Publications by authors named "Roland Stote"

38Publications

A computational study of the molecular basis of antibiotic resistance in a DXR mutant.

J Comput Aided Mol Des 2019 10 26;33(10):927-940. Epub 2019 Oct 26.

Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de La Santé et de La Recherche Médicale (INSERM), U1258 / Centre National de Recherche Scientifique (CNRS), UMR7104 / Université de Strasbourg, 1 rue Laurent Fries, P. Box 10142, 67404, Illkirch, CEDEX, France.

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http://dx.doi.org/10.1007/s10822-019-00229-5DOI Listing
October 2019

Unrolr: Structural analysis of protein conformations using stochastic proximity embedding.

J Comput Chem 2018 11;39(30):2551-2557

Biologie structurale intégrative Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de La Santé et de La Recherche Médicale (INSERM), U1258/Centre National de Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, Illkirch, France.

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http://doi.wiley.com/10.1002/jcc.25599
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http://dx.doi.org/10.1002/jcc.25599DOI Listing
November 2018

Publisher Correction: Post-translational modifications in DNA topoisomerase 2α highlight the role of a eukaryote-specific residue in the ATPase domain.

Sci Rep 2018 Jul 10;8(1):10673. Epub 2018 Jul 10.

Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.

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http://dx.doi.org/10.1038/s41598-018-28936-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6039497PMC
July 2018

Post-translational modifications in DNA topoisomerase 2α highlight the role of a eukaryote-specific residue in the ATPase domain.

Sci Rep 2018 06 18;8(1):9272. Epub 2018 Jun 18.

Université de Strasbourg, CNRS UMR7104, INSERM U1258, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.

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http://dx.doi.org/10.1038/s41598-018-27606-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006247PMC
June 2018

Alternative dimerization interfaces in the glucocorticoid receptor-α ligand binding domain.

Biochim Biophys Acta Gen Subj 2018 08 1;1862(8):1810-1825. Epub 2018 May 1.

Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104 - Inserm U1258 - Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France. Electronic address:

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http://dx.doi.org/10.1016/j.bbagen.2018.04.022DOI Listing
August 2018

Peptide-Protein Binding Investigated by Far-IR Spectroscopy and Molecular Dynamics Simulations.

Biophys J 2017 Jun;112(12):2575-2588

Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 UMR 7104 CNRS, Université de Strasbourg, Illkirch, France. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5479146PMC
June 2017

Allosteric Regulation in the Ligand Binding Domain of Retinoic Acid Receptorγ.

PLoS One 2017 26;12(1):e0171043. Epub 2017 Jan 26.

Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0171043PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5268703PMC
August 2017

Synthesis and biological evaluation of phosphate isosters of fosmidomycin and analogs as inhibitors of Escherichia coli and Mycobacterium smegmatis 1-deoxyxylulose 5-phosphate reductoisomerases.

Bioorg Med Chem 2017 01 30;25(2):684-689. Epub 2016 Nov 30.

Laboratoire Chimie et Biochimie de Molécules Bioactives - Université de Strasbourg/CNRS, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67081 Strasbourg, France. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09680896163111
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http://dx.doi.org/10.1016/j.bmc.2016.11.040DOI Listing
January 2017

Tautomers of a Fluorescent G Surrogate and Their Distinct Photophysics Provide Additional Information Channels.

Angew Chem Int Ed Engl 2016 07 8;55(28):7974-7978. Epub 2016 Jun 8.

Laboratoire de Biophotonique et Pharmacologie Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg 74 route du Rhin, 67401 Illkirch (France).

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http://dx.doi.org/10.1002/anie.201601688DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978544PMC
July 2016

PSSweb: protein structural statistics web server.

Nucleic Acids Res 2016 07 12;44(W1):W401-5. Epub 2016 May 12.

Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale U964, Centre National de la Recherche Scientifique UMR 7104, Université de Strasbourg, 67404 Illkirch, France.

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http://dx.doi.org/10.1093/nar/gkw332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987900PMC
July 2016

Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy.

Nucleic Acids Res 2016 Apr 20;44(7):3408-19. Epub 2016 Feb 20.

Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France

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http://dx.doi.org/10.1093/nar/gkw077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838372PMC
April 2016

Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes.

BMC Evol Biol 2015 Oct 12;15:222. Epub 2015 Oct 12.

Primordial Germ Cells' Ontogeny and Pluripotency Laboratory, Functional Genomics and Cancer Department, Genetics Institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.

