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Items: 49

1.

Genetic Predispositions of Glucocorticoid Resistance and Therapeutic Outcomes in Polymyalgia Rheumatica and Giant Cell Arteritis.

Smutny T, Barvik I, Veleta T, Pavek P, Soukup T.

J Clin Med. 2019 Apr 27;8(5). pii: E582. doi: 10.3390/jcm8050582. Review.

2.

Overlap of Promoter Recognition Specificity of Stress Response Sigma Factors SigD and SigH in Corynebacterium glutamicum ATCC 13032.

Dostálová H, Busche T, Holátko J, Rucká L, Štěpánek V, Barvík I, Nešvera J, Kalinowski J, Pátek M.

Front Microbiol. 2019 Jan 9;9:3287. doi: 10.3389/fmicb.2018.03287. eCollection 2018.

3.

The Core and Holoenzyme Forms of RNA Polymerase from Mycobacterium smegmatis.

Kouba T, Pospíšil J, Hnilicová J, Šanderová H, Barvík I, Krásný L.

J Bacteriol. 2019 Jan 28;201(4). pii: e00583-18. doi: 10.1128/JB.00583-18. Print 2019 Feb 15.

PMID:
30478083
4.

RNA-based boronate internucleosidic linkages: an entry into reversible templated ligation and loop formation.

Gimenez Molina A, Barvik I, Müller S, Vasseur JJ, Smietana M.

Org Biomol Chem. 2018 Nov 21;16(45):8824-8830. doi: 10.1039/c8ob02182a.

PMID:
30411775
5.

CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5' Capping with NAD<sup/>.

Vvedenskaya IO, Bird JG, Zhang Y, Zhang Y, Jiao X, Barvík I, Krásný L, Kiledjian M, Taylor DM, Ebright RH, Nickels BE.

Mol Cell. 2018 May 3;70(3):553-564.e9. doi: 10.1016/j.molcel.2018.03.014. Epub 2018 Apr 19.

6.

Are haplotypes in a single methotrexate pathway more predictive for response in rheumatoid arthritis than in different pathways?

Soukup T, Barvik I, Nekvindova J, Veleta T, Kubena AA, Duintjer Tebbens J, Pavek P, Dosedel M.

Pharmacogenomics. 2018 Apr;19(5):379-381. doi: 10.2217/pgs-2016-0182. Epub 2018 Mar 26.

PMID:
29577811
7.

Intracellular cavity of sensor domain controls allosteric gating of TRPA1 channel.

Zimova L, Sinica V, Kadkova A, Vyklicka L, Zima V, Barvik I, Vlachova V.

Sci Signal. 2018 Jan 23;11(514). pii: eaan8621. doi: 10.1126/scisignal.aan8621.

PMID:
29363587
8.

RNA-directed off/on switch of RNase H activity using boronic ester formation.

Reverte M, Barvik I, Vasseur JJ, Smietana M.

Org Biomol Chem. 2017 Oct 4;15(38):8204-8210. doi: 10.1039/c7ob02145c.

PMID:
28926069
9.

Solution structure of domain 1.1 of the σA factor from Bacillus subtilis is preformed for binding to the RNA polymerase core.

Zachrdla M, Padrta P, Rabatinová A, Šanderová H, Barvík I, Krásný L, Žídek L.

J Biol Chem. 2017 Jul 14;292(28):11610-11617. doi: 10.1074/jbc.M117.784074. Epub 2017 May 24.

10.

The First Extracellular Linker Is Important for Several Aspects of the Gating Mechanism of Human TRPA1 Channel.

Marsakova L, Barvik I, Zima V, Zimova L, Vlachova V.

Front Mol Neurosci. 2017 Jan 31;10:16. doi: 10.3389/fnmol.2017.00016. eCollection 2017.

11.

Tuning the hybridization properties of modified oligonucleotides: from flexible to conformationally constrained phosphonate internucleotide linkages.

Páv O, Barvík I, Liboska R, Petrová M, Šimák O, Rosenbergová Š, Novák P, Buděšínský M, Rosenberg I.

Org Biomol Chem. 2017 Jan 18;15(3):701-707. doi: 10.1039/c6ob02571d.

PMID:
27995239
12.

The plausible association of MTHFR and ADORA2A polymorphisms with nodules in rheumatoid arthritis patients treated with methotrexate.

