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  1. Article: Spatial arrangements of cyclodextrin host-guest complexes in solution studied by

    Lebedinskiy, Konstantin / Barvík, Ivan / Tošner, Zdeněk / Císařová, Ivana / Jindřich, Jindřich / Hrdina, Radim

    Beilstein journal of organic chemistry

    2024  Volume 20, Page(s) 331–335

    Abstract: ... ...

    Abstract 13
    Language English
    Publishing date 2024-02-20
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2192461-2
    ISSN 1860-5397
    ISSN 1860-5397
    DOI 10.3762/bjoc.20.33
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  2. Article ; Online: Synthesis and cholinesterase inhibitory activity study of Amaryllidaceae alkaloid analogues with

    Jansa, Petr / Barvík, Ivan / Hulcová, Daniela / Matoušová, Eliška

    Organic & biomolecular chemistry

    2022  Volume 20, Issue 19, Page(s) 3960–3966

    Abstract: Polycyclic compounds ... ...

    Abstract Polycyclic compounds with
    MeSH term(s) Acetylcholinesterase/metabolism ; Alkaloids/chemistry ; Amaryllidaceae/chemistry ; Amaryllidaceae/metabolism ; Amaryllidaceae Alkaloids/chemistry ; Amaryllidaceae Alkaloids/pharmacology ; Butyrylcholinesterase/metabolism ; Cholinesterase Inhibitors/chemistry ; Humans ; Molecular Docking Simulation ; Nitrogen ; Structure-Activity Relationship
    Chemical Substances Alkaloids ; Amaryllidaceae Alkaloids ; Cholinesterase Inhibitors ; Acetylcholinesterase (EC 3.1.1.7) ; Butyrylcholinesterase (EC 3.1.1.8) ; Nitrogen (N762921K75)
    Language English
    Publishing date 2022-05-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2097583-1
    ISSN 1477-0539 ; 1477-0520
    ISSN (online) 1477-0539
    ISSN 1477-0520
    DOI 10.1039/d2ob00553k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Overlapping SigH and SigE sigma factor regulons in

    Busche, Tobias / Dostálová, Hana / Rucká, Lenka / Holátko, Jiří / Barvík, Ivan / Štěpánek, Václav / Pátek, Miroslav / Kalinowski, Jörn

    Frontiers in microbiology

    2023  Volume 13, Page(s) 1059649

    Abstract: The sigma H ( ... ...

    Abstract The sigma H (σ
    Language English
    Publishing date 2023-02-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.1059649
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  4. Article ; Online: Phospho-Mimetic Mutation at Ser602 Inactivates Human TRPA1 Channel.

    Barvikova, Kristyna / Barvik, Ivan / Sinica, Viktor / Zimova, Lucie / Vlachova, Viktorie

    International journal of molecular sciences

    2020  Volume 21, Issue 21

    Abstract: The Transient Receptor Potential Ankyrin 1 (TRPA1) channel is an integrative molecular sensor for detecting environmental irritant compounds, endogenous proalgesic and inflammatory agents, pressure, and temperature. Different post-translational ... ...

    Abstract The Transient Receptor Potential Ankyrin 1 (TRPA1) channel is an integrative molecular sensor for detecting environmental irritant compounds, endogenous proalgesic and inflammatory agents, pressure, and temperature. Different post-translational modifications participate in the discrimination of the essential functions of TRPA1 in its physiological environment, but the underlying structural bases are poorly understood. Here, we explored the role of the cytosolic N-terminal residue Ser602 located near a functionally important allosteric coupling domain as a potential target of phosphorylation. The phosphomimetic mutation S602D completely abrogated channel activation, whereas the phosphonull mutations S602G and S602N produced a fully functional channel. Using mutagenesis, electrophysiology, and molecular simulations, we investigated the possible structural impact of a modification (mutation or phosphorylation) of Ser602 and found that this residue represents an important regulatory site through which the intracellular signaling cascades may act to reversibly restrict or "dampen" the conformational space of the TRPA1 channel and promote its transitions to the closed state.
    MeSH term(s) HEK293 Cells ; Humans ; Models, Molecular ; Molecular Dynamics Simulation ; Mutation ; Phosphorylation ; Protein Conformation ; Protein Domains ; Serine/metabolism ; TRPA1 Cation Channel/chemistry ; TRPA1 Cation Channel/genetics ; TRPA1 Cation Channel/metabolism
    Chemical Substances TRPA1 Cation Channel ; TRPA1 protein, human ; Serine (452VLY9402)
    Language English
    Publishing date 2020-10-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms21217995
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  5. Article ; Online: Design and NMR characterization of reversible head-to-tail boronate-linked macrocyclic nucleic acids.