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http://dx.doi.org/10.1186/s12862-015-0506-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603632PMC
October 2015

Far infrared spectra of solid state L-serine, L-threonine, L-cysteine, and L-methionine in different protonation states.

Spectrochim Acta A Mol Biomol Spectrosc 2015 16;150:301-7. Epub 2015 May 16.

Laboratoire de bio électrochimie et spectroscopie, UMR7140, Chimie de la Matière complexe, Université de Strasbourg, CNRS, 1 rue Blaise Pascal, F-67070 Strasbourg, France. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S13861425150061
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http://dx.doi.org/10.1016/j.saa.2015.05.031DOI Listing
September 2016

Molecular dynamics for computational proteomics of methylated histone H3.

Biochim Biophys Acta 2015 May 18;1850(5):1026-1040. Epub 2014 Sep 18.

Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Centre National de la Recherche Scientifique (CNRS) UMR7104, Université de Strasbourg, 67404 Illkirch, France.

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https://linkinghub.elsevier.com/retrieve/pii/S03044165140031
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http://dx.doi.org/10.1016/j.bbagen.2014.09.015DOI Listing
May 2015

Structural insights into the molecular mechanism of vitamin D receptor activation by lithocholic acid involving a new mode of ligand recognition.

J Med Chem 2014 Jun 21;57(11):4710-9. Epub 2014 May 21.

Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France.

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http://dx.doi.org/10.1021/jm5002524DOI Listing
June 2014

Protein structural statistics with PSS.

J Chem Inf Model 2013 Sep 9;53(9):2471-82. Epub 2013 Sep 9.

Laboratoire de Biochimie, UMR 7654 CNRS, Ecole Polytechnique , 91128 Palaiseau Cedex, France.

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http://dx.doi.org/10.1021/ci400233jDOI Listing
September 2013

Phosphorylation of the retinoic acid receptor alpha induces a mechanical allosteric regulation and changes in internal dynamics.

PLoS Comput Biol 2013 Apr 18;9(4):e1003012. Epub 2013 Apr 18.

Institute of Genetics and Molecular and Cellular Biology, Integrated Structural Biology Department, Illkirch, France.

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http://dx.doi.org/10.1371/journal.pcbi.1003012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3630199PMC
April 2013

Evolution of nuclear retinoic acid receptor alpha (RARα) phosphorylation sites. Serine gain provides fine-tuned regulation.

Mol Biol Evol 2011 Jul 5;28(7):2125-37. Epub 2011 Feb 5.

IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Institut National de Sante et de Recherche Medicale (INSERM), U596, Centre National de Recherche Scientifique (CNRS), UMR7104, Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France.

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http://mbe.oxfordjournals.org/content/early/2011/02/04/molbe
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http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msr035
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http://dx.doi.org/10.1093/molbev/msr035DOI Listing
July 2011

The structural and dynamic response of MAGI-1 PDZ1 with noncanonical domain boundaries to the binding of human papillomavirus E6.

J Mol Biol 2011 Mar 13;406(5):745-63. Epub 2011 Jan 13.

Equipe Oncoprotéines, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, BP 10413, 67412 Illkirch Cedex, France.

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http://dx.doi.org/10.1016/j.jmb.2011.01.015DOI Listing
March 2011

Force field parameters for the simulation of modified histone tails.

J Comput Chem 2010 Oct;31(13):2434-51

Structural Biology and Genomics Department, IGBMC, 1 rue Laurent Fries, BP 10142, F - 67404 Illkirch, Cedex, France.

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http://dx.doi.org/10.1002/jcc.21536DOI Listing
October 2010

Dynamic correlation networks in human peroxisome proliferator-activated receptor-γ nuclear receptor protein.

Eur Biophys J 2010 Oct 23;39(11):1503-12. Epub 2010 May 23.

Structural Biology and Genomics Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire, BP 10413 Illkirch, Strasbourg, France.

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http://link.springer.com/10.1007/s00249-010-0608-9
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http://dx.doi.org/10.1007/s00249-010-0608-9DOI Listing
October 2010

Far infrared spectra of solid state aliphatic amino acids in different protonation states.

J Chem Phys 2010 Mar;132(11):115105

Institut de Chimie, UMR 7177, Laboratoire de Spectroscopie Vibrationnelle et Electrochimie des Biomolécules, Université de Strasbourg, 1 rue Blaise Pascal, Strasbourg F-67070, France.

