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Items: 39

1.

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

Krebs FS, Esque J, Stote RH.

J Comput Aided Mol Des. 2019 Oct;33(10):927-940. doi: 10.1007/s10822-019-00229-5. Epub 2019 Oct 26.

PMID:
31654265
2.

Allostery in Its Many Disguises: From Theory to Applications.

Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T.

Structure. 2019 Apr 2;27(4):566-578. doi: 10.1016/j.str.2019.01.003. Epub 2019 Feb 7. Review.

3.

Recurrent activating mutations of PPARγ associated with luminal bladder tumors.

Rochel N, Krucker C, Coutos-Thévenot L, Osz J, Zhang R, Guyon E, Zita W, Vanthong S, Hernandez OA, Bourguet M, Badawy KA, Dufour F, Peluso-Iltis C, Heckler-Beji S, Dejaegere A, Kamoun A, de Reyniès A, Neuzillet Y, Rebouissou S, Béraud C, Lang H, Massfelder T, Allory Y, Cianférani S, Stote RH, Radvanyi F, Bernard-Pierrot I.

Nat Commun. 2019 Jan 16;10(1):253. doi: 10.1038/s41467-018-08157-y.

4.

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

Eberhardt J, Stote RH, Dejaegere A.

J Comput Chem. 2018 Nov 15;39(30):2551-2557. doi: 10.1002/jcc.25599.

PMID:
30447084
5.

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

Bedez C, Lotz C, Batisse C, Broeck AV, Stote RH, Howard E, Pradeau-Aubreton K, Ruff M, Lamour V.

Sci Rep. 2018 Jul 10;8(1):10673. doi: 10.1038/s41598-018-28936-3.

6.

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

Bedez C, Lotz C, Batisse C, Broeck AV, Stote RH, Howard E, Pradeau-Aubreton K, Ruff M, Lamour V.

Sci Rep. 2018 Jun 18;8(1):9272. doi: 10.1038/s41598-018-27606-8. Erratum in: Sci Rep. 2018 Jul 10;8(1):10673.

7.

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

Bianchetti L, Wassmer B, Defosset A, Smertina A, Tiberti ML, Stote RH, Dejaegere A.

Biochim Biophys Acta Gen Subj. 2018 Aug;1862(8):1810-1825. doi: 10.1016/j.bbagen.2018.04.022. Epub 2018 May 1.

PMID:
29723544
8.

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

Cote Y, Nominé Y, Ramirez J, Hellwig P, Stote RH.

Biophys J. 2017 Jun 20;112(12):2575-2588. doi: 10.1016/j.bpj.2017.05.018.

9.

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

Chebaro Y, Sirigu S, Amal I, Lutzing R, Stote RH, Rochette-Egly C, Rochel N, Dejaegere A.

PLoS One. 2017 Jan 26;12(1):e0171043. doi: 10.1371/journal.pone.0171043. eCollection 2017.

10.

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

Munier M, Tritsch D, Krebs F, Esque J, Hemmerlin A, Rohmer M, Stote RH, Grosdemange-Billiard C.

Bioorg Med Chem. 2017 Jan 15;25(2):684-689. doi: 10.1016/j.bmc.2016.11.040. Epub 2016 Nov 30.

PMID:
27955925
11.

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

Sholokh M, Improta R, Mori M, Sharma R, Kenfack C, Shin D, Voltz K, Stote RH, Zaporozhets OA, Botta M, Tor Y, Mély Y.

Angew Chem Int Ed Engl. 2016 Jul 4;55(28):7974-7978. doi: 10.1002/anie.201601688. Epub 2016 Jun 8.

12.

PSSweb: protein structural statistics web server.

Gaillard T, Stote RH, Dejaegere A.

Nucleic Acids Res. 2016 Jul 8;44(W1):W401-5. doi: 10.1093/nar/gkw332. Epub 2016 May 12.

13.

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

Voltz K, Léonard J, Touceda PT, Conyard J, Chaker Z, Dejaegere A, Godet J, Mély Y, Haacke S, Stote RH.

Nucleic Acids Res. 2016 Apr 20;44(7):3408-19. doi: 10.1093/nar/gkw077. Epub 2016 Feb 20.

14.

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

Gaillard T, Trivella A, Stote RH, Hellwig P.

Spectrochim Acta A Mol Biomol Spectrosc. 2015;150:301-7. doi: 10.1016/j.saa.2015.05.031. Epub 2015 May 16.

PMID:
26056980
15.

Molecular dynamics for computational proteomics of methylated histone H3.

Grauffel C, Stote RH, Dejaegere A.

Biochim Biophys Acta. 2015 May;1850(5):1026-1040. doi: 10.1016/j.bbagen.2014.09.015. Epub 2014 Sep 18.

PMID:
25240462
16.

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

Belorusova AY, Eberhardt J, Potier N, Stote RH, Dejaegere A, Rochel N.

J Med Chem. 2014 Jun 12;57(11):4710-9. doi: 10.1021/jm5002524. Epub 2014 May 21.

PMID:
24818857
17.

Protein structural statistics with PSS.

Gaillard T, Schwarz BB, Chebaro Y, Stote RH, Dejaegere A.

J Chem Inf Model. 2013 Sep 23;53(9):2471-82. doi: 10.1021/ci400233j. Epub 2013 Sep 9.

PMID:
23957210
18.

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

Chebaro Y, Amal I, Rochel N, Rochette-Egly C, Stote RH, Dejaegere A.

