Výsledky vyhledávání

Convergent vews on disordered protein dynamics from NMR and computational approaches

Autor: Nicola, Salvi, Vojtěch, Zapletal, Zuzana, Jaseňáková, Milan, Zachrdla, Petr, Padrta, Subhash, Narasimhan, Thorsten, Marquardsen, Jean-Max, Tyburn, Lukáš, Žídek, Martin, Blackledge, Fabien, Ferrage, Pavel, Kadeřávek

Publikováno v: Biophysical Journal
Biophysical Journal, 2022, 121 (20), pp.3785-3794. ⟨10.1016/j.bpj.2022.09.016⟩

International audience; Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) is a class of biologically important proteins exhibiting specific biophysical characteristics. They lack a hydrophobic core, and their conform

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e5898807fff2dd8639a7294778ef9a36
https://hal.science/hal-03861375/file/Salvi_BJ_text_preaccepted_4FF.pdf

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Characterisation of a transitionally occupied state of domain 1.1 of σA factor of RNA polymerase from Bacillus subtilis

Autor: Dávid Tužinčin, Petr Padrta, Kateřina Bendová, Libor Krásný, Lukas Zidek, Pavel Kadeřávek

σ factors are essential parts of bacterial RNA polymerase (RNAP) as they allow to recognize promotor sequences and initiate transcription. Domain 1.1 of vegetative σ factors occupies the primary channel of RNAP and also prevents binding of the σ f

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::eecd82dd2559b02fcc93d9388142389d
https://doi.org/10.22541/au.165897904.44818997/v1

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Boosting the resolution of low-field 15 N relaxation experiments on intrinsically disordered proteins with triple-resonance NMR

Autor: Jean-Max Tyburn, Vojtěch Zapletal, Milan Zachrdla, Nicolas Bolik-Coulon, Pavel Kadeřávek, Petr Padrta, Zuzana Jaseňáková, Thorsten Marquardsen, Fabien Ferrage, Lukáš Žídek

Publikováno v: Journal of Biomolecular NMR
Journal of Biomolecular NMR, 2020, 74 (2-3), pp.139-145. ⟨10.1007/s10858-019-00298-6⟩
Journal of Biomolecular NMR, Springer Verlag, 2020, 74 (2-3), pp.139-145. ⟨10.1007/s10858-019-00298-6⟩

Improving our understanding of nanosecond motions in disordered proteins requires the enhanced sampling of the spectral density function obtained from relaxation at low magnetic fields. High-resolution relaxometry and two-field NMR measurements of re

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::90dcc5a617604f244d5912c64a7b4cde
https://doi.org/10.1007/s10858-019-00298-6

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Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana

Autor: Zuzana Gelová, Jozef Hritz, Michaela Wimmerová, Petr Padrta, Blanka Pekárová, Olga Otrusinová, Jan Hejátko, Zuzana Jaseňáková, Agnieszka Szmitkowska, Pavel Kadeřávek, Lubomír Janda, Milan Zachrdla, Jaromír Marek, Hideo Iwaï, Séverine Jansen, Tomáš Klumpler, Lukáš Žídek, Gabriel Demo

Publikováno v: Journal of Biological Chemistry. 292:17525-17540

Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP-mediated phosphotransfer

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::33d499b0afebbfc6b334af28280d2ccc
https://doi.org/10.1074/jbc.m117.790212

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

Autor: Libor Krásný, Lukáš Žídek, Ivan Barvík, Petr Padrta, Milan Zachrdla, Alžbeta Rabatinová, Hana Šanderová

Publikováno v: Journal of Biological Chemistry. 292:11610-11617

Bacterial RNA polymerase (RNAP) requires σ factors to recognize promoter sequences. Domain 1.1 of primary σ factors (σ1.1) prevents their binding to promoter DNA in the absence of RNAP, and when in complex with RNAP, it occupies the DNA-binding ch

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::03155b7252ba338761a30f7c6a716712
https://doi.org/10.1074/jbc.m117.784074

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Boosting the resolution of low-field [Formula: see text] relaxation experiments on intrinsically disordered proteins with triple-resonance NMR

Autor: Zuzana, Jaseňáková, Vojtěch, Zapletal, Petr, Padrta, Milan, Zachrdla, Nicolas, Bolik-Coulon, Thorsten, Marquardsen, Jean-Max, Tyburn, Lukáš, Žídek, Fabien, Ferrage, Pavel, Kadeřávek

Publikováno v: Journal of biomolecular NMR. 74(2-3)

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::89e9c5c4d71347d6906489cd6c794db1
https://pubmed.ncbi.nlm.nih.gov/31960224

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Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase

Autor: Milan Zachrdla, Aleksandra Gruca, Petr Padrta, Malene Ringkjøbing Jensen, Vojtěch Kubáň, Libor Krásný, Hana Šanderová, Martin Blackledge, Marcin Grynberg, Zuzana Jaseňáková, Patryk Jarnot, Tomáš Koval, Lukáš Žídek, Dragana Vítovská, Hana Stegnerova, Pavel Srb, Joanna Ziemska-Legiecka, Jan Dohnálek

Publikováno v: Journal of the American Chemical Society
Journal of the American Chemical Society, 2019, 141 (42), pp.16817-16828. ⟨10.1021/jacs.9b07837⟩
Journal of the American Chemical Society, American Chemical Society, 2019, 141 (42), pp.16817-16828. ⟨10.1021/jacs.9b07837⟩

International audience; Electrostatic interactions play important roles in the functional mechanisms exploited by intrinsically disordered proteins (IDPs). The atomic resolution description of long-range and local structural propensities that can bot

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ac06acd53f1d3d29f2cb037ef3dccf1e
https://hal.univ-grenoble-alpes.fr/hal-02416081

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Spectral density mapping at multiple magnetic fields suitable for 13C NMR relaxation studies

Autor: Pavel Kadeřávek, Mária Šoltésová, Jozef Kowalewski, Josef Chmelík, Göran Widmalm, Jana Pavlíková Přecechtělová, Petr Padrta, Radovan Fiala, Vladimír Sklenář, Pavel Srb, Lukáš Žídek, Vojtěch Zapletal

Publikováno v: Journal of Magnetic Resonance. 266:23-40

Standard spectral density mapping protocols, well suited for the analysis of (15)N relaxation rates, introduce significant systematic errors when applied to (13)C relaxation data, especially if the dynamics is dominated by motions with short correlat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::dbad03024e0aeba44e81d6d40108ee95
https://doi.org/10.1016/j.jmr.2016.02.016

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Solution structure of domain 1.1 of the σ

Autor: Milan, Zachrdla, Petr, Padrta, Alžbeta, Rabatinová, Hana, Šanderová, Ivan, Barvík, Libor, Krásný, Lukáš, Žídek

Publikováno v: The Journal of biological chemistry. 292(28)

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::8465251897624fc277959396fb366a50
https://pubmed.ncbi.nlm.nih.gov/28539362

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Solution structure of the N-terminal domain ofBacillus subtilisδ subunit of RNA polymerase and its classification based on structural homologs

Autor: Lukáš Žídek, Jana Korelusová, Petr Padrta, Alžběta Švenková, Vladimír Sklenář, Jiří Nováček, Hana Šanderová, Libor Krásný, Jiří Jonák, Veronika Motáčková

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 78:1807-1810

RNA polymerase is an essential multisubunit enzyme responsible for transcription of genetic information from DNA into RNA. The RNA polymerase from Bacillus subtilis differs from its analogue from gram-negative bacteria in a presence of two additional

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::0660bca8a610d23e534b2e7879e730ce
https://doi.org/10.1002/prot.22708

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