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The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides
Quantum mechanical (QM) calculations at the level of density-functional tight-binding are applied to a protein–DNA complex (PDB: 2o8b) consisting of 3763 atoms, averaging 100 snapshots from molecular dynamics simulations. A detailed comparison of QM and force field (Amber) results is presented. It i...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9654426/ https://www.ncbi.nlm.nih.gov/pubmed/36362296 http://dx.doi.org/10.3390/ijms232113514 |
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author | Sladek, Vladimir Fedorov, Dmitri G. |
author_facet | Sladek, Vladimir Fedorov, Dmitri G. |
author_sort | Sladek, Vladimir |
collection | PubMed |
description | Quantum mechanical (QM) calculations at the level of density-functional tight-binding are applied to a protein–DNA complex (PDB: 2o8b) consisting of 3763 atoms, averaging 100 snapshots from molecular dynamics simulations. A detailed comparison of QM and force field (Amber) results is presented. It is shown that, when solvent screening is taken into account, the contributions of the backbones are small, and the binding of nucleotides in the double helix is governed by the base–base interactions. On the other hand, the backbones can make a substantial contribution to the binding of amino acid residues to nucleotides and other residues. The effect of charge transfer on the interactions is also analyzed, revealing that the actual charge of nucleotides and amino acid residues can differ by as much as 6 and 8% from the formal integer charge, respectively. The effect of interactions on topological models (protein -residue networks) is elucidated. |
format | Online Article Text |
id | pubmed-9654426 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-96544262022-11-15 The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides Sladek, Vladimir Fedorov, Dmitri G. Int J Mol Sci Article Quantum mechanical (QM) calculations at the level of density-functional tight-binding are applied to a protein–DNA complex (PDB: 2o8b) consisting of 3763 atoms, averaging 100 snapshots from molecular dynamics simulations. A detailed comparison of QM and force field (Amber) results is presented. It is shown that, when solvent screening is taken into account, the contributions of the backbones are small, and the binding of nucleotides in the double helix is governed by the base–base interactions. On the other hand, the backbones can make a substantial contribution to the binding of amino acid residues to nucleotides and other residues. The effect of charge transfer on the interactions is also analyzed, revealing that the actual charge of nucleotides and amino acid residues can differ by as much as 6 and 8% from the formal integer charge, respectively. The effect of interactions on topological models (protein -residue networks) is elucidated. MDPI 2022-11-04 /pmc/articles/PMC9654426/ /pubmed/36362296 http://dx.doi.org/10.3390/ijms232113514 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Sladek, Vladimir Fedorov, Dmitri G. The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides |
title | The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides |
title_full | The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides |
title_fullStr | The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides |
title_full_unstemmed | The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides |
title_short | The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides |
title_sort | importance of charge transfer and solvent screening in the interactions of backbones and functional groups in amino acid residues and nucleotides |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9654426/ https://www.ncbi.nlm.nih.gov/pubmed/36362296 http://dx.doi.org/10.3390/ijms232113514 |
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