@article{Steuer2021-07-07Guani-54762,
  year={2021},
  doi={10.1093/nar/gkab592},
  title={Guanidine-II aptamer conformations and ligand binding modes through the lens of molecular simulation},
  number={14},
  volume={49},
  issn={0305-1048},
  journal={Nucleic Acids Research},
  pages={7954--7965},
  author={Steuer, Jakob and Kukharenko, Oleksandra and Riedmiller, Kai and Hartig, Jörg S. and Peter, Christine}
}

<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/54762">
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/29"/>
    <dc:contributor>Riedmiller, Kai</dc:contributor>
    <dc:creator>Hartig, Jörg S.</dc:creator>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-09-01T11:55:28Z</dcterms:available>
    <dc:contributor>Kukharenko, Oleksandra</dc:contributor>
    <dc:creator>Riedmiller, Kai</dc:creator>
    <dc:creator>Kukharenko, Oleksandra</dc:creator>
    <dc:creator>Peter, Christine</dc:creator>
    <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by-nc/4.0/"/>
    <dc:contributor>Steuer, Jakob</dc:contributor>
    <dc:language>eng</dc:language>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-09-01T11:55:28Z</dc:date>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/54762/1/Steuer_2-wr0527ta93fh1.pdf"/>
    <dc:contributor>Peter, Christine</dc:contributor>
    <dcterms:abstract xml:lang="eng">Regulation of gene expression via riboswitches is a widespread mechanism in bacteria. Here, we investigate ligand binding of a member of the guanidine sensing riboswitch family, the guanidine-II riboswitch (Gd-II). It consists of two stem-loops forming a dimer upon ligand binding. Using extensive molecular dynamics simulations we have identified conformational states corresponding to ligand-bound and unbound states in a monomeric stem-loop of Gd-II and studied the selectivity of this binding. To characterize these states and ligand-dependent conformational changes we applied a combination of dimensionality reduction, clustering, and feature selection methods. In absence of a ligand, the shape of the binding pocket alternates between the conformation observed in presence of guanidinium and a collapsed conformation, which is associated with a deformation of the dimerization interface. Furthermore, the structural features responsible for the ability to discriminate against closely related analogs of guanidine are resolved. Based on these insights, we propose a mechanism that couples ligand binding to aptamer dimerization in the Gd-II system, demonstrating the value of computational methods in the field of nucleic acids research.</dcterms:abstract>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/54762"/>
    <dcterms:issued>2021-07-07</dcterms:issued>
    <dcterms:title>Guanidine-II aptamer conformations and ligand binding modes through the lens of molecular simulation</dcterms:title>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/29"/>
    <dc:creator>Steuer, Jakob</dc:creator>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/54762/1/Steuer_2-wr0527ta93fh1.pdf"/>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:contributor>Hartig, Jörg S.</dc:contributor>
    <dc:rights>Attribution-NonCommercial 4.0 International</dc:rights>
  </rdf:Description>
</rdf:RDF>