Xavier Periole

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Xavier Periole

Publications by authors named "Xavier Periole"

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36Publications

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Cholesterol binding to a conserved site modulates the conformation, pharmacology, and transport kinetics of the human serotonin transporter.

J Biol Chem 2018 Mar 19;293(10):3510-3523. Epub 2018 Jan 19.

From the Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus University Hospital, Skovagervej 2, DK-8240 Risskov, Denmark and

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March 2018

Dimer Interface of the Human Serotonin Transporter and Effect of the Membrane Composition.

Sci Rep 2018 Mar 23;8(1):5080. Epub 2018 Mar 23.

Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark.

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March 2018

Energetics Underlying Twist Polymorphisms in Amyloid Fibrils.

J Phys Chem B 2018 01 5;122(3):1081-1091. Epub 2018 Jan 5.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands.

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January 2018

A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition.

PLoS Comput Biol 2018 01 12;14(1):e1005907. Epub 2018 Jan 12.

Department of Chemistry, Aarhus University, Aarhus C, Denmark.

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January 2018

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex.

Nat Commun 2017 May 10;8:15214. Epub 2017 May 10.

Groningen Biomolecular Sciences and Biotechnology Institute &Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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May 2017

Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane.

J Phys Chem B 2017 04 28;121(15):3237-3249. Epub 2016 Sep 28.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands.

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April 2017

Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations.

Authors:
Xavier Periole

Chem Rev 2017 Jan 29;117(1):156-185. Epub 2016 Nov 29.

Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747AG Groningen, The Netherlands.

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January 2017

Computational 'microscopy' of cellular membranes.

J Cell Sci 2016 Jan 7;129(2):257-68. Epub 2016 Jan 7.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands

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January 2016

From light-harvesting to photoprotection: structural basis of the dynamic switch of the major antenna complex of plants (LHCII).

Sci Rep 2015 Oct 23;5:15661. Epub 2015 Oct 23.

Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.

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October 2015

Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex.

J Phys Chem B 2015 Jun 8;119(25):7791-803. Epub 2015 Jun 8.

‡Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.

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June 2015

Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent.

J Chem Theory Comput 2015 Jan 17;11(1):260-75. Epub 2014 Dec 17.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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January 2015

Lipid organization of the plasma membrane.

J Am Chem Soc 2014 Oct 1;136(41):14554-9. Epub 2014 Oct 1.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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October 2014

Phytochemicals perturb membranes and promiscuously alter protein function.

ACS Chem Biol 2014 Aug 17;9(8):1788-98. Epub 2014 Jun 17.

Zernike Institute for Advanced Materials, ‡Groningen Biomolecular Science and Biotechnology Institute, University of Groningen , Groningen, The Netherlands.

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August 2014

The power of coarse graining in biomolecular simulations.

Wiley Interdiscip Rev Comput Mol Sci 2014 May;4(3):225-248

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen Groningen, The Netherlands.

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May 2014

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations.

J Chem Theory Comput 2013 Aug 16;9(8):3282-92. Epub 2013 Jul 16.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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August 2013

The Martini coarse-grained force field.

Methods Mol Biol 2013 ;924:533-65

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.

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February 2013

Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1.

J Am Chem Soc 2013 Feb 13;135(8):3112-20. Epub 2013 Feb 13.

Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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February 2013

Improved Parameters for the Martini Coarse-Grained Protein Force Field.

J Chem Theory Comput 2013 Jan 28;9(1):687-97. Epub 2012 Nov 28.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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January 2013

Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models.

Proteins 2012 Jul 13;80(7):1744-54. Epub 2012 Apr 13.

Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158-2330, USA.

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July 2012

Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.

J Am Chem Soc 2012 Jul 25;134(26):10959-65. Epub 2012 Jun 25.

Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.

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July 2012

Rhodopsin forms a dimer with cytoplasmic helix 8 contacts in native membranes.

Biochemistry 2012 Mar 27;51(9):1819-21. Epub 2012 Feb 27.

Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, New York 10065, United States.

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March 2012

Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields.

J Chem Theory Comput 2012 Mar 29;8(3):1003-14. Epub 2012 Feb 29.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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March 2012

In silico design of robust bolalipid membranes.

Biomacromolecules 2012 Jan 1;13(1):196-205. Epub 2011 Dec 1.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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January 2012

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition.

J Chem Theory Comput 2009 Sep 19;5(9):2531-43. Epub 2009 Aug 19.

Department of Chemistry and Biochemistry and Institute for Macromolecular Assemblies, The City College of New York, 160 Convent Ave, New York, New York 10031, and Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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September 2009

Probing the free energy landscape of the FBP28WW domain using multiple techniques.

J Comput Chem 2009 May;30(7):1059-68

Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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May 2009

Factors that affect the degree of twist in beta-sheet structures: a molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide.

J Phys Chem B 2009 Feb;113(6):1728-37

Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands.

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February 2009

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials.

Proteins 2008 Sep;72(4):1171-88

Howard Hughes Medical Institute and Columbia University, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, USA.

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September 2008

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

J Chem Theory Comput 2008 May;4(5):819-34

Dept of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada, Chemical Engineering Department, The University of Michigan, 2300 Hayward Street, Ann Arbor, Michigan 48109, and Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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May 2008

Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain.

Proteins 2007 Nov;69(3):536-50

Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands.

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November 2007

G protein-coupled receptors self-assemble in dynamics simulations of model bilayers.

J Am Chem Soc 2007 Aug 21;129(33):10126-32. Epub 2007 Jul 21.

Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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August 2007

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent.

J Chem Phys 2007 Jan;126(1):014903

Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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January 2007

Acid-base equilibria in rhodopsin: dependence of the protonation state of glu134 on its environment.

Biochemistry 2004 Jun;43(22):6858-64

Department of Physiology and Biophysics, Box 1218, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, USA.

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June 2004

Molecular dynamics simulations of transducin: interdomain and front to back communication in activation and nucleotide exchange.

J Mol Biol 2004 Apr;338(3):469-81

Department of Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY 10029, USA.

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April 2004