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

Title: String method solution of the gating pathways for a pentameric ligand-gated ion channel

Authors:
; ; ; ; ORCiD logo; ;
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1368687
DOE Contract Number:  
AC02-76SF00515; APP1104259; U01-11567710; DP170101732
Resource Type:
Journal Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 114; Journal Issue: 21; Journal ID: ISSN 0027-8424
Country of Publication:
United States
Language:
English

Citation Formats

Lev, Bogdan, Murail, Samuel, Poitevin, Frédéric, Cromer, Brett A., Baaden, Marc, Delarue, Marc, and Allen, Toby W. String method solution of the gating pathways for a pentameric ligand-gated ion channel. United States: N. p., 2017. Web. doi:10.1073/pnas.1617567114.
Lev, Bogdan, Murail, Samuel, Poitevin, Frédéric, Cromer, Brett A., Baaden, Marc, Delarue, Marc, & Allen, Toby W. String method solution of the gating pathways for a pentameric ligand-gated ion channel. United States. doi:10.1073/pnas.1617567114.
Lev, Bogdan, Murail, Samuel, Poitevin, Frédéric, Cromer, Brett A., Baaden, Marc, Delarue, Marc, and Allen, Toby W. Tue . "String method solution of the gating pathways for a pentameric ligand-gated ion channel". United States. doi:10.1073/pnas.1617567114.
@article{osti_1368687,
title = {String method solution of the gating pathways for a pentameric ligand-gated ion channel},
author = {Lev, Bogdan and Murail, Samuel and Poitevin, Frédéric and Cromer, Brett A. and Baaden, Marc and Delarue, Marc and Allen, Toby W.},
abstractNote = {},
doi = {10.1073/pnas.1617567114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
issn = {0027-8424},
number = 21,
volume = 114,
place = {United States},
year = {2017},
month = {5}
}

Works referenced in this record:

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


Crystal structure of human glycine receptor-α3 bound to antagonist strychnine
journal, September 2015

  • Huang, Xin; Chen, Hao; Michelsen, Klaus
  • Nature, Vol. 526, Issue 7572
  • DOI: 10.1038/nature14972

Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289

Crystal structure of a human GABAA receptor
journal, June 2014


PNAS Plus: From the Cover: A gating mechanism of pentameric ligand-gated ion channels
journal, September 2013

  • Calimet, N.; Simoes, M.; Changeux, J. -P.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 42
  • DOI: 10.1073/pnas.1313785110

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
journal, June 2011

  • Buch, I.; Giorgino, T.; De Fabritiis, G.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 25
  • DOI: 10.1073/pnas.1103547108

Comparison of simple potential functions for simulating liquid water
journal, July 1983

  • Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
  • The Journal of Chemical Physics, Vol. 79, Issue 2
  • DOI: 10.1063/1.445869

On the nature of partial agonism in the nicotinic receptor superfamily
journal, July 2008

  • Lape, Remigijus; Colquhoun, David; Sivilotti, Lucia G.
  • Nature, Vol. 454, Issue 7205
  • DOI: 10.1038/nature07139

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
journal, April 1998

  • MacKerell, A. D.; Bashford, D.; Bellott, M.
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp973084f

Agonist and Antagonist Binding in Human Glycine Receptors
journal, September 2014

  • Yu, Rilei; Hurdiss, Eliott; Greiner, Timo
  • Biochemistry, Vol. 53, Issue 38
  • DOI: 10.1021/bi500815f

The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters
journal, October 2013


CHARMM: The biomolecular simulation program
journal, July 2009

  • Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
  • Journal of Computational Chemistry, Vol. 30, Issue 10
  • DOI: 10.1002/jcc.21287

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
journal, June 2010

  • Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo
  • The Journal of Physical Chemistry B, Vol. 114, Issue 23
  • DOI: 10.1021/jp101759q

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

Finding Transition Pathways Using the String Method with Swarms of Trajectories
journal, March 2008

  • Pan, Albert C.; Sezer, Deniz; Roux, Benoît
  • The Journal of Physical Chemistry B, Vol. 112, Issue 11
  • DOI: 10.1021/jp0777059

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

Pore opening and closing of a pentameric ligand-gated ion channel
journal, November 2010

  • Zhu, F.; Hummer, G.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 46
  • DOI: 10.1073/pnas.1009313107

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

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

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

Site-Directed Spin Labeling Reveals Pentameric Ligand-Gated Ion Channel Gating Motions
journal, November 2013


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

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

Allostery and the Monod-Wyman-Changeux Model After 50 Years
journal, June 2012


Cis–trans isomerization at a proline opens the pore of a neurotransmitter-gated ion channel
journal, November 2005

  • Lummis, Sarah C. R.; Beene, Darren L.; Lee, Lori W.
  • Nature, Vol. 438, Issue 7065
  • DOI: 10.1038/nature04130