    Debiais, Mégane / Gimenez Molina, Alejandro / Müller, Sabine / Vasseur, Jean-Jacques / Barvik, Ivan / Baraguey, Carine / Smietana, Michael

    Organic & biomolecular chemistry

    2022  Volume 20, Issue 14, Page(s) 2889–2895

    Abstract: Inspired by the ability of boronic acids to bind with compounds containing diol moieties, we envisioned the formation in solution of boronate ester-based macrocycles by the head-to-tail assembly of a nucleosidic precursor that contains both a boronic ... ...

    Abstract Inspired by the ability of boronic acids to bind with compounds containing diol moieties, we envisioned the formation in solution of boronate ester-based macrocycles by the head-to-tail assembly of a nucleosidic precursor that contains both a boronic acid and the natural 2',3'-diol of ribose. DOSY NMR spectroscopy experiments in water and anhydrous DMF revealed the dynamic assembly of this precursor into dimeric and trimeric macrocycles in a concentration-dependent fashion as well as the reversibility of the self-assembly process. NMR experimental values and quantum mechanics calculations provided further insight into the sugar pucker conformation profile of these macrocycles.
    MeSH term(s) Boronic Acids/chemistry ; Esters/chemistry ; Magnetic Resonance Spectroscopy ; Nucleic Acids
    Chemical Substances Boronic Acids ; Esters ; Nucleic Acids
    Language English
    Publishing date 2022-04-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2097583-1
    ISSN 1477-0539 ; 1477-0520
    ISSN (online) 1477-0539
    ISSN 1477-0520
    DOI 10.1039/d2ob00232a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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

    Smutny, Tomas / Barvik, Ivan / Veleta, Tomas / Pavek, Petr / Soukup, Tomas

    Journal of clinical medicine

    2019  Volume 8, Issue 5

    Abstract: Polymyalgia rheumatica (PMR) and giant cell arteritis (GCA) are closely related chronic inflammatory diseases. Glucocorticoids (GCs) are first-choice drugs for PMR and GCA, although some patients show poor responsiveness to the initial GC regimen or ... ...

    Abstract Polymyalgia rheumatica (PMR) and giant cell arteritis (GCA) are closely related chronic inflammatory diseases. Glucocorticoids (GCs) are first-choice drugs for PMR and GCA, although some patients show poor responsiveness to the initial GC regimen or experience flares after GC tapering. To date, no valid biomarkers have been found to predict which patients are at most risk for developing GC resistance. In this review, we summarize PMR- and GCA-related gene polymorphisms and we associate these gene variants with GC resistance and therapeutic outcomes. A limited number of GC resistance associated-polymorphisms have been published so far, mostly related to
    Language English
    Publishing date 2019-04-27
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662592-1
    ISSN 2077-0383
    ISSN 2077-0383
    DOI 10.3390/jcm8050582
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  7. Article: Proximal C-Terminus Serves as a Signaling Hub for TRPA1 Channel Regulation via Its Interacting Molecules and Supramolecular Complexes.

    Zimova, Lucie / Barvikova, Kristyna / Macikova, Lucie / Vyklicka, Lenka / Sinica, Viktor / Barvik, Ivan / Vlachova, Viktorie

    Frontiers in physiology

    2020  Volume 11, Page(s) 189

    Abstract: Our understanding of the general principles of the polymodal regulation of transient receptor potential (TRP) ion channels has grown impressively in recent years as a result of intense efforts in protein structure determination by cryo-electron ... ...

