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  1. Article ; Online: Editorial

    Maya Topf / Edina Rosta / Gregory R. Bowman / Massimiliano Bonomi

    Frontiers in Molecular Biosciences, Vol

    Experiments and Simulations: A Pas de Deux to Unravel Biological Function

    2021  Volume 8

    Keywords modeling ; molecular dynamic (MD) ; integrative approaches ; functional dynamics ; experimental-computational method ; molecular simulation ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Toward Understanding CB[7]-Based Supramolecular Diels-Alder Catalysis

    Dénes Berta / István Szabó / Oren A. Scherman / Edina Rosta

    Frontiers in Chemistry, Vol

    2020  Volume 8

    Abstract: Cucurbiturils (CBs) are robust and versatile macrocyclic compounds, often used as molecular hosts in complex supramolecular systems. In previous work, remarkable catalytic activity has been observed for asymmetric cycloadditions under very mild ... ...

    Abstract Cucurbiturils (CBs) are robust and versatile macrocyclic compounds, often used as molecular hosts in complex supramolecular systems. In previous work, remarkable catalytic activity has been observed for asymmetric cycloadditions under very mild conditions. Herein, we investigate the nature of supramolecular catalysis using DFT calculations and QM/MM techniques. We discuss induced conformational changes, electrostatic shielding effects from the highly polar aqueous environment and cooperativity in hydrogen bonding of the substrates in explicit water using QM/MM simulation techniques. Our results show little specificity for the chosen molecules, suggesting an excellent opportunity to expand the scope for catalytic use of these supramolecular macrocyclic containers.
    Keywords QM/MM ; Diels-Alder (DA) chemistry ; catalysis ; confinement & solvent effect ; quantum chemistry ab initio ; Chemistry ; QD1-999
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations

    Xiaoliang Pan / Edina Rosta / Yihan Shao

    Molecules, Vol 23, Iss 10, p

    2018  Volume 2500

    Abstract: In QM/MM calculations, it is essential to handle electrostatic interactions between the QM and MM subsystems accurately and efficiently. To achieve maximal efficiency, it is convenient to adopt a hybrid scheme, where the QM electron density is used ... ...

    Abstract In QM/MM calculations, it is essential to handle electrostatic interactions between the QM and MM subsystems accurately and efficiently. To achieve maximal efficiency, it is convenient to adopt a hybrid scheme, where the QM electron density is used explicitly in the evaluation of short-range QM/MM electrostatic interactions, while a multipolar representation for the QM electron density is employed to account for the long-range QM/MM electrostatic interactions. In order to avoid energy discontinuity at the cutoffs, which separate the short- and long-range QM/MM electrostatic interactions, a switching function should be utilized to ensure a smooth potential energy surface. In this study, we benchmarked the accuracy of such hybrid embedding schemes for QM/MM electrostatic interactions using different multipolar representations, switching functions and cutoff distances. For test systems (neutral and anionic oxyluciferin in MM (aqueous and enzyme) environments), the best accuracy was acquired with a combination of QM electrostatic potential (ESP) charges and dipoles and two switching functions (long-range electrostatic corrections (LREC) and Switch) in the treatment of long-range QM/MM electrostatics. It allowed us to apply a 10Å distance cutoff and still obtain QM/MM electrostatics/polarization energies within 0.1 kcal/mol and time-dependent density functional theory (TDDFT)/MM vertical excitation energies within 10−3 eV from theoretical reference values.
    Keywords electrostatics ; multipolar expansion ; multiscale modeling ; QM/MM ; Organic chemistry ; QD241-441
    Subject code 541
    Language English
    Publishing date 2018-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis

    Lindsay McGregor / Tamás Földes / Soi Bui / Martine Moulin / Nicolas Coquelle / Matthew P. Blakeley / Edina Rosta / Roberto A. Steiner

    IUCrJ, Vol 8, Iss 1, Pp 46-

    2021  Volume 59

    Abstract: Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O2 to dehydroisourate (DHU) via a peroxo intermediate. DHU then undergoes hydration to 5- ... ...

