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Issue 45, 2009
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ProteinDNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies

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Abstract

We use a physics-based approach termed ADAPT to analyse the sequence-specific interactions of three proteins which bind to DNA on the side of the minor groove. The analysis is able to estimate the binding energy for all potential sequences, overcoming the combinatorial problem via a divide-and-conquer approach which breaks the proteinDNA interface down into a series of overlapping oligomeric fragments. All possible base sequences are studied for each fragment. Energy minimisation with an all-atom representation and a conventional force field allows for conformational adaptation of the DNA and of the protein side chains for each new sequence. As a result, the analysis depends linearly on the length of the binding site and complexes as large as the nucleosome can be treated, although this requires access to grid computing facilities. The results on the three complexes studied are in good agreement with experiment. Although they all involve significant DNA deformation, it is found that this does not necessarily imply that the recognition will be dominated by the sequence-dependent mechanical properties of DNA.

Graphical abstract: Protein–DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies

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Publication details

The article was received on 02 Jun 2009, accepted on 24 Sep 2009 and first published on 07 Oct 2009


Article type: Paper
DOI: 10.1039/B910888M
Citation: Phys. Chem. Chem. Phys., 2009,11, 10712-10721
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    ProteinDNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies

    K. Zakrzewska, B. Bouvier, A. Michon, C. Blanchet and R. Lavery, Phys. Chem. Chem. Phys., 2009, 11, 10712
    DOI: 10.1039/B910888M

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