    Abstract Our understanding of the general principles of the polymodal regulation of transient receptor potential (TRP) ion channels has grown impressively in recent years as a result of intense efforts in protein structure determination by cryo-electron microscopy. In particular, the high-resolution structures of various TRP channels captured in different conformations, a number of them determined in a membrane mimetic environment, have yielded valuable insights into their architecture, gating properties and the sites of their interactions with annular and regulatory lipids. The correct repertoire of these channels is, however, organized by supramolecular complexes that involve the localization of signaling proteins to sites of action, ensuring the specificity and speed of signal transduction events. As such, TRP ankyrin 1 (TRPA1), a major player involved in various pain conditions, localizes into cholesterol-rich sensory membrane microdomains, physically interacts with calmodulin, associates with the scaffolding A-kinase anchoring protein (AKAP) and forms functional complexes with the related TRPV1 channel. This perspective will contextualize the recent biochemical and functional studies with emerging structural data with the aim of enabling a more thorough interpretation of the results, which may ultimately help to understand the roles of TRPA1 under various physiological and pathophysiological pain conditions. We demonstrate that an alteration to the putative lipid-binding site containing a residue polymorphism associated with human asthma affects the cold sensitivity of TRPA1. Moreover, we present evidence that TRPA1 can interact with AKAP to prime the channel for opening. The structural bases underlying these interactions remain unclear and are definitely worth the attention of future studies.
    Language English
    Publishing date 2020-03-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564217-0
    ISSN 1664-042X
    ISSN 1664-042X
    DOI 10.3389/fphys.2020.00189
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  8. Article ; Online: Recognition of 2',5'-linked oligoadenylates by human ribonuclease L: molecular dynamics study.

    Maláč, Kamil / Barvík, Ivan

    Journal of molecular modeling

    2014  Volume 20, Issue 4, Page(s) 2123

    Abstract: The capability of current MD simulations to be used as a tool in rational design of agonists of medically interesting enzyme RNase L was tested. Dimerization and enzymatic activity of RNase L is stimulated by 2',5'-linked oligoadenylates (pA₂₅A₂₅A; 2-5A). ...

    Abstract The capability of current MD simulations to be used as a tool in rational design of agonists of medically interesting enzyme RNase L was tested. Dimerization and enzymatic activity of RNase L is stimulated by 2',5'-linked oligoadenylates (pA₂₅A₂₅A; 2-5A). First, it was necessary to ensure that a complex of monomeric human RNase L and 25A was stable in MD simulations. It turned out that Glu131 had to be protonated. The non-protonated Glu131 caused dissociation of 2-5A from RNase L. Because of the atypical 2'-5' internucleotide linkages and a specific spatial arrangement of the 25A trimer, when a single molecule carries all possible conformers of the glycosidic torsion angle, several versions of the AMBER force field were tested. One that best maintained functionally important interactions of 25A and RNase L was selected for subsequent MD simulations. Furthermore, we wonder whether powerful GPUs are able to produce MD trajectories long enough to convincingly demonstrate effects of subtle perturbations of interactions between 25A and RNase L. Detrimental impacts of various point mutations of RNase L (R155A, F126A, W60A, K89A) on 2-5A binding were observed on a time scale of 200 ns. Finally, 2-5A analogues with a bridged 3'--O,4'--C-alkylene linkage (B) introduced into the adenosine units (A) were used to assess ability of MD simulations to distinguish on the time scale of hundreds of nanoseconds between agonists of RNase L (pA₂₅A₂₅B, pB₂₅A₂₅A, pB₂₅A₂₅B) and inactive analogs (pA₂₅B₂₅A, pA₂₅B₂₅B, pB₂₅B₂₅A, pB₂₅B₂₅B). Agonists were potently bound to RNase L during 200 ns MD runs. For inactive 2-5A analogs, by contrast, significant disruptions of their interactions with RNase L already within 100 ns MD runs were found.
    MeSH term(s) Adenine Nucleotides/chemistry ; Adenine Nucleotides/metabolism ; Endoribonucleases/chemistry ; Endoribonucleases/metabolism ; Enzyme Activation ; Humans ; Hydrogen Bonding ; Molecular Conformation ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Oligoribonucleotides/chemistry ; Oligoribonucleotides/metabolism ; Protein Binding ; Protein Multimerization
    Chemical Substances Adenine Nucleotides ; Oligoribonucleotides ; 2',5'-oligoadenylate (61172-40-5) ; Endoribonucleases (EC 3.1.-) ; 2-5A-dependent ribonuclease (EC 3.1.26.-)
    Language English
    Publishing date 2014-03-16
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1284729-X
    ISSN 0948-5023 ; 1610-2940
    ISSN (online) 0948-5023
    ISSN 1610-2940
    DOI 10.1007/s00894-014-2123-x
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  9. Article ; Online: Substrate recognition by norovirus polymerase: microsecond molecular dynamics study.

