On the polarization of ligands by proteins.
Identifieur interne : 000141 ( Main/Exploration ); précédent : 000140; suivant : 000142On the polarization of ligands by proteins.
Auteurs : Soohaeng Yoo Willow [États-Unis] ; Bing Xie [États-Unis] ; Jason Lawrence [États-Unis] ; Robert S. Eisenberg [États-Unis] ; David D L. Minh [États-Unis]Source :
- Physical chemistry chemical physics : PCCP [ 1463-9084 ] ; 2020.
Abstract
Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we use a quantum mechanics/molecular mechanics (QM/MM) approach, in which the ligand is the QM region, to compute the ligand polarization energy of 286 protein-ligand complexes from the PDBBind Core Set (release 2016). Calculations were performed both with and without implicit solvent based on the domain decomposition Conductor-like Screening Model. We observe that the ligand polarization energy is linearly correlated with the magnitude of the electric field acting on the ligand, the magnitude of the induced dipole moment, and the classical polarization energy. The influence of protein and cation charges on the ligand polarization diminishes with the distance and is below 2 kcal mol-1 at 9 Å and 1 kcal mol-1 at 12 Å. Compared to these embedding field charges, implicit solvent has a relatively minor effect on ligand polarization. Considering both polarization and solvation appears essential to computing negative binding energies in some crystallographic complexes. Solvation, but not polarization, is essential for achieving moderate correlation with experimental binding free energies.
DOI: 10.1039/d0cp00376j
PubMed: 32421120
Affiliations:
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Eisenberg</name><affiliation wicri:level="1"><nlm:affiliation>Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois 60616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois 60616</wicri:regionArea><wicri:noRegion>Illinois 60616</wicri:noRegion></affiliation></author><author><name sortKey="Minh, David D L" sort="Minh, David D L" uniqKey="Minh D" first="David D L" last="Minh">David D L. Minh</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, USA. dminh@iit.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616</wicri:regionArea><wicri:noRegion>Illinois 60616</wicri:noRegion></affiliation></author></analytic><series><title level="j">Physical chemistry chemical physics : PCCP</title><idno type="eISSN">1463-9084</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we use a quantum mechanics/molecular mechanics (QM/MM) approach, in which the ligand is the QM region, to compute the ligand polarization energy of 286 protein-ligand complexes from the PDBBind Core Set (release 2016). Calculations were performed both with and without implicit solvent based on the domain decomposition Conductor-like Screening Model. We observe that the ligand polarization energy is linearly correlated with the magnitude of the electric field acting on the ligand, the magnitude of the induced dipole moment, and the classical polarization energy. The influence of protein and cation charges on the ligand polarization diminishes with the distance and is below 2 kcal mol-1 at 9 Å and 1 kcal mol-1 at 12 Å. Compared to these embedding field charges, implicit solvent has a relatively minor effect on ligand polarization. Considering both polarization and solvation appears essential to computing negative binding energies in some crystallographic complexes. Solvation, but not polarization, is essential for achieving moderate correlation with experimental binding free energies.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32421120</PMID><DateRevised><Year>2020</Year><Month>06</Month><Day>04</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1463-9084</ISSN><JournalIssue CitedMedium="Internet"><Volume>22</Volume><Issue>21</Issue><PubDate><Year>2020</Year><Month>Jun</Month><Day>04</Day></PubDate></JournalIssue><Title>Physical chemistry chemical physics : PCCP</Title><ISOAbbreviation>Phys Chem Chem Phys</ISOAbbreviation></Journal><ArticleTitle>On the polarization of ligands by proteins.</ArticleTitle><Pagination><MedlinePgn>12044-12057</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1039/d0cp00376j</ELocationID><Abstract><AbstractText>Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we use a quantum mechanics/molecular mechanics (QM/MM) approach, in which the ligand is the QM region, to compute the ligand polarization energy of 286 protein-ligand complexes from the PDBBind Core Set (release 2016). Calculations were performed both with and without implicit solvent based on the domain decomposition Conductor-like Screening Model. We observe that the ligand polarization energy is linearly correlated with the magnitude of the electric field acting on the ligand, the magnitude of the induced dipole moment, and the classical polarization energy. The influence of protein and cation charges on the ligand polarization diminishes with the distance and is below 2 kcal mol-1 at 9 Å and 1 kcal mol-1 at 12 Å. Compared to these embedding field charges, implicit solvent has a relatively minor effect on ligand polarization. Considering both polarization and solvation appears essential to computing negative binding energies in some crystallographic complexes. Solvation, but not polarization, is essential for achieving moderate correlation with experimental binding free energies.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Willow</LastName><ForeName>Soohaeng Yoo</ForeName><Initials>SY</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, USA. dminh@iit.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xie</LastName><ForeName>Bing</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, USA. dminh@iit.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lawrence</LastName><ForeName>Jason</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Computer Science, Illinois Institute of Technology, Chicago, Illinois 60616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eisenberg</LastName><ForeName>Robert S</ForeName><Initials>RS</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-4860-5434</Identifier><AffiliationInfo><Affiliation>Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois 60616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Minh</LastName><ForeName>David D L</ForeName><Initials>DDL</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-4802-2618</Identifier><AffiliationInfo><Affiliation>Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, USA. dminh@iit.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Phys Chem Chem Phys</MedlineTA><NlmUniqueID>100888160</NlmUniqueID><ISSNLinking>1463-9076</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>5</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>5</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>5</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32421120</ArticleId><ArticleId IdType="doi">10.1039/d0cp00376j</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Willow, Soohaeng Yoo" sort="Willow, Soohaeng Yoo" uniqKey="Willow S" first="Soohaeng Yoo" last="Willow">Soohaeng Yoo Willow</name></noRegion><name sortKey="Eisenberg, Robert S" sort="Eisenberg, Robert S" uniqKey="Eisenberg R" first="Robert S" last="Eisenberg">Robert S. Eisenberg</name><name sortKey="Lawrence, Jason" sort="Lawrence, Jason" uniqKey="Lawrence J" first="Jason" last="Lawrence">Jason Lawrence</name><name sortKey="Minh, David D L" sort="Minh, David D L" uniqKey="Minh D" first="David D L" last="Minh">David D L. Minh</name><name sortKey="Xie, Bing" sort="Xie, Bing" uniqKey="Xie B" first="Bing" last="Xie">Bing Xie</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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