Soukup T, Dosedel M, Nekvindova J, Antonin Kubena A, Tacheci I, Duintjer Tebbens J, Vlcek J, Bradna P, Barvik I, Pavek P.

Pharmacogenet Genomics. 2017 Feb;27(2):43-50. doi: 10.1097/FPC.0000000000000256.

PMID:
27846189
13.

Non-canonical transcription initiation: the expanding universe of transcription initiating substrates.

Barvík I, Rejman D, Panova N, Šanderová H, Krásný L.

FEMS Microbiol Rev. 2017 Mar 1;41(2):131-138. doi: 10.1093/femsre/fuw041. Review.

PMID:
27799279
14.

The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA.

Bird JG, Zhang Y, Tian Y, Panova N, Barvík I, Greene L, Liu M, Buckley B, Krásný L, Lee JK, Kaplan CD, Ebright RH, Nickels BE.

Nature. 2016 Jul 21;535(7612):444-7. Epub 2016 Jul 6.

15.

Influence of major-groove chemical modifications of DNA on transcription by bacterial RNA polymerases.

Raindlová V, Janoušková M, Slavíčková M, Perlíková P, Boháčová S, Milisavljevič N, Šanderová H, Benda M, Barvík I, Krásný L, Hocek M.

Nucleic Acids Res. 2016 Apr 20;44(7):3000-12. doi: 10.1093/nar/gkw171. Epub 2016 Mar 21.

16.

Insights into the Mechanism of Action of Bactericidal Lipophosphonoxins.

Panova N, Zborníková E, Šimák O, Pohl R, Kolář M, Bogdanová K, Večeřová R, Seydlová G, Fišer R, Hadravová R, Šanderová H, Vítovská D, Šiková M, Látal T, Lovecká P, Barvík I, Krásný L, Rejman D.

PLoS One. 2015 Dec 30;10(12):e0145918. doi: 10.1371/journal.pone.0145918. eCollection 2015.

17.

Synthesis and structural characterization of monomeric and dimeric peptide nucleic acids prepared by using microwave-promoted multicomponent reactions.

Ovadia R, Lebrun A, Barvik I, Vasseur JJ, Baraguey C, Alvarez K.

Org Biomol Chem. 2015 Dec 7;13(45):11052-71. doi: 10.1039/c5ob01604e. Epub 2015 Sep 23.

PMID:
26394794
18.

Structural modeling and patch-clamp analysis of pain-related mutation TRPA1-N855S reveal inter-subunit salt bridges stabilizing the channel open state.

Zíma V, Witschas K, Hynkova A, Zímová L, Barvík I, Vlachova V.

Neuropharmacology. 2015 Jun;93:294-307. doi: 10.1016/j.neuropharm.2015.02.018. Epub 2015 Feb 25.

PMID:
25724085
19.

The impact of C677T and A1298C MTHFR polymorphisms on methotrexate therapeutic response in East Bohemian region rheumatoid arthritis patients.

Soukup T, Dosedel M, Pavek P, Nekvindova J, Barvik I, Bubancova I, Bradna P, Kubena AA, Carazo AF, Veleta T, Vlcek J.

Rheumatol Int. 2015 Jul;35(7):1149-61. doi: 10.1007/s00296-015-3219-z. Epub 2015 Jan 25.

PMID:
25618758
20.

Recognition of 2',5'-linked oligoadenylates by human ribonuclease L: molecular dynamics study.

Maláč K, Barvík I.

J Mol Model. 2014 Apr;20(4):2123. doi: 10.1007/s00894-014-2123-x. Epub 2014 Mar 16.

PMID:
24633766
21.

5'-O-Methylphosphonate nucleic acids--new modified DNAs that increase the Escherichia coli RNase H cleavage rate of hybrid duplexes.

Šipova H, Špringer T, Rejman D, Šimak O, Petrová M, Novák P, Rosenbergová Š, Páv O, Liboska R, Barvík I, Štěpanek J, Rosenberg I, Homola J.

Nucleic Acids Res. 2014 Apr;42(8):5378-89. doi: 10.1093/nar/gku125. Epub 2014 Feb 12.

22.

Complex between human RNase HI and the phosphonate-DNA/RNA duplex: molecular dynamics study.

Maláč K, Barvík I.

