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  1. Article ; Online: The molecular mechanism of the ligand exchange reaction of an antibody against a glutathione-coated gold cluster.

    Rojas-Cervellera, Víctor / Raich, Lluís / Akola, Jaakko / Rovira, Carme

    Nanoscale

    2017  Volume 9, Issue 9, Page(s) 3121–3127

    Abstract: The labeling of proteins with heavy atom clusters is of paramount importance in biomedical research, but its detailed molecular mechanism remains unknown. Here we uncover it for the particular case of the anti-influenza N9 neuraminidase NC10 antibody ... ...

    Abstract The labeling of proteins with heavy atom clusters is of paramount importance in biomedical research, but its detailed molecular mechanism remains unknown. Here we uncover it for the particular case of the anti-influenza N9 neuraminidase NC10 antibody against a glutathione-coated gold cluster by means of ab initio QM/MM calculations. We show that the labeling reaction follows an associative double S
    Language English
    Publishing date 2017-03-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2515664-0
    ISSN 2040-3372 ; 2040-3364
    ISSN (online) 2040-3372
    ISSN 2040-3364
    DOI 10.1039/c6nr08498b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: How do Water Solvent and Glutathione Ligands Affect the Structure and Electronic Properties of Au25(SR)18(-)?

    Rojas-Cervellera, Víctor / Rovira, Carme / Akola, Jaakko

    The journal of physical chemistry letters

    2015  Volume 6, Issue 19, Page(s) 3859–3865

    Abstract: The effects of aqueous solvent and biological ligands on the structural and electronic properties of thiolate-protected Au25(SR)18(-) clusters have been studied by performing quantum mechanics/molecular mechanics (QM/MM) simulations. Analysis of bond ... ...

    Abstract The effects of aqueous solvent and biological ligands on the structural and electronic properties of thiolate-protected Au25(SR)18(-) clusters have been studied by performing quantum mechanics/molecular mechanics (QM/MM) simulations. Analysis of bond distances and angles show that the solvated nanocluster experiences modest structural changes, which are reflected as flexibility of the Au core. The hydrophilic glutathione ligands shield the metallic core effectively and distort its symmetry via sterical hindrance effects. We show that the previously reported agreement between the calculated HOMO-LUMO gap of the cluster and the optical measurement is due to cancellation of errors, where the typical underestimation of the theoretical band gap compensates the effect of the missing solvent. The use of a hybrid functional results in a HOMO-LUMO gap value of 1.5 eV for the solvated nanocluster with glutathione ligands, in good agreement with optical measurements. Our results demonstrate that ligand/solvent effects should be considered for a proper comparison between theory and experiment.
    Language English
    Publishing date 2015-10-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.5b01382
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The reaction mechanism of retaining glycosyltransferases.

    Ardèvol, Albert / Iglesias-Fernández, Javier / Rojas-Cervellera, Víctor / Rovira, Carme

    Biochemical Society transactions

    2016  Volume 44, Issue 1, Page(s) 51–60

    Abstract: The catalytic mechanism of retaining glycosyltransferases (ret-GTs) remains a controversial issue in glycobiology. By analogy to the well-established mechanism of retaining glycosidases, it was first suggested that ret-GTs follow a double-displacement ... ...

    Abstract The catalytic mechanism of retaining glycosyltransferases (ret-GTs) remains a controversial issue in glycobiology. By analogy to the well-established mechanism of retaining glycosidases, it was first suggested that ret-GTs follow a double-displacement mechanism. However, only family 6 GTs exhibit a putative nucleophile protein residue properly located in the active site to participate in catalysis, prompting some authors to suggest an unusual single-displacement mechanism [named as front-face or SNi (substitution nucleophilic internal)-like]. This mechanism has now received strong support, from both experiment and theory, for several GT families except family 6, for which a double-displacement reaction is predicted. In the last few years, we have uncovered the molecular mechanisms of several retaining GTs by means of quantum mechanics/molecular mechanics (QM/MM) metadynamics simulations, which we overview in the present work.
    MeSH term(s) Animals ; Glycosides/chemistry ; Glycosides/metabolism ; Glycosylation ; Glycosyltransferases/chemistry ; Glycosyltransferases/metabolism ; Humans ; Models, Molecular ; Quantum Theory
    Chemical Substances Glycosides ; Glycosyltransferases (EC 2.4.-)
    Language English
    Publishing date 2016-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 184237-7
    ISSN 1470-8752 ; 0300-5127
    ISSN (online) 1470-8752
    ISSN 0300-5127
    DOI 10.1042/BST20150177
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Staple motifs, initial steps in the formation of thiolate-protected gold nanoparticles: how do they form?

    Rojas-Cervellera, Víctor / Giralt, Ernest / Rovira, Carme

    Inorganic chemistry

    2012  Volume 51, Issue 21, Page(s) 11422–11429

    Abstract: Recent structural determinations have shown that thiolate-protected gold nanoparticles are not as regular and symmetric as initially thought, but characteristic substructures (staple motifs) are formed on their surface. However, their mechanism of ... ...

