Robust and Accurate Computational Estimation of the Polarizability Tensors of Macromolecules.
Identifieur interne : 000125 ( Main/Exploration ); précédent : 000124; suivant : 000126Robust and Accurate Computational Estimation of the Polarizability Tensors of Macromolecules.
Auteurs : Muhamed Amin [Allemagne] ; Hebatallah Samy [Égypte] ; Jochen Küpper [Allemagne]Source :
- The journal of physical chemistry letters [ 1948-7185 ] ; 2019.
Descripteurs français
- KwdFr :
- Acides aminés (composition chimique), Anabaena variabilis (composition chimique), Analyse de régression (MeSH), Cyanobactéries (composition chimique), Glutarédoxines (composition chimique), Humains (MeSH), Inhibiteur de la liaison au diazépam (composition chimique), Plastocyanine (composition chimique), Simulation numérique (MeSH), Théorie quantique (MeSH), Électricité statique (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Amino Acids, Diazepam Binding Inhibitor, Glutaredoxins, Plastocyanin.
- chemistry : Anabaena variabilis, Cyanobacteria.
- Computer Simulation, Humans, Quantum Theory, Regression Analysis, Static Electricity.
Abstract
Alignment of molecules through electric fields minimizes the averaging over orientations, e.g., in single-particle-imaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor, which is usually calculated using quantum chemistry methods. These methods are not feasible for large molecules. Here, we calculate the polarizability tensor of proteins using a regression model that correlates the polarizabilities of the 20 amino acids with perfect conductors of the same shape. The dielectric constant of the molecules could be estimated from the slope of the regression line based on the Clausius-Mossotti equation. We benchmark our predictions against the quantum chemistry results for the Trp cagemini protein and the measured dielectric constants of larger proteins. Our method has applications in computing laser alignment of macromolecules, for instance, benefiting single-particle imaging, as well as for estimation of the optical and electrostatic characteristics of proteins and other macromolecules.
DOI: 10.1021/acs.jpclett.9b00963
PubMed: 31074620
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Robust and Accurate Computational Estimation of the Polarizability Tensors of Macromolecules.</title><author><name sortKey="Amin, Muhamed" sort="Amin, Muhamed" uniqKey="Amin M" first="Muhamed" last="Amin">Muhamed Amin</name><affiliation wicri:level="1"><nlm:affiliation>Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg , Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg </wicri:regionArea><wicri:noRegion>22607 Hamburg </wicri:noRegion><wicri:noRegion>22607 Hamburg </wicri:noRegion><wicri:noRegion>22607 Hamburg </wicri:noRegion></affiliation></author><author><name sortKey="Samy, Hebatallah" sort="Samy, Hebatallah" uniqKey="Samy H" first="Hebatallah" last="Samy">Hebatallah Samy</name><affiliation wicri:level="1"><nlm:affiliation>University of Science and Technology, Zewail City , 6th of October City, Giza , Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>University of Science and Technology, Zewail City , 6th of October City, Giza </wicri:regionArea><wicri:noRegion>Giza </wicri:noRegion></affiliation></author><author><name sortKey="Kupper, Jochen" sort="Kupper, Jochen" uniqKey="Kupper J" first="Jochen" last="Küpper">Jochen Küpper</name><affiliation wicri:level="1"><nlm:affiliation>Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg , Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg </wicri:regionArea><wicri:noRegion>22607 Hamburg </wicri:noRegion><wicri:noRegion>22607 Hamburg </wicri:noRegion><wicri:noRegion>22607 Hamburg </wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Physics , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg , Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Physics , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg </wicri:regionArea><wicri:noRegion>22761 Hamburg </wicri:noRegion><wicri:noRegion>22761 Hamburg </wicri:noRegion><wicri:noRegion>22761 Hamburg </wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry , Universität Hamburg , Martin-Luther-King-Platz 6 , 20146 Hamburg , Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Chemistry , Universität Hamburg , Martin-Luther-King-Platz 6 , 20146 Hamburg </wicri:regionArea><wicri:noRegion>20146 Hamburg </wicri:noRegion><wicri:noRegion>20146 Hamburg </wicri:noRegion><wicri:noRegion>20146 Hamburg </wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>The Hamburg Center for Ultrafast Imaging , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg , Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>The Hamburg Center for Ultrafast Imaging , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg </wicri:regionArea><wicri:noRegion>22761 Hamburg </wicri:noRegion><wicri:noRegion>22761 Hamburg </wicri:noRegion><wicri:noRegion>22761 Hamburg </wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:31074620</idno><idno type="pmid">31074620</idno><idno type="doi">10.1021/acs.jpclett.9b00963</idno><idno type="wicri:Area/Main/Corpus">000144</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000144</idno><idno type="wicri:Area/Main/Curation">000144</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000144</idno><idno type="wicri:Area/Main/Exploration">000144</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Robust and Accurate Computational Estimation of the Polarizability Tensors of Macromolecules.