Výsledky vyhledávání - "Nad'a Špačková"

Protein environment affects the water–tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants

Autor: Filip Šebesta, Séverine Jansen, Jaroslav V. Burda, Milan Zachrdla, Nad'a Špačková, Jiří Kozelka, Pavel Srb, Zuzana Trošanová, Lukáš Žídek

Publikováno v: Physical Chemistry Chemical Physics. 20:12664-12677

Water molecules can interact with aromatic moieties using either their O-H bonds or their lone-pairs of electrons. In proteins, water-π interactions have been reported to occur with tryptophan and histidine residues, and dynamic exchange between O-H

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe2a24a239bd882421c0527eedc53e30
https://doi.org/10.1039/c7cp08623g

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Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

Autor: Tadeusz Kulinski, Joanna Sarzyñska, Thomas E. Cheatham, Nad'a Špačková, Eva Fadrná, Jaroslav Koča, Jiří Šponer, Modesto Orozco

Publikováno v: Journal of chemical theory and computation. 5(9)

We have carried out a set of explicit solvent molecular dynamics (MD) simulations on two DNA quadruplex (G-DNA) molecules, namely the antiparallel d(G4T4G4)2 dimeric quadruplex with diagonal loops and the parallel-stranded human telomeric monomolecul

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe20c36abe5c03da2dace78e2723f8ba
https://pubmed.ncbi.nlm.nih.gov/26616629

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Structural Dynamics of the Box C/D RNA Kink-Turn and Its Complex with Proteins: The Role of the A-Minor 0 Interaction, Long-Residency Water Bridges, and Structural Ion-Binding Sites Revealed by Molecular Simulations

Autor: Kamila Réblová, Nad'a Špačková, Jiri Sponer

Publikováno v: The Journal of Physical Chemistry B. 114:10581-10593

Kink-turns (K-turns) are recurrent elbow-like RNA motifs that participate in protein-assisted RNA folding and contribute to RNA dynamics. We carried out a set of molecular dynamics (MD) simulations using parm99 and parmbsc0 force fields to investigat

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https://doi.org/10.1021/jp102572k

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Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion

Autor: Nad'a Špačková, Vladimir Sychrovsky, Lukáš Trantírek, Zuzana Vokáčová, Koen Robeyns, Jiri Sponer, Luc Van Meervelt, Wulf Blankenfeldt, Silvie Foldynová-Trantírková

Publikováno v: Nucleic Acids Research

We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted fro

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::afafaa8339078cf1ede039e56e5874f7
https://doi.org/10.1093/nar/gkp783

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Molecular dynamics simulations and their application to four-stranded DNA

Autor: Nad'a Špačková, Jiří Šponer

Publikováno v: Methods (San Diego, Calif.)

This review provides a critical assessment of the advantages and limitations of modeling methods available for guanine quadruplex (G-DNA) molecules. We characterize the relations of simulations to the experimental techniques and explain the actual me

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3b1b1ea94b1f612fdc118cc0ffeda6fa
https://doi.org/10.1016/j.ymeth.2007.02.004

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Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme

Autor: Nad'a Špačková, Jana Sefcikova, Maryna V. Krasovska, Nils G. Walter, Jiří Šponer

Publikováno v: Biopolymers. 85:392-406

The self-cleaving hepatitis delta virus (HDV) ribozyme is essential for the replication of HDV, a liver disease causing pathogen in humans. The catalytically critical nucleotide C75 of the ribozyme is buttressed by a trefoil turn pivoting around an e

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2f99122239e525b38deca1f2f3fc9e5b
https://doi.org/10.1002/bip.20693

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Calculation of Structural Behavior of Indirect NMR Spin−Spin Couplings in the Backbone of Nucleic Acids

Autor: Jiří Šponer, Zuzana Vokáčová, Bohdan Schneider, ‡ and Nad'a Špačková, Vladimír Sychrovský

Publikováno v: The Journal of Physical Chemistry B. 110:22894-22902

Calculated indirect NMR spin-spin coupling constants (J-couplings) between (31)P, (13)C, and (1)H nuclei were related to the backbone torsion angles of nucleic acids (NAs), and it was shown that J-couplings can facilitate accurate and reliable struct

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f171b877f0469ca871f9dc19092cc09d
https://doi.org/10.1021/jp065000l

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Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence

Autor: Nad'a Špačková, Filip Lankaš, Jiri Sponer, Peter Karran, Flavia Barone, Filomena Mazzei, Margherita Bignami

Publikováno v: Biophysical Chemistry. 118:31-41

DNA 7-hydro-8-oxoguanine (8-oxoG) is implicated in frameshift formation in an G(6) sequence of the HPRT gene in mismatch repair (MMR) defective cells. Using oligonucleotides based on this frameshift hotspot, we investigated how a single 8-oxoG modifi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4b7672a04548e28a6cd3a71228c21422
https://doi.org/10.1016/j.bpc.2005.06.003

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Structural Dynamics of Precursor and Product of the RNA Enzyme from the Hepatitis Delta Virus as Revealed by Molecular Dynamics Simulations

Autor: Nils G. Walter, Maryna V. Krasovska, Jiří Šponer, Jana Sefcikova, Nad'a Špačková

Publikováno v: Journal of Molecular Biology. 351:731-748

The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme involved in the replication of a human pathogen, the hepatitis delta virus. Recent crystal structures of the precursor and product of self-cleavage, together with detailed kinetic

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https://doi.org/10.1016/j.jmb.2005.06.016

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Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5‘-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA

Autor: Nohad Gresh, Nad'a Špačková, Judit E. Šponer, Jerzy Leszczynski, Jiri Sponer

Publikováno v: Scopus-Elsevier

SIBFA polarizable molecular mechanics (PMM) and quantum-chemical (ab initio Hartree−Fock and DFT) computations are performed on the binding of hydrated Zn(II) and Mg(II) cations to 5‘-guanosine mon...

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https://doi.org/10.1021/jp022659s

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