ArticleInternational journal of molecular sciences2022
The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides.
Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 17 citations in OpenAlex.
- Visualization of Properties in the Fragment Molecular Orbital Method Using Facio.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Untangling the Complexity of Binding Across Biomolecular Interfaces with Interaction Network Models.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE.Journal of chemical information and modeling · 2025Article
- Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments.Molecules (Basel, Switzerland) · 2024Article
- CaInternational journal of molecular sciences · 2023Article
- Review
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Authors and funding
2 authors at 2 institutions in 2 countries.
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Abstract
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.
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