Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device.
Identifieur interne : 001194 ( PubMed/Corpus ); précédent : 001193; suivant : 001195Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device.
Auteurs : Olivier Delalande ; Nicolas Ferey ; Benoist Laurent ; Marc Gueroult ; Brigitte Hartmann ; Marc BaadenSource :
- Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing [ 2335-6936 ] ; 2010.
English descriptors
- KwdEn :
- Binding Sites, Calcium (metabolism), Cations (metabolism), Computational Biology, Deoxyribonuclease I (chemistry), Deoxyribonuclease I (metabolism), Metals (metabolism), Models, Biological, Models, Molecular, Molecular Dynamics Simulation, Molecular Probe Techniques, Molecular Probes, Software, Static Electricity.
- MESH :
- chemical , chemistry : Deoxyribonuclease I.
- chemical , metabolism : Calcium, Cations, Deoxyribonuclease I, Metals.
- Binding Sites, Computational Biology, Models, Biological, Models, Molecular, Molecular Dynamics Simulation, Molecular Probe Techniques, Molecular Probes, Software, Static Electricity.
Abstract
Metal ions drive important parts of biology, yet it remains experimentally challenging to locate their binding sites. Here we present an innovative computational approach. We use interactive steering of charged ions or small molecules in an electrostatic potential map in order to identify potential binding sites. The user interacts with a haptic device and experiences tactile feedback related to the strength of binding at a given site. The potential field is the first level of resolution used in this model. Any type of potential field can be used, implicitly taking into account various conditions such as ionic strength, dielectric constants or the presence of a membrane. At a second level, we represent the accessibility of all binding sites by modelling the shape of the target macromolecule via non-bonded van der Waals interactions between its static atomic or coarse-grained structure and the probe molecule(s). The third independent level concerns the representation of the molecular probe itself. Ion selectivity can be assessed by using multiple interacting ions as probes. This method was successfully applied to the DNase I enzyme, where we recently identified two new cation binding sites by computationally expensive extended molecular dynamics simulations.
PubMed: 19908373
Links to Exploration step
pubmed:19908373Le document en format XML
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Pacific Symposium on Biocomputing</title><idno type="ISSN">2335-6936</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Calcium (metabolism)</term><term>Cations (metabolism)</term><term>Computational Biology</term><term>Deoxyribonuclease I (chemistry)</term><term>Deoxyribonuclease I (metabolism)</term><term>Metals (metabolism)</term><term>Models, Biological</term><term>Models, Molecular</term><term>Molecular Dynamics Simulation</term><term>Molecular Probe Techniques</term><term>Molecular Probes</term><term>Software</term><term>Static Electricity</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Deoxyribonuclease I</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Calcium</term><term>Cations</term><term>Deoxyribonuclease I</term><term>Metals</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Computational Biology</term><term>Models, Biological</term><term>Models, Molecular</term><term>Molecular Dynamics Simulation</term><term>Molecular Probe Techniques</term><term>Molecular Probes</term><term>Software</term><term>Static Electricity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Metal ions drive important parts of biology, yet it remains experimentally challenging to locate their binding sites. Here we present an innovative computational approach. We use interactive steering of charged ions or small molecules in an electrostatic potential map in order to identify potential binding sites. The user interacts with a haptic device and experiences tactile feedback related to the strength of binding at a given site. The potential field is the first level of resolution used in this model. Any type of potential field can be used, implicitly taking into account various conditions such as ionic strength, dielectric constants or the presence of a membrane. At a second level, we represent the accessibility of all binding sites by modelling the shape of the target macromolecule via non-bonded van der Waals interactions between its static atomic or coarse-grained structure and the probe molecule(s). The third independent level concerns the representation of the molecular probe itself. Ion selectivity can be assessed by using multiple interacting ions as probes. This method was successfully applied to the DNase I enzyme, where we recently identified two new cation binding sites by computationally expensive extended molecular dynamics simulations.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">19908373</PMID><DateCreated><Year>2009</Year><Month>11</Month><Day>12</Day></DateCreated><DateCompleted><Year>2013</Year><Month>11</Month><Day>13</Day></DateCompleted><DateRevised><Year>2013</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">2335-6936</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2010</Year></PubDate></JournalIssue><Title>Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing</Title><ISOAbbreviation>Pac Symp Biocomput</ISOAbbreviation></Journal><ArticleTitle>Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device.</ArticleTitle><Pagination><MedlinePgn>205-15</MedlinePgn></Pagination><Abstract><AbstractText>Metal ions drive important parts of biology, yet it remains experimentally challenging to locate their binding sites. Here we present an innovative computational approach. We use interactive steering of charged ions or small molecules in an electrostatic potential map in order to identify potential binding sites. The user interacts with a haptic device and experiences tactile feedback related to the strength of binding at a given site. The potential field is the first level of resolution used in this model. Any type of potential field can be used, implicitly taking into account various conditions such as ionic strength, dielectric constants or the presence of a membrane. At a second level, we represent the accessibility of all binding sites by modelling the shape of the target macromolecule via non-bonded van der Waals interactions between its static atomic or coarse-grained structure and the probe molecule(s). The third independent level concerns the representation of the molecular probe itself. Ion selectivity can be assessed by using multiple interacting ions as probes. This method was successfully applied to the DNase I enzyme, where we recently identified two new cation binding sites by computationally expensive extended molecular dynamics simulations.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Delalande</LastName><ForeName>Olivier</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Laboratoire de Biochimie Théorique, CNRS UPR9080/IBPC, 13 rue Pierre et Marie Curie, F-75005, Paris, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ferey</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Laurent</LastName><ForeName>Benoist</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Gueroult</LastName><ForeName>Marc</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Hartmann</LastName><ForeName>Brigitte</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Baaden</LastName><ForeName>Marc</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Singapore</Country><MedlineTA>Pac Symp Biocomput</MedlineTA><NlmUniqueID>9711271</NlmUniqueID></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D002412">Cations</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D008670">Metals</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015335">Molecular Probes</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.21.1</RegistryNumber><NameOfSubstance UI="D003850">Deoxyribonuclease I</NameOfSubstance></Chemical><Chemical><RegistryNumber>SY7Q814VUP</RegistryNumber><NameOfSubstance UI="D002118">Calcium</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName MajorTopicYN="N" UI="D001665">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D002118">Calcium</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000378">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D002412">Cations</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000378">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D019295">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D003850">Deoxyribonuclease I</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000737">chemistry</QualifierName><QualifierName MajorTopicYN="N" UI="Q000378">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D008670">Metals</DescriptorName><QualifierName MajorTopicYN="Y" UI="Q000378">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D008954">Models, Biological</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D008958">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D056004">Molecular Dynamics Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D015336">Molecular Probe Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D015335">Molecular Probes</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D012984">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D055672">Static Electricity</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>11</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>11</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>11</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pii">9789814295291_0023</ArticleId><ArticleId IdType="pubmed">19908373</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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