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A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins

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cris.lastimport.scopus2024-02-12T20:42:49Z
dc.abstract.enWe present a method to rapidly identify hydrogen-mediated interactions in proteins (e.g., hydrogen bonds, hydrogen bonds, water-mediated hydrogen bonds, salt bridges, and aromatic -hydrogen interactions) through heavy atom geometry alone, that is, without needing to explicitly determine hydrogen atom positions using either experimental or theoretical methods. By including specific real (or virtual) partner atoms as defined by the atom type of both the donor and acceptor heavy atoms, a set of unique angles can be rapidly calculated. By comparing the distance between the donor and the acceptor and these unique angles to the statistical preferences observed in the Protein Data Bank (PDB), we were able to identify a set of conserved geometries (15 for donor atoms and 7 for acceptor atoms) for hydrogen-mediated interactions in proteins. This set of identified interactions includes every polar atom type present in the Protein Data Bank except OE1 (glutamate/glutamine sidechain) and a clear geometric preference for the methionine sulfur atom (SD) to act as a hydrogen bond acceptor. This method could be readily applied to protein design eorts.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorRoth, Jennifer K.
dc.contributor.authorGórna, Maria
dc.contributor.authorMerski, Matthew
dc.contributor.authorSkrzeczkowski, Jakub
dc.date.accessioned2024-01-24T17:37:51Z
dc.date.available2024-01-24T17:37:51Z
dc.date.copyright2020-11-15
dc.date.issued2020
dc.description.accesstimeAT_PUBLICATION
dc.description.financeŚrodki finansowe przyznane na realizację projektu w zakresie badań naukowych lub prac rozwojowych
dc.description.number22
dc.description.versionFINAL_PUBLISHED
dc.description.volume25
dc.identifier.doi10.3390/MOLECULES25225326
dc.identifier.issn1420-3049
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/101569
dc.identifier.weblinkhttps://www.mdpi.com/1420-3049/25/22/5326/pdf
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofMolecules
dc.relation.pages5326
dc.rightsCC-BY
dc.sciencecloudnosend
dc.subject.enhydrogen bond
dc.subject.enCH- bond
dc.subject.enprotein crystal structure
dc.subject.enmethionine
dc.subject.enprotein geometry
dc.titleA Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins
dc.typeJournalArticle
dspace.entity.typePublication