July 2, 2021 Journal article Open Access

Pecina, Adam; Rosa-Gastaldo, Daniele; Riccardi, Laura; Franco-Ulloa, Sebastian; Milan, Emil; Scrimin, Paolo; Mancin, Fabrizio; De Vivo, Marco

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  <identifier identifierType="URL">https://zenodo.org/record/5155228</identifier>
  <creators>
    <creator>
      <creatorName>Pecina, Adam</creatorName>
      <givenName>Adam</givenName>
      <familyName>Pecina</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-3890-7831</nameIdentifier>
      <affiliation>Istituto Italiano di Tecnologia</affiliation>
    </creator>
    <creator>
      <creatorName>Rosa-Gastaldo, Daniele</creatorName>
      <givenName>Daniele</givenName>
      <familyName>Rosa-Gastaldo</familyName>
      <affiliation>Università di Padova</affiliation>
    </creator>
    <creator>
      <creatorName>Riccardi, Laura</creatorName>
      <givenName>Laura</givenName>
      <familyName>Riccardi</familyName>
      <affiliation>Istituto Italiano di Tecnologia</affiliation>
    </creator>
    <creator>
      <creatorName>Franco-Ulloa, Sebastian</creatorName>
      <givenName>Sebastian</givenName>
      <familyName>Franco-Ulloa</familyName>
      <affiliation>Istituto Italiano di Tecnologia</affiliation>
    </creator>
    <creator>
      <creatorName>Milan, Emil</creatorName>
      <givenName>Emil</givenName>
      <familyName>Milan</familyName>
      <affiliation>Università di Padova</affiliation>
    </creator>
    <creator>
      <creatorName>Scrimin,  Paolo</creatorName>
      <givenName>Paolo</givenName>
      <familyName>Scrimin</familyName>
      <affiliation>Università di Padova</affiliation>
    </creator>
    <creator>
      <creatorName>Mancin,  Fabrizio</creatorName>
      <givenName>Fabrizio</givenName>
      <familyName>Mancin</familyName>
      <affiliation>Università di Padova</affiliation>
    </creator>
    <creator>
      <creatorName>De Vivo, Marco</creatorName>
      <givenName>Marco</givenName>
      <familyName>De Vivo</familyName>
      <affiliation>Istituto Italiano di Tecnologia</affiliation>
    </creator>
  </creators>
  <titles>
    <title>On the Metal-Aided Catalytic Mechanism for Phosphodiester Bond Cleavage Performed by Nanozymes</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>functionalized nanoparticles</subject>
    <subject>artificial enzymes</subject>
    <subject>monolayer-protected gold clusters</subject>
    <subject>metal-dependent catalysis</subject>
    <subject>molecular simulations</subject>
    <subject>MD</subject>
    <subject>NMR</subject>
    <subject>nanotechnology</subject>
    <subject>CompNanozymes</subject>
    <subject>Marie Skłodowska-Curie grant agreement No 843117"</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-07-02</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="JournalArticle"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/5155228</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1021/acscatal.1c01215</relatedIdentifier>
  </relatedIdentifiers>
  <version>published</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Recent studies have shown that gold nanoparticles (AuNPs) functionalized with Zn(II) complexes can cleave phosphate esters and nucleic acids. Remarkably, such synthetic nanonucleases appear to catalyze metal (Zn)-aided hydrolytic reactions of nucleic acids similar to metallonuclease enzymes. To clarify the reaction mechanism of these nanocatalysts, here we have comparatively analyzed two nanonucleases with a &amp;gt;10-fold difference in the catalytic efficiency for the hydrolysis of the 2-hydroxypropyl-4-nitrophenylphosphate (HPNP, a typical RNA model substrate). We have used microsecond-long atomistic simulations, integrated with NMR experiments, to investigate the structure and dynamics of the outer coating monolayer of these nanoparticles, either alone or in complex with HPNP, in solution. We show that the most efficient one is characterized by coating ligands that promote a well-organized monolayer structure, with the formation of solvated bimetallic catalytic sites. Importantly, we have found that these nanoparticles can mimic two-metal-ion enzymes for nucleic acid processing, with Zn ions that promote HPNP binding at the reaction center. Thus, the two-metal-ion-aided hydrolytic strategy of such nanonucleases helps in explaining their catalytic efficiency for substrate hydrolysis, in accordance with the experimental evidence. These mechanistic insights reinforce the parallelism between such functionalized AuNPs and proteins toward the rational design of more efficient catalysts.&lt;/p&gt;</description>
    <description descriptionType="Other">This project (CompNanozymes) has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 843117.</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/100010661</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/843117/">843117</awardNumber>
      <awardTitle>Metal-dependent catalysis of nanozymes: First steps towards computational nanoenzymology</awardTitle>
    </fundingReference>
  </fundingReferences>
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