Xavier Periole

Xavier Periole

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Xavier Periole

Xavier Periole

Publications by authors named "Xavier Periole"

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DNA-encircled lipid bilayers.

Nanoscale 2018 Oct 1;10(39):18463-18467. Epub 2018 Oct 1.

Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany.

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http://xlink.rsc.org/?DOI=C8NR06505E
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http://dx.doi.org/10.1039/c8nr06505eDOI Listing
October 2018

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

J Biol Chem 2018 03 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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http://dx.doi.org/10.1074/jbc.M117.809046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5846164PMC
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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http://dx.doi.org/10.1038/s41598-018-22912-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5865177PMC
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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http://dx.doi.org/10.1021/acs.jpcb.7b10233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5857390PMC
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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http://dx.doi.org/10.1371/journal.pcbi.1005907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5811071PMC
January 2018

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

Nat Commun 2017 05 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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http://dx.doi.org/10.1038/ncomms15214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5436218PMC
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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http://dx.doi.org/10.1021/acs.jpcb.6b06865DOI Listing
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 01 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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http://dx.doi.org/10.1021/acs.chemrev.6b00344DOI Listing
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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http://dx.doi.org/10.1242/jcs.176040DOI Listing
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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http://www.nature.com/articles/srep15661
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http://dx.doi.org/10.1038/srep15661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4616226PMC
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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http://dx.doi.org/10.1021/acs.jpcb.5b00809DOI Listing
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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http://dx.doi.org/10.1021/ct500477kDOI Listing
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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http://dx.doi.org/10.1021/ja507832eDOI Listing
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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http://dx.doi.org/10.1021/cb500086eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136704PMC
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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http://dx.doi.org/10.1002/wcms.1169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4171755PMC
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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http://dx.doi.org/10.1021/ct400219nDOI Listing
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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http://dx.doi.org/10.1007/978-1-62703-017-5_20DOI Listing
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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http://pubs.acs.org/doi/10.1021/ja310577u
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http://dx.doi.org/10.1021/ja310577uDOI Listing
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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http://dx.doi.org/10.1021/ct300646gDOI Listing
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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http://doi.wiley.com/10.1002/prot.24068
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http://dx.doi.org/10.1002/prot.24068DOI Listing
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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http://dx.doi.org/10.1021/ja303286eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406292PMC
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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http://dx.doi.org/10.1021/bi3001598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3332060PMC
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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http://dx.doi.org/10.1021/ct200599dDOI Listing
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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http://dx.doi.org/10.1021/bm201454jDOI Listing
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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http://dx.doi.org/10.1021/ct9002114DOI Listing
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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http://dx.doi.org/10.1002/jcc.21128DOI Listing
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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http://dx.doi.org/10.1021/jp8078259DOI Listing
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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http://dx.doi.org/10.1002/prot.22005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761145PMC
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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http://dx.doi.org/10.1021/ct700324xDOI Listing
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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http://dx.doi.org/10.1002/prot.21491DOI Listing
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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http://dx.doi.org/10.1021/ja0706246DOI Listing
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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http://dx.doi.org/10.1063/1.2404954DOI Listing
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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http://dx.doi.org/10.1021/bi049949eDOI Listing
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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http://dx.doi.org/10.1016/j.jmb.2004.02.064DOI Listing
April 2004