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Comparison of DNA binding across protein superfamilies

AuthorsContreras-Moreira, Bruno CSIC ORCID ; Sancho Sanz, Javier; Espinosa Angarica, Vladimir
Keywordsprotein-DNA complex
binding specificity
Issue Date2010
PublisherJohn Wiley & Sons
CitationContreras-Moreira B, Sancho J, Espinosa V. Comparison of DNA binding across protein superfamilies. Proteins Structure Function and Bioinformatics 78 (1): 52-62 (2010)
AbstractSpecific protein-DNA interactions are central to a wide group of processes in the cell and have been studied both experimentally and computational ly over the years. Despite the increasing collection of protein-DNA complexes, so far only a few studies have aimed at dissecting the structural characteristics of DNA binding among evolutionarily related proteins. Some questions that remain to be answered are: a) what is the contribution of the different readout mechanisms in members of a given structural superfamily, b) what is the degree of interface similarity among superfamily members and how this affects binding specificity, c) how DNA-binding protein superfamilies distribute across taxa, and d) is there a general or family-specific code for the recognition of DNA. We have recently developed a straightforward method to dissect the interface of protein-DNA complexes at the atomic level and here we apply it to study 175 proteins belonging to 9 representative superfamilies. Our results indicate that evolutionarily unrelated DNA-binding domains broadly conserve specificity statistics, such as the ratio of indirect/direct readout and the frequency of atomic interactions, therefore supporting the existence of a set of recognition rules. It is also found that interface conservation follows trends that are superfamily-specific. Finally, this paper identifies tendencies in the phylogenetic distribution of transcription factors, which might be related to the evolution of regulatory networks, and postulates that the modular nature of zinc finger proteins can explain its role in large genomes, as it allows for larger binding interfaces in a single protein molecule.
Publisher version (URL)http://dx.doi.org/10.1002/prot.22525
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