</title><author><name sortKey="Amin, Muhamed" sort="Amin, Muhamed" uniqKey="Amin M" first="Muhamed" last="Amin">Muhamed Amin</name><affiliation wicri:level="1"><nlm:affiliation>Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg , Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg </wicri:regionArea><wicri:noRegion>22607 Hamburg </wicri:noRegion><wicri:noRegion>22607 Hamburg </wicri:noRegion><wicri:noRegion>22607 Hamburg </wicri:noRegion></affiliation></author><author><name sortKey="Samy, Hebatallah" sort="Samy, Hebatallah" uniqKey="Samy H" first="Hebatallah" last="Samy">Hebatallah Samy</name><affiliation wicri:level="1"><nlm:affiliation>University of Science and Technology, Zewail City , 6th of October City, Giza , Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>University of Science and Technology, Zewail City , 6th of October City, Giza </wicri:regionArea><wicri:noRegion>Giza </wicri:noRegion></affiliation></author><author><name sortKey="Kupper, Jochen" sort="Kupper, Jochen" uniqKey="Kupper J" first="Jochen" last="Küpper">Jochen Küpper</name><affiliation wicri:level="1"><nlm:affiliation>Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg , Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg </wicri:regionArea><wicri:noRegion>22607 Hamburg </wicri:noRegion><wicri:noRegion>22607 Hamburg </wicri:noRegion><wicri:noRegion>22607 Hamburg </wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Physics , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg , Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Physics , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg </wicri:regionArea><wicri:noRegion>22761 Hamburg </wicri:noRegion><wicri:noRegion>22761 Hamburg </wicri:noRegion><wicri:noRegion>22761 Hamburg </wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry , Universität Hamburg , Martin-Luther-King-Platz 6 , 20146 Hamburg , Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Chemistry , Universität Hamburg , Martin-Luther-King-Platz 6 , 20146 Hamburg </wicri:regionArea><wicri:noRegion>20146 Hamburg </wicri:noRegion><wicri:noRegion>20146 Hamburg </wicri:noRegion><wicri:noRegion>20146 Hamburg </wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>The Hamburg Center for Ultrafast Imaging , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg , Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>The Hamburg Center for Ultrafast Imaging , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg </wicri:regionArea><wicri:noRegion>22761 Hamburg </wicri:noRegion><wicri:noRegion>22761 Hamburg </wicri:noRegion><wicri:noRegion>22761 Hamburg </wicri:noRegion></affiliation></author></analytic><series><title level="j">The journal of physical chemistry letters</title><idno type="eISSN">1948-7185</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acids (chemistry)</term><term>Anabaena variabilis (chemistry)</term><term>Computer Simulation (MeSH)</term><term>Cyanobacteria (chemistry)</term><term>Diazepam Binding Inhibitor (chemistry)</term><term>Glutaredoxins (chemistry)</term><term>Humans (MeSH)</term><term>Plastocyanin (chemistry)</term><term>Quantum Theory (MeSH)</term><term>Regression Analysis (MeSH)</term><term>Static Electricity (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Acides aminés (composition chimique)</term><term>Anabaena variabilis (composition chimique)</term><term>Analyse de régression (MeSH)</term><term>Cyanobactéries (composition chimique)</term><term>Glutarédoxines (composition chimique)</term><term>Humains (MeSH)</term><term>Inhibiteur de la liaison au diazépam (composition chimique)</term><term>Plastocyanine (composition chimique)</term><term>Simulation numérique (MeSH)</term><term>Théorie quantique (MeSH)</term><term>Électricité statique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Amino Acids</term><term>Diazepam Binding Inhibitor</term><term>Glutaredoxins</term><term>Plastocyanin</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Anabaena variabilis</term><term>Cyanobacteria</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Acides aminés</term><term>Anabaena variabilis</term><term>Cyanobactéries</term><term>Glutarédoxines</term><term>Inhibiteur de la liaison au diazépam</term><term>Plastocyanine</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Simulation</term><term>Humans</term><term>Quantum Theory</term><term>Regression Analysis</term><term>Static Electricity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de régression</term><term>Humains</term><term>Simulation numérique</term><term>Théorie quantique</term><term>Électricité statique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Alignment of molecules through electric fields minimizes the averaging over orientations, e.g., in single-particle-imaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor, which is usually calculated using quantum chemistry methods. These methods are not feasible for large molecules. Here, we calculate the polarizability tensor of proteins using a regression model that correlates the polarizabilities of the 20 amino acids with perfect conductors of the same shape. The dielectric constant of the molecules could be estimated from the slope of the regression line based on the Clausius-Mossotti equation. We benchmark our predictions against the quantum chemistry results for the Trp cagemini protein and the measured dielectric constants of larger proteins. Our method has applications in computing laser alignment of macromolecules, for instance, benefiting single-particle imaging, as well as for estimation of the optical and electrostatic characteristics of proteins and other macromolecules.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31074620</PMID><DateCompleted><Year>2019</Year><Month>08</Month><Day>09</Day></DateCompleted><DateRevised><Year>2019</Year><Month>08</Month><Day>09</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1948-7185</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>11</Issue><PubDate><Year>2019</Year><Month>Jun</Month><Day>06</Day></PubDate></JournalIssue><Title>The journal of physical chemistry letters</Title><ISOAbbreviation>J Phys Chem Lett</ISOAbbreviation></Journal><ArticleTitle>Robust and Accurate Computational Estimation of the Polarizability Tensors of Macromolecules.