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.

doi:10.3390/ijms232113514

Open AccessArticle

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides

by

Vladimir Sladek

^1,*

and

Dmitri G. Fedorov

^2,*

¹

Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia

²

Research Center for Computational Design of Advanced Functional Materials (CD-FMat) National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Ibaraki, Japan

^*

Authors to whom correspondence should be addressed.

Int. J. Mol. Sci. 2022, 23(21), 13514; https://doi.org/10.3390/ijms232113514

Submission received: 14 October 2022 / Revised: 26 October 2022 / Accepted: 28 October 2022 / Published: 4 November 2022

(This article belongs to the Special Issue Proteins and Protein-Ligand Interactions)

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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.

Keywords: fragment molecular orbital; molecular dynamics; molecular mechanics; non-covalent interactions; residue interaction networks; dielectric constant

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MDPI and ACS Style

Sladek, V.; Fedorov, D.G. The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides. Int. J. Mol. Sci. 2022, 23, 13514. https://doi.org/10.3390/ijms232113514

AMA Style

Sladek V, Fedorov DG. The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides. International Journal of Molecular Sciences. 2022; 23(21):13514. https://doi.org/10.3390/ijms232113514

Chicago/Turabian Style

Sladek, Vladimir, and Dmitri G. Fedorov. 2022. "The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides" International Journal of Molecular Sciences 23, no. 21: 13514. https://doi.org/10.3390/ijms232113514

APA Style

Sladek, V., & Fedorov, D. G. (2022). The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides. International Journal of Molecular Sciences, 23(21), 13514. https://doi.org/10.3390/ijms232113514

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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

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