Protein-DNA complexation: contact profiles in DNA grooves

  • M. Yu. Zhitnikova O. Ya. Usikov Institute for Radiophysics and Electronics, Natl. Acad. of Sci. of Ukraine, Acad. Proskury Street, 12, Kharkiv, 61085, Ukraine https://orcid.org/0000-0003-0003-7375
  • A. V. Shestopalova O. Ya. Usikov Institute for Radiophysics and Electronics, Natl. Acad. of Sci. of Ukraine, Acad. Proskury Street, 12, Kharkiv, 61085, Ukraine; V.N. Karazin Kharkiv National University, Svobody sq., 4, Kharkiv, 61022, Ukraine
Keywords: protein-DNA recognition, protein-DNA contacts, DNA structure, binding site prediction, structural variations

Abstract

Background: Investigation of the specific protein-DNA complexation mechanisms allows to establish general principles of molecular recognition, which must be taken into account while developing artificial nanostructures based on DNA, and to improve the prediction efficiency of the protein binding sites on DNA. One of the main characteristics of the protein-DNA complexes are the number and type of contacts in the binding sites of DNA and proteins. Conformational changes in the DNA double helix can cause changes in these characteristics.

Objectives: The purpose of our study is to establish the features of the interactions between nucleotides and amino acid residues in the binding sites of protein-DNA complexes and their dependence on the conformation of deoxyribose and the angle γ of the polynucleotide chain.

Materials and methods: At research of protein-DNA recognition process we have analyzed the contacts between amino acids and nucleotides of the 128 protein-DNA complexes from the structural databases. Conformational parameters of DNA backbone were calculated using the 3DNA/CompDNA program. The number of contacts was determined using a geometric criterion. Two protein and DNA atoms were considered to be in contact if the distance between their centers is less than 4.5 Å. Amino acid residues were arranged according to hydrophobicity scale as hydrophobic or nonpolar and polar.

Results: The analysis of contacts between polar and hydrophobic residues and nucleotides with different conformations of the sugar-phosphate backbone showed that nucleotides form more contacts with polar amino acids in both grooves than with hydrophobic ones regardless of nucleotide conformation. But the profile of such contacts differs in minor and major grooves and depends on the conformation of both deoxyribose and γ angle. The contact profiles are characterized by the sequence-specificity or the different propensity of nucleotides to form contacts with the residues in both grooves.

Conclusions: Our analysis have shown, that the amount and type of protein-nucleic contacts and their distribution in the grooves depend on the conformation of the sugar-phosphate backbone, the nucleotide sequence and the type of amino acids in the binding sites.

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Author Biography

M. Yu. Zhitnikova, O. Ya. Usikov Institute for Radiophysics and Electronics, Natl. Acad. of Sci. of Ukraine, Acad. Proskury Street, 12, Kharkiv, 61085, Ukraine

м.н.с відділу біологічної фізики

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Published
2017-12-22
Cited
How to Cite
Zhitnikova, M. Y., & Shestopalova, A. V. (2017). Protein-DNA complexation: contact profiles in DNA grooves. Biophysical Bulletin, 2(38), 54-65. https://doi.org/10.26565/2075-3810-2017-38-06
Section
Molecular biophysics