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http://dx.doi.org/10.1063/1.3356027DOI Listing
March 2010

Dynamics of beta3 integrin I-like and hybrid domains: insight from simulations on the mechanism of transition between open and closed forms.

Proteins 2009 Sep;76(4):977-94

Laboratoire de Biophysicochimie Moléculaire, Institut de Chimie de Strasbourg, Université de Strasbourg, Strasbourg, France.

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http://doi.wiley.com/10.1002/prot.22404
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http://dx.doi.org/10.1002/prot.22404DOI Listing
September 2009

Molecular basis for Bcl-2 homology 3 domain recognition in the Bcl-2 protein family: identification of conserved hot spot interactions.

J Biol Chem 2009 Jun 17;284(26):17499-511. Epub 2009 Mar 17.

Laboratoire de Biophysicochimie Moléculaire, Institut de Chimie, UMR 7177, Université de Strasbourg, F-67000 Strasbourg, France.

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http://dx.doi.org/10.1074/jbc.M805542200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788401PMC
June 2009

Comparative normal mode analysis of LFA-1 integrin I-domains.

J Mol Biol 2007 Nov 12;374(1):231-49. Epub 2007 Jul 12.

Laboratoire de Biophysicochimie Moléculaire, Institut de Chimie de Strasbourg, Université Louis Pasteur, BP 1032, Strasbourg, France.

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http://dx.doi.org/10.1016/j.jmb.2007.07.006DOI Listing
November 2007

Critical role of desolvation in the binding of 20-hydroxyecdysone to the ecdysone receptor.

J Biol Chem 2007 Nov 11;282(45):32924-34. Epub 2007 Sep 11.

Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, Illkirch, France.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M705559200
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http://dx.doi.org/10.1074/jbc.M705559200DOI Listing
November 2007

Metal ion dependent adhesion sites in integrins: a combined DFT and QMC study on Mn2+.

J Phys Chem B 2007 Aug 3;111(30):9099-103. Epub 2007 Jul 3.

Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 1072, 20080 Donostia, Spain.

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https://pubs.acs.org/doi/10.1021/jp071065s
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http://dx.doi.org/10.1021/jp071065sDOI Listing
August 2007

Protein-protein recognition and interaction hot spots in an antigen-antibody complex: free energy decomposition identifies "efficient amino acids".

Proteins 2007 May;67(2):418-34

Structural Biology and Genomics Department, UMR 7104, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS / INSERM / ULP, F-67404 Illkirch Cedex, France.

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http://dx.doi.org/10.1002/prot.21259DOI Listing
May 2007

On the affinity regulation of the metal-ion-dependent adhesion sites in integrins.

J Am Chem Soc 2006 Mar;128(11):3554-63

Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center, P. K. 1072, 20080 Donostia, Spain.

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http://dx.doi.org/10.1021/ja054142aDOI Listing
March 2006

Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes.

J Chem Phys 2004 Nov;121(19):9539-48

Laboratoire de Chimie Biophysique ISIS (UMR 7006-CNRS), Université Louis Pasteur, 8 allée Gaspard Monge, 67000 Strasbourg, France.

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http://aip.scitation.org/doi/10.1063/1.1789935
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http://dx.doi.org/10.1063/1.1789935DOI Listing
November 2004

Functionality maps of the ATP binding site of DNA gyrase B: generation of a consensus model of ligand binding.

J Med Chem 2004 Aug;47(18):4373-90

Département de Biologie et Génomique Structurales, IGBMC UMR 7104, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard S. Brant BP 10413, F-67412 Illkirch, France.

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http://dx.doi.org/10.1021/jm0311184DOI Listing
August 2004

Structure of the His44 --> Ala single point mutant of the distal finger motif of HIV-1 nucleocapsid protein: a combined NMR, molecular dynamics simulation, and fluorescence study.

Biochemistry 2004 Jun;43(24):7687-97

Laboratoire de Chimie Biophysique, ISIS UMR 7006 CNRS, Université Louis Pasteur, 8 allée Gaspard Monge, BP 70028, F-67083 Strasbourg Cedex, France.

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http://dx.doi.org/10.1021/bi036137uDOI Listing
June 2004

NO rebinding to myoglobin: a reactive molecular dynamics study.

Biophys Chem 2002 Jul;98(1-2):183-207

Laboratoire de Chimie Biophysique, ISIS UMR 7006, Universite Louis Pasteur, 67000, Strasbourg, France.

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http://dx.doi.org/10.1016/s0301-4622(02)00093-5DOI Listing
July 2002