</ArticleTitle><Pagination><MedlinePgn>2938-2943</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1021/acs.jpclett.9b00963</ELocationID><Abstract><AbstractText>Alignment of molecules through electric fields minimizes the averaging over orientations, e.g., in single-particle-imaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor, which is usually calculated using quantum chemistry methods. These methods are not feasible for large molecules. Here, we calculate the polarizability tensor of proteins using a regression model that correlates the polarizabilities of the 20 amino acids with perfect conductors of the same shape. The dielectric constant of the molecules could be estimated from the slope of the regression line based on the Clausius-Mossotti equation. We benchmark our predictions against the quantum chemistry results for the Trp cagemini protein and the measured dielectric constants of larger proteins. Our method has applications in computing laser alignment of macromolecules, for instance, benefiting single-particle imaging, as well as for estimation of the optical and electrostatic characteristics of proteins and other macromolecules.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Amin</LastName><ForeName>Muhamed</ForeName><Initials>M</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-3146-150X</Identifier><AffiliationInfo><Affiliation>Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg , Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Samy</LastName><ForeName>Hebatallah</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>University of Science and Technology, Zewail City , 6th of October City, Giza , Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Küpper</LastName><ForeName>Jochen</ForeName><Initials>J</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-4395-9345</Identifier><AffiliationInfo><Affiliation>Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85 , 22607 Hamburg , Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Physics , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg , Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Chemistry , Universität Hamburg , Martin-Luther-King-Platz 6 , 20146 Hamburg , Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>The Hamburg Center for Ultrafast Imaging , Universität Hamburg , Luruper Chaussee 149 , 22761 Hamburg , Germany.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>05</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Phys Chem Lett</MedlineTA><NlmUniqueID>101526034</NlmUniqueID><ISSNLinking>1948-7185</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000596">Amino Acids</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D026261">Diazepam Binding Inhibitor</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D054477">Glutaredoxins</NameOfSubstance></Chemical><Chemical><RegistryNumber>9014-09-9</RegistryNumber><NameOfSubstance UI="D010970">Plastocyanin</NameOfSubstance></Chemical></ChemicalList><MeshHeadingList><MeshHeading><DescriptorName UI="D000596" MajorTopicYN="N">Amino Acids</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D046870" MajorTopicYN="N">Anabaena variabilis</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="Y">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000458" MajorTopicYN="N">Cyanobacteria</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D026261" MajorTopicYN="N">Diazepam Binding Inhibitor</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D054477" MajorTopicYN="N">Glutaredoxins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010970" MajorTopicYN="N">Plastocyanin</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011789" MajorTopicYN="N">Quantum Theory</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012044" MajorTopicYN="N">Regression Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055672" MajorTopicYN="N">Static Electricity</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>5</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>8</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>5</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31074620</ArticleId><ArticleId IdType="doi">10.1021/acs.jpclett.9b00963</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li><li>Égypte</li></country></list><tree><country name="Allemagne"><noRegion><name sortKey="Amin, Muhamed" sort="Amin, Muhamed" uniqKey="Amin M" first="Muhamed" last="Amin">Muhamed Amin</name></noRegion><name sortKey="Kupper, Jochen" sort="Kupper, Jochen" uniqKey="Kupper J" first="Jochen" last="Küpper">Jochen Küpper</name><name sortKey="Kupper, Jochen" sort="Kupper, Jochen" uniqKey="Kupper J" first="Jochen" last="Küpper">Jochen Küpper</name><name sortKey="Kupper, Jochen" sort="Kupper, Jochen" uniqKey="Kupper J" first="Jochen" last="Küpper">Jochen Küpper</name><name sortKey="Kupper, Jochen" sort="Kupper, Jochen" uniqKey="Kupper J" first="Jochen" last="Küpper">Jochen Küpper</name></country><country name="Égypte"><noRegion><name sortKey="Samy, Hebatallah" sort="Samy, Hebatallah" uniqKey="Samy H" first="Hebatallah" last="Samy">Hebatallah Samy</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/GlutaredoxinV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000125 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000125 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= GlutaredoxinV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:31074620
|texte= Robust and Accurate Computational Estimation of the Polarizability Tensors of Macromolecules.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:31074620" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a GlutaredoxinV1
| This area was generated with Dilib version V0.6.37. |  |