J Mol Graph Model. 2013 Jul;44:81-90. doi: 10.1016/j.jmgm.2013.05.004. Epub 2013 May 17.

PMID:
23751958
23.

Substrate recognition by norovirus polymerase: microsecond molecular dynamics study.

Maláč K, Barvík I.

J Comput Aided Mol Des. 2013 Apr;27(4):373-88. doi: 10.1007/s10822-013-9652-8. Epub 2013 Apr 26.

PMID:
23619980
24.

The δ subunit of RNA polymerase is required for rapid changes in gene expression and competitive fitness of the cell.

Rabatinová A, Šanderová H, Jirát Matějčková J, Korelusová J, Sojka L, Barvík I, Papoušková V, Sklenár V, Žídek L, Krásný L.

J Bacteriol. 2013 Jun;195(11):2603-11. doi: 10.1128/JB.00188-13. Epub 2013 Mar 29.

25.

C-terminal acidic cluster is involved in Ca2+-induced regulation of human transient receptor potential ankyrin 1 channel.

Sura L, Zíma V, Marsakova L, Hynkova A, Barvík I, Vlachova V.

J Biol Chem. 2012 May 25;287(22):18067-77. doi: 10.1074/jbc.M112.341859. Epub 2012 Mar 29.

26.

4'-Alkoxy oligodeoxynucleotides: a novel class of RNA mimics.

Liboska R, Snášel J, Barvík I, Buděšínský M, Pohl R, Točík Z, Páv O, Rejman D, Novák P, Rosenberg I.

Org Biomol Chem. 2011 Dec 21;9(24):8261-7. doi: 10.1039/c1ob06148h. Epub 2011 Nov 3.

PMID:
22051918
27.

Synthesis and properties of ApA analogues with shortened phosphonate internucleotide linkage.

Králíková S, Buděšínský M, Barvík I, Masojídková M, Točík Z, Rosenberg I.

Nucleosides Nucleotides Nucleic Acids. 2011 Jul-Aug;30(7-8):524-43. doi: 10.1080/15257770.2011.581259.

PMID:
21888544
28.

Synthesis of oligoribonucleotides with phosphonate-modified linkages.

Páv O, Košiová I, Barvík I, Pohl R, Buděšínský M, Rosenberg I.

Org Biomol Chem. 2011 Sep 7;9(17):6120-6. doi: 10.1039/c1ob05488k. Epub 2011 Jul 18.

PMID:
21769370
29.

Dynamic and programmable DNA-templated boronic ester formation.

Martin AR, Barvik I, Luvino D, Smietana M, Vasseur JJ.

Angew Chem Int Ed Engl. 2011 Apr 26;50(18):4193-6. doi: 10.1002/anie.201007170. Epub 2011 Mar 28. No abstract available.

PMID:
21445950
30.

Rapid changes in gene expression: DNA determinants of promoter regulation by the concentration of the transcription initiating NTP in Bacillus subtilis.

Sojka L, Kouba T, Barvík I, Sanderová H, Maderová Z, Jonák J, Krásny L.

Nucleic Acids Res. 2011 Jun;39(11):4598-611. doi: 10.1093/nar/gkr032. Epub 2011 Feb 7.

31.

3'-Deoxy phosphoramidate dinucleosides as improved inhibitors of hepatitis C virus subgenomic replicon and NS5B polymerase activity.

Priet S, Zlatev I, Barvik I, Geerts K, Leyssen P, Neyts J, Dutartre H, Canard B, Vasseur JJ, Morvan F, Alvarez K.

J Med Chem. 2010 Sep 23;53(18):6608-17. doi: 10.1021/jm100102v. Erratum in: J Med Chem. 2011 Jul 14;54(13):4936.

PMID:
20799693
32.

The N-terminal region is crucial for the thermostability of the G-domain of Bacillus stearothermophilus EF-Tu.

Sanderová H, Tiserová H, Barvík I, Sojka L, Jonák J, Krásný L.

Biochim Biophys Acta. 2010 Jan;1804(1):147-55. doi: 10.1016/j.bbapap.2009.09.024. Epub 2009 Sep 30.

PMID:
19800034
33.

Conformational evaluation of labeled C3'-O-P-(13)CH(2)-O-C4'' phosphonate internucleotide linkage, a phosphodiester isostere.

Tocík Z, Budesínský M, Barvík I Jr, Rosenberg I.