    Maláč, Kamil / Barvík, Ivan

    Journal of computer-aided molecular design

    2013  Volume 27, Issue 4, Page(s) 373–388

    Abstract: Molecular dynamics simulations of complexes between Norwalk virus RNA dependent RNA polymerase and its natural CTP and 2dCTP (both containing the O5'-C5'-C4'-O4' sequence of atoms bridging the triphosphate and sugar moiety) or modified coCTP (C5'-O5'-C4'- ...

    Abstract Molecular dynamics simulations of complexes between Norwalk virus RNA dependent RNA polymerase and its natural CTP and 2dCTP (both containing the O5'-C5'-C4'-O4' sequence of atoms bridging the triphosphate and sugar moiety) or modified coCTP (C5'-O5'-C4'-O4'), cocCTP (C5'-O5'-C4'-C4'') substrates were produced by means of CUDA programmable graphical processing units and the ACEMD software package. It enabled us to gain microsecond MD trajectories clearly showing that similar nucleoside triphosphates can bind surprisingly differently into the active site of the Norwalk virus RNA dependent RNA polymerase. It corresponds to their different modes of action (CTP-substrate, 2dCTP-poor substrate, coCTP-chain terminator, cocCTP-inhibitor). Moreover, extremely rare events-as repetitive pervasion of Arg182 into a potentially reaction promoting arrangement-were captured.
    MeSH term(s) Caliciviridae Infections/virology ; Cytidine Triphosphate/analogs & derivatives ; Cytidine Triphosphate/metabolism ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Norovirus/enzymology ; Norovirus/metabolism ; RNA-Dependent RNA Polymerase/metabolism ; Substrate Specificity
    Chemical Substances Cytidine Triphosphate (65-47-4) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
    Language English
    Publishing date 2013-04-26
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 808166-9
    ISSN 1573-4951 ; 0920-654X
    ISSN (online) 1573-4951
    ISSN 0920-654X
    DOI 10.1007/s10822-013-9652-8
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2625: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
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  10. Article ; Online: Complex between human RNase HI and the phosphonate-DNA/RNA duplex: molecular dynamics study.

    Maláč, Kamil / Barvík, Ivan

    Journal of molecular graphics & modelling

    2013  Volume 44, Page(s) 81–90

    Abstract: Our 200ns MD simulations show that even fully modified oligonucleotides bearing the 3'-O-P-CH2-O-5' (but not 3'-O-CH2-P-O-5') phosphonate linkages can be successfully attached to the surface of Human RNase H. It enables to explain that oligonucleotides ... ...

    Abstract Our 200ns MD simulations show that even fully modified oligonucleotides bearing the 3'-O-P-CH2-O-5' (but not 3'-O-CH2-P-O-5') phosphonate linkages can be successfully attached to the surface of Human RNase H. It enables to explain that oligonucleotides consisting of the alternating 3'-O-P-CH2-O-5' phosphonate and phosphodiester linkages are capable to elicit the RNase H activity (while the 3'-O-CH2-P-O-5' phosphonates are completely inactive). Stability of the binuclear active site of Human RNase H was achieved using the one-atom model for Mg(2+) in conjunction with a polarized phosphate group of the scissile bond, which is wedged between both magnesium ions. The reference MD simulation (lasting for 1000ns), which was produced using a well-established seven-point (with dummy atoms) model for Mg(2+) led to essentially the same results. The MD run (lasting for 500ns) produced for the Thermus thermophilus Argonaute enzyme shows the transferability of our approach for the stabilization of a binuclear active site. Glu512 was bound in the T. thermophilus Argonaute active site to the 2'-OH of the nucleotide adjacent to the scissile phosphate and one of the two active-site divalent metal ions in exactly the same way as Glu186 in Human RNase H. Glu512 thus completes the catalytic tetrad of Argonaute.
    MeSH term(s) Binding Sites ; Catalytic Domain ; DNA/chemistry ; Humans ; Ligands ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Organophosphonates/chemistry ; Protein Binding ; Protein Conformation ; RNA/chemistry ; Ribonuclease H/chemistry
    Chemical Substances Ligands ; Organophosphonates ; RNA (63231-63-0) ; DNA (9007-49-2) ; Ribonuclease H (EC 3.1.26.4) ; ribonuclease HI (EC 3.1.26.4)
    Language English
    Publishing date 2013-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1396450-1
    ISSN 1873-4243 ; 1093-3263
    ISSN (online) 1873-4243
    ISSN 1093-3263
    DOI 10.1016/j.jmgm.2013.05.004
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3491: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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