PLoS Comput Biol. 2013 Apr;9(4):e1003012. doi: 10.1371/journal.pcbi.1003012. Epub 2013 Apr 18.

19.

Structural basis for hijacking of cellular LxxLL motifs by papillomavirus E6 oncoproteins.

Zanier K, Charbonnier S, Sidi AO, McEwen AG, Ferrario MG, Poussin-Courmontagne P, Cura V, Brimer N, Babah KO, Ansari T, Muller I, Stote RH, Cavarelli J, Vande Pol S, Travé G.

Science. 2013 Feb 8;339(6120):694-8. doi: 10.1126/science.1229934.

20.

Design, synthesis, and functional evaluation of leukocyte function associated antigen-1 antagonists in early and late stages of cancer development.

San Sebastián E, Zimmerman T, Zubia A, Vara Y, Martin E, Sirockin F, Dejaegere A, Stote RH, Lopez X, Pantoja-Uceda D, Valcárcel M, Mendoza L, Vidal-Vanaclocha F, Cossío FP, Blanco FJ.

J Med Chem. 2013 Feb 14;56(3):735-47. doi: 10.1021/jm3016848. Epub 2013 Jan 22.

PMID:
23339734
21.

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

Charbonnier S, Nominé Y, Ramírez J, Luck K, Chapelle A, Stote RH, Travé G, Kieffer B, Atkinson RA.

J Mol Biol. 2011 Mar 11;406(5):745-63. doi: 10.1016/j.jmb.2011.01.015. Epub 2011 Jan 13.

PMID:
21238461
22.

Force field parameters for the simulation of modified histone tails.

Grauffel C, Stote RH, Dejaegere A.

J Comput Chem. 2010 Oct;31(13):2434-51. doi: 10.1002/jcc.21536.

PMID:
20652987
23.

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

Fidelak J, Ferrer S, Oberlin M, Moras D, Dejaegere A, Stote RH.

Eur Biophys J. 2010 Oct;39(11):1503-12. doi: 10.1007/s00249-010-0608-9. Epub 2010 May 23.

PMID:
20496064
24.

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

Trivella A, Gaillard T, Stote RH, Hellwig P.

J Chem Phys. 2010 Mar 21;132(11):115105. doi: 10.1063/1.3356027.

PMID:
20331320
25.

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

Gaillard T, Dejaegere A, Stote RH.

Proteins. 2009 Sep;76(4):977-94. doi: 10.1002/prot.22404.

PMID:
19350618
26.

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

Moroy G, Martin E, Dejaegere A, Stote RH.

J Biol Chem. 2009 Jun 26;284(26):17499-511. doi: 10.1074/jbc.M805542200. Epub 2009 Mar 17.

27.

Histone H3 tails containing dimethylated lysine and adjacent phosphorylated serine modifications adopt a specific conformation during mitosis and meiosis.

Eberlin A, Grauffel C, Oulad-Abdelghani M, Robert F, Torres-Padilla ME, Lambrot R, Spehner D, Ponce-Perez L, Würtz JM, Stote RH, Kimmins S, Schultz P, Dejaegere A, Tora L.

Mol Cell Biol. 2008 Mar;28(5):1739-54. doi: 10.1128/MCB.01180-07. Epub 2008 Jan 7.

28.

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

Gaillard T, Martin E, San Sebastian E, Cossío FP, Lopez X, Dejaegere A, Stote RH.

J Mol Biol. 2007 Nov 16;374(1):231-49. Epub 2007 Jul 12.

PMID:
17919656
29.

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

Browning C, Martin E, Loch C, Wurtz JM, Moras D, Stote RH, Dejaegere AP, Billas IM.

J Biol Chem. 2007 Nov 9;282(45):32924-34. Epub 2007 Sep 11.

30.

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

Sebastian ES, Matxain JM, Eriksson LA, Stote RH, Dejaegere A, Cossio FP, Lopez X.

J Phys Chem B. 2007 Aug 2;111(30):9099-103. Epub 2007 Jul 3.

PMID:
17608410
31.
32.

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

San Sebastian E, Mercero JM, Stote RH, Dejaegere A, Cossío FP, Lopez X.

J Am Chem Soc. 2006 Mar 22;128(11):3554-63.

PMID:
16536528
33.

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

Wan S, Stote RH, Karplus M.

J Chem Phys. 2004 Nov 15;121(19):9539-48.

PMID:
15538876
34.

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

Schechner M, Sirockin F, Stote RH, Dejaegere AP.

J Med Chem. 2004 Aug 26;47(18):4373-90.

PMID:
15317451
35.

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.

Stote RH, Kellenberger E, Muller H, Bombarda E, Roques BP, Kieffer B, Mély Y.

Biochemistry. 2004 Jun 22;43(24):7687-97.

PMID:
15196011
36.

Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints.

Martí-Renom MA, Stote RH, Querol E, Aviles FX, Karplus M.

Proteins. 2000 Aug 15;40(3):482-93.

PMID:
10861940
37.

Characterization of flexible molecules in solution: the RGDW peptide.

Bartels C, Stote RH, Karplus M.

J Mol Biol. 1998 Dec 18;284(5):1641-60.

PMID:
9878376
38.

Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints.

Martí-Renom MA, Stote RH, Querol E, Avilés FX, Karplus M.

J Mol Biol. 1998 Nov 20;284(1):145-72.

PMID:
9811548
39.

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