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JOURNALS // Computer Research and Modeling // Archive

Computer Research and Modeling, 2009 Volume 1, Issue 3, Pages 281–286 (Mi crm646)

This article is cited in 1 paper

ANALYSIS AND MODELING OF COMPLEX LIVING SYSTEMS

Contact specificity in protein–DNA complexes

A. A. Anashkinaa, N. G. Esipovaa, Y. N. Kuznetsovb, V. G. Tumanyana

a Engelhardt Institute of Molecular Biology RAS, Vavilov str. 32, Moscow 119991, Russia
b Russian Academy of Sciences Institute of Control Sciences, Profsoyuznaya str. 65, Moscow GSP-7, B-342, 117997, Russia

Abstract: In this work we investigated contacts between proteins and nucleic acids by Voronoi–Delaunay tessellation. About one third of all contacts are contacts between nucleotides and positively charged residues Arg and Lys, 32,3 %. Ser and Thr together take part in 15 % of contacts. Asn forms 6 % контактов, as well as Gly. Contribution of each other residue type does not exceed 5 %. Statistically significant are contacts Asp-G, Trp-C, Glu-C, Asp-C and His-T. General mechanism of charged residues participation in specific protein-DNA interactions is suggested.

Keywords: Voronoi–Delaunay tessellation, protein–DNA complexes.

Received: 14.04.2009

DOI: 10.20537/2076-7633-2009-1-3-281-286



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