Theoretical design of a specific DNA-Zinc-finger protein interaction with semi-empirical quantum chemical methods

Gábor Nagy, B. Gyurcsik, Eufrozina A. Hoffmann, T. Körtvélyesi

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

The interactions of a zinc-finger (ZF) protein with DNA containing the specific recognition site of the ZF and with a non-specific DNA were studied with the semi-empirical quantum chemical method of PM6/Mozyme. The ZF protein (1MEY)-DNA complex structures were generated by docking calculations. The complex structures were reoptimized with the PM6/Mozyme method with implicit solvation in water. The structures were also calculated in the gas phase. The interaction enthalpies between the protein and DNA within the complexes obtained in the PM6/Mozyme with solvation optimized structures were calculated with the single-point PM6-DH2/Mozyme method (PM6 with dispersion, H-bond correction and Mozyme) with solvation. The results supported the specific and non-specific interactions in the complexes obtained from the docking experiments. The binding enthalpies of the specific and non-specific DNA binding to the protein differed significantly. The interactions between the nucleic acid strands in duplexes were also evaluated; these interactions between the base pairs were different because of the different "G...C:A...T" ratios in the DNA molecules studied. The stacking interactions between the nucleic bases were also characterized in the DNA duplexes.

Original languageEnglish
Pages (from-to)928-934
Number of pages7
JournalJournal of Molecular Graphics and Modelling
Volume29
Issue number7
DOIs
Publication statusPublished - Jun 2011

Fingerprint

Zinc
DNA
deoxyribonucleic acid
zinc
proteins
Proteins
Solvation
solvation
interactions
Enthalpy
enthalpy
Nucleic acids
nucleic acids
strands
Nucleic Acids
Gases
vapor phases
Molecules
Water
water

Keywords

  • DNA
  • Docking
  • PM6-DH2
  • Semi-empirical quantum chemical methods
  • Zinc-finger protein

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry

Cite this

Theoretical design of a specific DNA-Zinc-finger protein interaction with semi-empirical quantum chemical methods. / Nagy, Gábor; Gyurcsik, B.; Hoffmann, Eufrozina A.; Körtvélyesi, T.

In: Journal of Molecular Graphics and Modelling, Vol. 29, No. 7, 06.2011, p. 928-934.

Research output: Contribution to journalArticle

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