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  1. Article ; Online: Molecular dynamics simulations reveal the parallel stranded d(GGGA)

    Pokorná, Pavlína / Mlýnský, Vojtěch / Bussi, Giovanni / Šponer, Jiří / Stadlbauer, Petr

    International journal of biological macromolecules

    2024  Volume 261, Issue Pt 2, Page(s) 129712

    Abstract: G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through complex processes. Characterization of the G4 folding landscape may help to elucidate biological roles of G4s but is challenging both experimentally and computationally. ... ...

    Abstract G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through complex processes. Characterization of the G4 folding landscape may help to elucidate biological roles of G4s but is challenging both experimentally and computationally. Here, we achieved complete folding of a three-quartet parallel DNA G4 with (GGGA)
    MeSH term(s) Molecular Dynamics Simulation ; Nucleic Acid Conformation ; DNA/chemistry ; G-Quadruplexes ; Nucleic Acids
    Chemical Substances DNA (9007-49-2) ; Nucleic Acids
    Language English
    Publishing date 2024-01-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2024.129712
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  2. Article ; Online: Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations.

    Zhang, Zhengyue / Mlýnský, Vojtěch / Krepl, Miroslav / Šponer, Jiří / Stadlbauer, Petr

    Journal of chemical information and modeling

    2024  Volume 64, Issue 9, Page(s) 3896–3911

    Abstract: Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and ... ...

    Abstract Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
    MeSH term(s) G-Quadruplexes ; Molecular Dynamics Simulation ; Mechanical Phenomena ; Biomechanical Phenomena ; DNA/chemistry
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2024-04-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.4c00227
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  3. Article ; Online: The Reactivity-Enhancing Role of Water Clusters in Ammonia Aqueous Solutions.

    Cassone, Giuseppe / Saija, Franz / Sponer, Jiri / Shaik, Sason

    The journal of physical chemistry letters

    2023  Volume 14, Issue 35, Page(s) 7808–7813

    Abstract: Among the many prototypical acid-base systems, ammonia aqueous solutions hold a privileged place, owing to their omnipresence in various planets and their universal solvent character. Although the theoretical optimal water-ammonia molar ratio to form ... ...

    Abstract Among the many prototypical acid-base systems, ammonia aqueous solutions hold a privileged place, owing to their omnipresence in various planets and their universal solvent character. Although the theoretical optimal water-ammonia molar ratio to form NH
    Language English
    Publishing date 2023-08-25
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c01810
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  4. Article ; Online: Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations.

    Stadlbauer, Petr / Mlýnský, Vojtěch / Krepl, Miroslav / Šponer, Jiří

    Journal of chemical information and modeling

    2023  Volume 63, Issue 15, Page(s) 4716–4731

    Abstract: Guanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many biological processes. GQs formed in single-stranded regions often need to be unwound by cellular machinery, so their mechanochemical properties are important. Here, we ... ...

    Abstract Guanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many biological processes. GQs formed in single-stranded regions often need to be unwound by cellular machinery, so their mechanochemical properties are important. Here, we performed steered molecular dynamics simulations of human telomeric GQs to study their unfolding. We examined four pulling regimes, including a very slow setup with pulling velocity and force load accessible to high-speed atomic force microscopy. We identified multiple factors affecting the unfolding mechanism, i.e.,: (i) the more the direction of force was perpendicular to the GQ channel axis (determined by GQ topology), the more the base unzipping mechanism happened, (ii) the more parallel the direction of force was, GQ opening and cross-like GQs were more likely to occur, (iii) strand slippage mechanism was possible for GQs with an all-
    MeSH term(s) Humans ; Guanine/chemistry ; G-Quadruplexes ; Molecular Dynamics Simulation ; Mechanical Phenomena ; Telomere
    Chemical Substances Guanine (5Z93L87A1R)
    Language English
    Publishing date 2023-07-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.3c00171
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  5. Article ; Online: Insoluble organic matter - an "organic" cradle of life: Comment on the paper "Insoluble organic matter in chondrites: Archetypal melanin-like PAH-based multifunctionality at the origin of life?" by Marco d'Ischia et al.

