Unravelling Protein-DNA Interactions at Molecular Level: A DFT and NCI Study

Journal of Chemical Theory and Computation
Jorge GonzalezJudith Millán

Abstract

Histone-DNA interactions were probed computationally at a molecular level, by characterizing the bimolecular clusters constituted by selected amino acid derivatives with polar (asparagine and glutamine), nonpolar (alanine, valine, and isoleucine), and charged (arginine) side chains and methylated pyrimidinic (1-methylcytosine and 1-methylthymine) and puric (9-methyladenine and 9-methylguanine) DNA bases. The computational approach combined different methodologies: a molecular mechanics (MMFFs forced field) conformational search and structural and vibrational density-functional calculations (M06-2X with double and triple-ζ Pople's basis sets). To dissect the interactions, intermolecular forces were analyzed with the Non-Covalent Interactions (NCI) analysis. The results for the 24 different clusters studied show a noticeable correlation between the calculated binding energies and the propensities for protein-DNA base interactions found in the literature. Such correlation holded even for the interaction of the selected amino acid derivatives with Watson and Crick pairs. Therefore, the balance between hydrogen bonds and van der Waals interactions (specially stacking) in the control of the final shape of the investigated amino acid-...Continue Reading

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Citations

Dec 20, 2016·Journal of Chemical Theory and Computation·Olga A StasyukPavel Hobza
Apr 22, 2017·The Journal of Physical Chemistry. B·Natarajan Sathiyamoorthy Venkataramanan, Ambigapathy Suvitha
Dec 19, 2017·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Corentin LefebvreEric Hénon
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Apr 8, 2017·The Journal of Chemical Physics·Ewa Pastorczak, Clémence Corminboeuf
Aug 21, 2020·Chembiochem : a European Journal of Chemical Biology·Judith MillanRodrigo Martínez
Apr 14, 2017·Journal of Chemical Theory and Computation·Cui LiuDong-Xia Zhao
Jan 3, 2020·Journal of Chemical Information and Modeling·Francesca Peccati
Feb 27, 2021·Scientific Reports·Yudibeth Sixto-LópezSarita Montaño

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