A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins
We 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 π-hydrogen interactions) through heavy atom geometry alone, that is, without needing to explicitly determine hydrogen at...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-11-01
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| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/25/22/5326 |
| _version_ | 1797547824847519744 |
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| author | Matthew Merski Jakub Skrzeczkowski Jennifer K. Roth Maria W. Górna |
| author_facet | Matthew Merski Jakub Skrzeczkowski Jennifer K. Roth Maria W. Górna |
| author_sort | Matthew Merski |
| collection | DOAJ |
| description | We 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 π-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 efforts. |
| first_indexed | 2024-03-10T14:50:50Z |
| format | Article |
| id | doaj.art-669aa07f5cc44d59807458a5ed45b5f5 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T14:50:50Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-669aa07f5cc44d59807458a5ed45b5f52023-11-20T21:01:24ZengMDPI AGMolecules1420-30492020-11-012522532610.3390/molecules25225326A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in ProteinsMatthew Merski0Jakub Skrzeczkowski1Jennifer K. Roth2Maria W. Górna3Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, PolandBiological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, PolandDepartment of Psychology, Carlow University, Pittsburgh, PA 15213, USABiological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, PolandWe 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 π-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 efforts.https://www.mdpi.com/1420-3049/25/22/5326hydrogen bondCH-π bondprotein crystal structuremethionineprotein geometry |
| spellingShingle | Matthew Merski Jakub Skrzeczkowski Jennifer K. Roth Maria W. Górna A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins Molecules hydrogen bond CH-π bond protein crystal structure methionine protein geometry |
| title | A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins |
| title_full | A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins |
| title_fullStr | A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins |
| title_full_unstemmed | A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins |
| title_short | A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins |
| title_sort | geometric definition of short to medium range hydrogen mediated interactions in proteins |
| topic | hydrogen bond CH-π bond protein crystal structure methionine protein geometry |
| url | https://www.mdpi.com/1420-3049/25/22/5326 |
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