    Abstract Recent structural determinations have shown that thiolate-protected gold nanoparticles are not as regular and symmetric as initially thought, but characteristic substructures (staple motifs) are formed on their surface. However, their mechanism of formation, especially the fate of the sulfur protons upon thiol binding, remains one of the most intriguing unanswered questions in gold cluster chemistry. By means of ab initio molecular dynamics (AIMD), we monitor the trajectory of thiol protons reacting with a gold cluster, demonstrating that the staple motif forms in a multiple-pathway chemical reaction, releasing molecular hydrogen. The results obtained also reconcile the conclusions of structural determinations with the interpretations of spectroscopic experiments on solution, suggesting the presence of intact thiols or chemisorbed hydrogen.
    MeSH term(s) Gold/chemistry ; Hydrogen/chemistry ; Molecular Dynamics Simulation ; Nanoparticles/chemistry ; Oxidation-Reduction ; Protons ; Sulfhydryl Compounds/chemistry ; Sulfur/chemistry
    Chemical Substances Protons ; Sulfhydryl Compounds ; Sulfur (70FD1KFU70) ; Gold (7440-57-5) ; Hydrogen (7YNJ3PO35Z)
    Language English
    Publishing date 2012-11-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1484438-2
    ISSN 1520-510X ; 0020-1669
    ISSN (online) 1520-510X
    ISSN 0020-1669
    DOI 10.1021/ic301079k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Formation of a covalent glycosyl-enzyme species in a retaining glycosyltransferase.

    Rojas-Cervellera, Víctor / Ardèvol, Albert / Boero, Mauro / Planas, Antoni / Rovira, Carme

    Chemistry (Weinheim an der Bergstrasse, Germany)

    2013  Volume 19, Issue 42, Page(s) 14018–14023

    Abstract: Elusive glycosyl-enzyme adduct: Using classical MD simulations and QM/MM metadynamics, the long-time sought glycosyl-enzyme covalent intermediate of a retaining glycosyltransferase, with a putative nucleophile residue in the active site, has been trapped ...

    Abstract Elusive glycosyl-enzyme adduct: Using classical MD simulations and QM/MM metadynamics, the long-time sought glycosyl-enzyme covalent intermediate of a retaining glycosyltransferase, with a putative nucleophile residue in the active site, has been trapped (MD=molecular dynamics; QM/MM=quantum mechanics/molecular mechanics).
    MeSH term(s) Computer Simulation ; Enzymes/chemistry ; Enzymes/metabolism ; Glycosyltransferases/chemistry ; Glycosyltransferases/metabolism ; Models, Molecular ; Quantum Theory
    Chemical Substances Enzymes ; Glycosyltransferases (EC 2.4.-)
    Language English
    Publishing date 2013-10-11
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1478547-x
    ISSN 1521-3765 ; 0947-6539
    ISSN (online) 1521-3765
    ISSN 0947-6539
    DOI 10.1002/chem.201302898
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers.

    Espinosa Leal, Leonardo Andrés / Karpenko, Alexander / Swasey, Steven / Gwinn, Elisabeth G / Rojas-Cervellera, Victor / Rovira, Carme / Lopez-Acevedo, Olga

    The journal of physical chemistry letters

    2015  Volume 6, Issue 20, Page(s) 4061–4066

    Abstract: DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be ... ...

    Abstract DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.
    MeSH term(s) Circular Dichroism ; Cytosine/chemistry ; Gases/chemistry ; Hydrogen Bonding ; Models, Molecular ; Quantum Theory ; Silver/chemistry
    Chemical Substances Gases ; Silver (3M4G523W1G) ; Cytosine (8J337D1HZY)
    Language English
    Publishing date 2015-10-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.5b01864
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: An Epoxide Intermediate in Glycosidase Catalysis.

    Sobala, Lukasz F / Speciale, Gaetano / Zhu, Sha / Raich, Lluís / Sannikova, Natalia / Thompson, Andrew J / Hakki, Zalihe / Lu, Dan / Shamsi Kazem Abadi, Saeideh / Lewis, Andrew R / Rojas-Cervellera, Víctor / Bernardo-Seisdedos, Ganeko / Zhang, Yongmin / Millet, Oscar / Jiménez-Barbero, Jesús / Bennet, Andrew J / Sollogoub, Matthieu / Rovira, Carme / Davies, Gideon J /
    Williams, Spencer J

    ACS central science

    2020  Volume 6, Issue 5, Page(s) 760–770

    Abstract: Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or ... ...

    Abstract Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or neighboring-group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational, and kinetic evidence for neighboring-group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99
    Language English
    Publishing date 2020-04-16
    Publishing country United States
    Document type Journal Article
    ISSN 2374-7943
    ISSN 2374-7943
    DOI 10.1021/acscentsci.0c00111
    Database MEDical Literature Analysis and Retrieval System OnLINE

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