    Šponer, Judit E / Šponer, Jiří

    Physics of life reviews

    2021  Volume 38, Page(s) 135–136

    MeSH term(s) Carbon ; Extraterrestrial Environment ; Melanins ; Meteoroids
    Chemical Substances Melanins ; Carbon (7440-44-0)
    Language English
    Publishing date 2021-05-21
    Publishing country Netherlands
    Document type Journal Article ; Comment
    ZDB-ID 2148883-6
    ISSN 1873-1457 ; 1571-0645
    ISSN (online) 1873-1457
    ISSN 1571-0645
    DOI 10.1016/j.plrev.2021.05.003
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  6. Article ; Online: Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.

    Kührová, Petra / Mlýnský, Vojtěch / Otyepka, Michal / Šponer, Jiří / Banáš, Pavel

    Journal of chemical information and modeling

    2023  Volume 63, Issue 7, Page(s) 2133–2146

    Abstract: RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion ... ...

    Abstract RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion atmosphere. Although RNA molecules are formally single-stranded, canonical (Watson-Crick) duplexes are key components of folded RNAs. A double-stranded (ds) RNA is also important for the design of RNA-based nanostructures and assemblies. Despite the fact that the description of canonical dsRNA is considered the least problematic part of RNA modeling, the imperfect shape and flexibility of dsRNA can lead to imbalances in the simulations of larger RNAs and RNA-containing assemblies. We present a comprehensive set of molecular dynamics (MD) simulations of four canonical A-RNA duplexes. Our focus was directed toward the characterization of the influence of varying ion concentrations and of the size of the solvation box. We compared several water models and four RNA force fields. The simulations showed that the A-RNA shape was most sensitive to the RNA force field, with some force fields leading to a reduced inclination of the A-RNA duplexes. The ions and water models played a minor role. The effect of the box size was negligible, and even boxes with a small fraction of the bulk solvent outside the RNA hydration sphere were sufficient for the simulation of the dsRNA.
    MeSH term(s) RNA/chemistry ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Water/chemistry ; Ions/chemistry
    Chemical Substances RNA (63231-63-0) ; Water (059QF0KO0R) ; Ions
    Language English
    Publishing date 2023-03-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.2c01438
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  7. Article ; Online: Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations.

    Pokorná, Pavlína / Krepl, Miroslav / Campagne, Sébastien / Šponer, Jiří

    The journal of physical chemistry. B

    2022  Volume 126, Issue 45, Page(s) 9207–9221

    Abstract: RNA-protein complexes use diverse binding strategies, ranging from structurally well-defined interfaces to completely disordered regions. Experimental characterization of flexible segments is challenging and can be aided by atomistic molecular dynamics ( ... ...

    Abstract RNA-protein complexes use diverse binding strategies, ranging from structurally well-defined interfaces to completely disordered regions. Experimental characterization of flexible segments is challenging and can be aided by atomistic molecular dynamics (MD) simulations. Here, we used an extended set of microsecond-scale MD trajectories (400 μs in total) to study two FUS-RNA constructs previously characterized by nuclear magnetic resonance (NMR) spectroscopy. The FUS protein contains a well-structured RNA recognition motif domain followed by a presumably disordered RGG tail that binds RNA stem-loop hairpins. Our simulations not only provide several suggestions complementing the experiments but also reveal major methodological difficulties in studies of such complex RNA-protein interfaces. Despite efforts to stabilize the binding via system-specific force-field adjustments, we have observed progressive distortions of the RNA-protein interface inconsistent with experimental data. We propose that the dynamics is so rich that its converged description is not achievable even upon stabilizing the system. Still, after careful analysis of the trajectories, we have made several suggestions regarding the binding. We identify substates in the RNA loops, which can explain the NMR data. The RGG tail localized in the minor groove remains disordered, sampling countless transient interactions with the RNA. There are long-range couplings among the different elements contributing to the recognition, which can lead to allosteric communication throughout the system. Overall, the RNA-FUS systems form dynamical ensembles that cannot be fully represented by single static structures. Thus, albeit imperfect, MD simulations represent a viable tool to investigate dynamic RNA-protein complexes.
    MeSH term(s) RNA Recognition Motif ; Molecular Dynamics Simulation ; RNA/chemistry ; Molecular Conformation ; Proteins/chemistry
    Chemical Substances RNA (63231-63-0) ; Proteins
    Language English
    Publishing date 2022-11-08
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.2c06168
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  8. Article ; Online: 121 Advanced computational studies of G-quadruplex folding and topological preferences.