    Abstract Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O2 to dehydroisourate (DHU) via a peroxo intermediate. DHU then undergoes hydration to 5-hydroxyisourate (5HIU). At different stages of the reaction both catalytic O2 and water occupy the `peroxo hole' above the organic substrate. Here, high-resolution neutron/X-ray crystallographic analysis at room temperature has been integrated with molecular dynamics simulations to investigate the hydration step of the reaction. The joint neutron/X-ray structure of perdeuterated Aspergillus flavus UOX in complex with its 8-azaxanthine (8AZA) inhibitor shows that the catalytic water molecule (W1) is present in the peroxo hole as neutral H2O, oriented at 45° with respect to the ligand. It is stabilized by Thr57 and Asn254 on different UOX protomers as well as by an O—H.π interaction with 8AZA. The active site Lys10–Thr57 dyad features a charged Lys10–NH3+ side chain engaged in a strong hydrogen bond with Thr57OG1, while the Thr57OG1–HG1 bond is rotationally dynamic and oriented toward the π system of the ligand, on average. Our analysis offers support for a mechanism in which W1 performs a nucleophilic attack on DHUC5 with Thr57HG1 central to a Lys10-assisted proton-relay system. Room-temperature crystallography and simulations also reveal conformational heterogeneity for Asn254 that modulates W1 stability in the peroxo hole. This is proposed to be an active mechanism to facilitate W1/O2 exchange during catalysis.
    Keywords neutron/x-ray diffraction ; urate oxidase ; protein perdeuteration ; cofactor-independent oxidase ; biomolecular simulations ; Science ; Q
    Subject code 540
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher International Union of Crystallography
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Resolving sub-angstrom ambient motion through reconstruction from vibrational spectra

    Jack Griffiths / Tamás Földes / Bart de Nijs / Rohit Chikkaraddy / Demelza Wright / William M. Deacon / Dénes Berta / Charlie Readman / David-Benjamin Grys / Edina Rosta / Jeremy J. Baumberg

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 8

    Abstract: Tracking single molecule movements is a challenging task, but highly desired for applications and fundamental studies. Here the authors reconstruct the sub-angstrom relative movements of a molecule interacting with a metal adatom, by measuring its ... ...

    Abstract Tracking single molecule movements is a challenging task, but highly desired for applications and fundamental studies. Here the authors reconstruct the sub-angstrom relative movements of a molecule interacting with a metal adatom, by measuring its vibrational spectrum in a self-assembled monolayer, continuously modified by the adatom in a nanoparticle-on-mirror construct.
    Keywords Science ; Q
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Optical probes of molecules as nano-mechanical switches

    Dean Kos / Giuliana Di Martino / Alexandra Boehmke / Bart de Nijs / Dénes Berta / Tamás Földes / Sara Sangtarash / Edina Rosta / Hatef Sadeghi / Jeremy J. Baumberg

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 8

    Abstract: The development of molecular electronics at single molecule level calls for new tools beyond electrical characterisation. Kos et al. show an optical probe of molecular junctions in a plasmonic nanocavity geometry, which supports in situ interrogation of ... ...

    Abstract The development of molecular electronics at single molecule level calls for new tools beyond electrical characterisation. Kos et al. show an optical probe of molecular junctions in a plasmonic nanocavity geometry, which supports in situ interrogation of molecular configurations.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: SARAH Domain-Mediated MST2-RASSF Dimeric Interactions.

    Goar Sánchez-Sanz / Bartłomiej Tywoniuk / David Matallanas / David Romano / Lan K Nguyen / Boris N Kholodenko / Edina Rosta / Walter Kolch / Nicolae-Viorel Buchete

    PLoS Computational Biology, Vol 12, Iss 10, p e

    2016  Volume 1005051

    Abstract: RASSF enzymes act as key apoptosis activators and tumor suppressors, being downregulated in many human cancers, although their exact regulatory roles remain unknown. A key downstream event in the RASSF pathway is the regulation of MST kinases, which are ... ...

    Abstract RASSF enzymes act as key apoptosis activators and tumor suppressors, being downregulated in many human cancers, although their exact regulatory roles remain unknown. A key downstream event in the RASSF pathway is the regulation of MST kinases, which are main effectors of RASSF-induced apoptosis. The regulation of MST1/2 includes both homo- and heterodimerization, mediated by helical SARAH domains, though the underlying molecular interaction mechanism is unclear. Here, we study the interactions between RASSF1A, RASSF5, and MST2 SARAH domains by using both atomistic molecular simulation techniques and experiments. We construct and study models of MST2 homodimers and MST2-RASSF SARAH heterodimers, and we identify the factors that control their high molecular stability. In addition, we also analyze both computationally and experimentally the interactions of MST2 SARAH domains with a series of synthetic peptides particularly designed to bind to it, and hope that our approach can be used to address some of the challenging problems in designing new anti-cancer drugs.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2016-10-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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