Biopolymers. 2009 Jul;91(7):514-29. doi: 10.1002/bip.21162.

PMID:
19213047
34.

Phosphoramidate dinucleosides as hepatitis C virus polymerase inhibitors.

Zlatev I, Dutartre H, Barvik I, Neyts J, Canard B, Vasseur JJ, Alvarez K, Morvan F.

J Med Chem. 2008 Sep 25;51(18):5745-57. doi: 10.1021/jm800617c.

PMID:
18800766
35.

On the stereochemistry of C3'-O-P-CH2-O-C4'' phosphonate internucleotide bond, a phosphate isostere.

Tocík Z, Budĕsínský M, Barvík I Jr, Rosenberg I.

Nucleic Acids Symp Ser (Oxf). 2008;(52):427-8. doi: 10.1093/nass/nrn217.

PMID:
18776436
36.

Ring enlargement of cyclic acetals and ketals: a way to seven-membered nucleoside phostones.

Páv O, Barvík I, Budesínský M, Masojídková M, Rosenberg I.

Org Lett. 2007 Dec 20;9(26):5469-72. Epub 2007 Nov 30.

PMID:
18047360
37.

YbxF, a protein associated with exponential-phase ribosomes in Bacillus subtilis.

Sojka L, Fucík V, Krásný L, Barvík I, Jonák J.

J Bacteriol. 2007 Jul;189(13):4809-14. Epub 2007 Apr 27.

38.

Temperature modulates binding specificity and affinity of the d-trehalose/d-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis.

Herman P, Barvik I Jr, Staiano M, Vitale A, Vecer J, Rossi M, D'Auria S.

Biochim Biophys Acta. 2007 May;1774(5):540-4. Epub 2007 Mar 20.

PMID:
17448739
39.

Novel isosteric, isopolar phosphonate analogs of oligonucleotides: preparation and properties.

Tocík Z, Barvík I Jr, Budesínský M, Rosenberg I.

Biopolymers. 2006 Nov;83(4):400-13.

PMID:
16845669
40.

Impact of the guanidinium group on hybridization and cellular uptake of cationic oligonucleotides.

Deglane G, Abes S, Michel T, Prévot P, Vives E, Debart F, Barvik I, Lebleu B, Vasseur JJ.

Chembiochem. 2006 Apr;7(4):684-92.

PMID:
16518865
41.

E. coli RNase HI and the phosphonate-DNA/RNA hybrid: molecular dynamics simulations.

Barvik I Jr.

Nucleosides Nucleotides Nucleic Acids. 2005;24(5-7):435-41.

PMID:
16247966
42.

The role of calcium in the conformational dynamics and thermal stability of the D-galactose/D-glucose-binding protein from Escherichia coli.

Herman P, Vecer J, Barvik I Jr, Scognamiglio V, Staiano M, de Champdoré M, Varriale A, Rossi M, D'Auria S.

Proteins. 2005 Oct 1;61(1):184-95.

PMID:
16080150
44.

-CH2- lengthening of the internucleotide linkage in the ApA dimer can improve its conformational compatibility with its natural polynucleotide counterpart.

Hanus J, Barvík I, Ruszová-Chmelová K, Stepánek J, Turpin PY, Bok J, Rosenberg I, Petrová-Endová M.

Nucleic Acids Res. 2001 Dec 15;29(24):5182-94.

45.
46.

Nonlinearity and trapping in excitation transfer: Dimers and trimers.

Barvík I I, Esser B, Schanz H.

Phys Rev B Condens Matter. 1995 Oct 1;52(13):9377-9386. No abstract available.

PMID:
9979983
47.

Effect of trapping on transport coherence. II. Continuous-time random-walk treatment.

Herman P, Barvík I I.

Phys Rev B Condens Matter. 1993 Aug 1;48(5):3130-3141. No abstract available.

PMID:
10008735
48.

Interpolation between the Grover-Silbey and the generalized stochastic Liouville equation theories.

Cápek V V, Barvík I I.

Phys Rev A. 1992 Dec 15;46(12):7431-7438. No abstract available.

PMID:
9908092
49.

Towards memory effects for electrons and phonons on nonrigid lattices.

Barvík I I, Cápek V V.

Phys Rev B Condens Matter. 1989 Nov 15;40(14):9973-9976. No abstract available.

PMID:
9991529

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