    Šponer, Jiří

    Journal of biomolecular structure & dynamics

    2015  Volume 33 Suppl 1, Page(s) 76–77

    Language English
    Publishing date 2015
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2015.1032754
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  9. Article ; Online: Formic acid, the precursor of formamide, from serpentinization: Comment on the paper: "Mineral self-organization on a lifeless planet" by Juan Manuel García-Ruiz, Mark A. van Zuilen and Wolfgang Bach.

    Šponer, Judit E / Šponer, Jiří

    Physics of life reviews

    2020  Volume 34-35, Page(s) 94–95

    MeSH term(s) Formamides ; Formates ; Minerals ; Planets
    Chemical Substances Formamides ; Formates ; Minerals ; formic acid (0YIW783RG1)
    Language English
    Publishing date 2020-06-18
    Publishing country Netherlands
    Document type Journal Article ; Comment
    ZDB-ID 2148883-6
    ISSN 1873-1457 ; 1571-0645
    ISSN (online) 1873-1457
    ISSN 1571-0645
    DOI 10.1016/j.plrev.2020.06.002
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  10. Article: Residues flanking the ARKme3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations

    Pokorná, Pavlína / Krepl, Miroslav / Šponer, Jiří

    Biochimica et biophysica acta. 2021 Jan., v. 1865, no. 1

    2021  

    Abstract: The chromodomain (CD) of HP1 proteins is an established H3K9ᵐᵉ³ reader that also binds H1, EHMT2 and H3K23 lysine-methylated targets. Structural experiments have provided atomistic pictures of its recognition of the conserved ARKᵐᵉ³S/T motif, but ... ...

    Abstract The chromodomain (CD) of HP1 proteins is an established H3K9ᵐᵉ³ reader that also binds H1, EHMT2 and H3K23 lysine-methylated targets. Structural experiments have provided atomistic pictures of its recognition of the conserved ARKᵐᵉ³S/T motif, but structural dynamics' contribution to the recognition may have been masked by ensemble averaging.We acquired ~350 μs of explicit solvent molecular dynamics (MD) simulations of the CD domain interacting with several peptides using the latest AMBER force fields.The simulations reproduced the experimentally observed static binding patterns well but also revealed visible structural dynamics at the interfaces. While the buried K₀ᵐᵉ³ and A₋₂ target residues are tightly bound, several flanking sidechains sample diverse sites on the CD surface. Different amino acid positions of the targets can substitute for each other by forming mutually replaceable interactions with CD, thereby explaining the lack of strict requirement for cationic H3 target residues at the −3 position. The Q₋₄ residue of H3 targets further stabilizes the binding. The recognition pattern of the H3K23 ATKᵐᵉ³A motif, for which no structure is available, is predicted.The CD reads a longer target segment than previously thought, ranging from positions −7 to +3. The CD anionic clamp can be neutralized not only by the −3 and −1 residues, but also by −7, −6, −5 and +3 residues.Structural dynamics, not immediately apparent from the structural data, contribute to molecular recognition between the HP1 CD domain and its targets. Mutual replaceability of target residues increases target sequence flexibility.
    Keywords amino acids ; molecular dynamics ; peptides ; solvents
    Language English
    Dates of publication 2021-01
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 840755-1
    ISSN 0304-4165
    ISSN 0304-4165
    DOI 10.1016/j.bbagen.2020.129771
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