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Oxford University Press, Nucleic Acids Research, 5(42), p. 3381-3394, 2013

DOI: 10.1093/nar/gkt1273

Elsevier, Biophysical Journal, 3(100), p. 69a, 2011

DOI: 10.1016/j.bpj.2010.12.579

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Bioinformatic analysis of the protein/DNA interface

Journal article published in 2013 by Bohdan Schneider ORCID, Jiří Černý, J. Cerny ORCID, Daniel Svozil ORCID, Petr Čech, Agnel Praveen Joseph, P. Cech, Jean-Christophe Gelly, Alexandre G. de Brevern
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Abstract To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Genet., 41:271–287)] and dinucleotide conformers [Svozil, Kalina, Omelka and Schneider (2008) (DNA conformations and their sequence preferences. Nucleic Acids Res., 36:3690–3706)], respectively. Assembling the mutually interacting protein blocks and dinucleotide conformers into ‘interaction matrices’ revealed their correlations and conformer preferences at the interface relative to their occurrence outside the interface. The analyzed data demonstrated important differences between complexes of various types of proteins such as transcription factors and nucleases, distinct interaction patterns for the DNA minor groove relative to the major groove and phosphate and importance of water-mediated contacts. Water molecules mediate proportionally the largest number of contacts in the minor groove and form the largest proportion of contacts in complexes of transcription factors. The generally known induction of A-DNA forms by complexation was more accurately attributed to A-like and intermediate A/B conformers rare in naked DNA molecules.