veit, S.; Godt, A.
  • Journal of Magnetic Resonance, Vol. 142, Issue 2
  • DOI: 10.1006/jmre.1999.1944

X-ray structure of the human α4β2 nicotinic receptor
journal, October 2016

  • Morales-Perez, Claudio L.; Noviello, Colleen M.; Hibbs, Ryan E.
  • Nature, Vol. 538, Issue 7625
  • DOI: 10.1038/nature19785

X-ray structure of the mouse serotonin 5-HT3 receptor
journal, August 2014

  • Hassaine, Ghérici; Deluz, Cédric; Grasso, Luigino
  • Nature, Vol. 512, Issue 7514
  • DOI: 10.1038/nature13552

Molecular Architecture of Full-Length KcsA : Role of Cytoplasmic Domains in Ion Permeation and Activation Gating
journal, January 2001

  • Cortes, D. Marien; Cuello, Luis G.; Perozo, Eduardo
  • The Journal of General Physiology, Vol. 117, Issue 2
  • DOI: 10.1085/jgp.117.2.165

Modified reconstitution method used in patch-clamp studies of Escherichia coli ion channels
journal, September 1989


Gating Movement of Acetylcholine Receptor Caught by Plunge-Freezing
journal, October 2012


Linking Crystallographic Model and Data Quality
journal, May 2012


Principles of activation and permeation in an anion-selective Cys-loop receptor
journal, May 2011


X-ray structure of a prokaryotic pentameric ligand-gated ion channel
journal, March 2008


Glycine receptor mechanism elucidated by electron cryo-microscopy
journal, September 2015


Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter
journal, May 2014


Conformational Changes Underlying Desensitization of the Pentameric Ligand-Gated Ion Channel ELIC
journal, June 2015


Structural mechanism of C-type inactivation in K+ channels
journal, July 2010

  • Cuello, Luis G.; Jogini, Vishwanath; Cortes, D. Marien
  • Nature, Vol. 466, Issue 7303
  • DOI: 10.1038/nature09153

Structure of the M2 Transmembrane Segment of GLIC, a Prokaryotic Cys Loop Receptor Homologue from Gloeobacter violaceus , Probed by Substituted Cysteine Accessibility
journal, March 2011

  • Parikh, Rishi B.; Bali, Moez; Akabas, Myles H.
  • Journal of Biological Chemistry, Vol. 286, Issue 16
  • DOI: 10.1074/jbc.M111.221895

The determination of pair distance distributions by pulsed ESR using Tikhonov regularization
journal, February 2005

  • Chiang, Yun-Wei; Borbat, Peter P.; Freed, Jack H.
  • Journal of Magnetic Resonance, Vol. 172, Issue 2
  • DOI: 10.1016/j.jmr.2004.10.012

PROCHECK: a program to check the stereochemical quality of protein structures
journal, April 1993

  • Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.
  • Journal of Applied Crystallography, Vol. 26, Issue 2
  • DOI: 10.1107/S0021889892009944

Cooperativity in Cytochrome P450 3A4: LINKAGES IN SUBSTRATE BINDING, SPIN STATE, UNCOUPLING, AND PRODUCT FORMATION
journal, January 2007

  • Denisov, Ilia G.; Baas, Bradley J.; Grinkova, Yelena V.
  • Journal of Biological Chemistry, Vol. 282, Issue 10
  • DOI: 10.1074/jbc.M609589200

Mutations that stabilize the open state of the Erwinia chrisanthemi ligand-gated ion channel fail to change the conformation of the pore domain in crystals
journal, April 2012

  • Gonzalez-Gutierrez, G.; Lukk, T.; Agarwal, V.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 16
  • DOI: 10.1073/pnas.1119268109

Endogenous neurosteroids regulate GABAA receptors through two discrete transmembrane sites
journal, November 2006

  • Hosie, Alastair M.; Wilkins, Megan E.; da Silva, Helena M. A.
  • Nature, Vol. 444, Issue 7118
  • DOI: 10.1038/nature05324

X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel
journal, January 2011

  • Nury, Hugues; Van Renterghem, Catherine; Weng, Yun
  • Nature, Vol. 469, Issue 7330
  • DOI: 10.1038/nature09647

iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM
journal, March 2011

  • Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910048675

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels
journal, February 2013

  • Sauguet, Ludovic; Poitevin, Frédéric; Murail, Samuel
  • The EMBO Journal, Vol. 32, Issue 5
  • DOI: 10.1038/emboj.2013.17

Acetylcholine receptor channel structure probed in cysteine-substitution mutants
journal, October 1992


Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

A locally closed conformation of a bacterial pentameric proton-gated ion channel
journal, May 2012

  • Prevost, Marie S.; Sauguet, Ludovic; Nury, Hugues
  • Nature Structural & Molecular Biology, Vol. 19, Issue 6
  • DOI: 10.1038/nsmb.2307

Structural basis for the coupling between activation and inactivation gates in K+ channels
journal, July 2010

  • Cuello, Luis G.; Jogini, Vishwanath; Cortes, D. Marien
  • Nature, Vol. 466, Issue 7303
  • DOI: 10.1038/nature09136

Ionic radii in aqueous solutions
journal, December 1988


Sites of alcohol and volatile anaesthetic action on GABAA and glycine receptors
journal, September 1997

  • Mihic, S. John; Ye, Qing; Wick, Marilee J.
  • Nature, Vol. 389, Issue 6649
  • DOI: 10.1038/38738

A Quantitative Description of KcsA Gating I: Macroscopic Currents
journal, October 2007

  • Chakrapani, Sudha; Cordero-Morales, Julio F.; Perozo, Eduardo
  • The Journal of General Physiology, Vol. 130, Issue 5
  • DOI: 10.1085/jgp.200709843

Channel gating governed symmetrically by conserved leucine residues in the M2 domain of nicotinic receptors
journal, August 1995

  • Labarca, Cesar; Nowak, Mark W.; Zhang, Haiyun
  • Nature, Vol. 376, Issue 6540
  • DOI: 10.1038/376514a0

Mutations in the channel domain alter desensitization of a neuronal nicotinic receptor
journal, October 1991

  • Revah, F.; Bertrand, D.; Galzi, J. -L
  • Nature, Vol. 353, Issue 6347
  • DOI: 10.1038/353846a0

Desensitization Mechanism in Prokaryotic Ligand-gated Ion Channel
journal, April 2012

  • Velisetty, Phanindra; Chakrapani, Sudha
  • Journal of Biological Chemistry, Vol. 287, Issue 22
  • DOI: 10.1074/jbc.M112.348045

The impact of receptor desensitization on fast synaptic transmission
journal, March 1996