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Title: How B-DNA dynamics decipher sequence-selective protein recognition
Author: Battistini, Federica
Hospital, Adam
Buitrago Ospina, Diana Camila
Gallego Perez, Diego
Dans, Pablo D.
Gelpí Buchaca, Josep Lluís
Orozco López, Modesto
Keywords: Genètica molecular
Molecular genetics
Issue Date: 17-Jul-2019
Publisher: Elsevier Ltd
Abstract: The rules governing sequence-specific DNA-protein recognition are under a long-standing debate regarding the prevalence of base versus shape readout mechanisms to explain sequence specificity and of the conformational selection versus induced fit binding paradigms to explain binding-related conformational changes in DNA. Using a combination of atomistic simulations on a subset of representative sequences and mesoscopic simulations at the protein-DNA interactome level, we demonstrate the prevalence of the shape readout model in determining sequence-specificity and of the conformational selection paradigm in defining the general mechanism for binding-related conformational changes in DNA. Our results suggest that the DNA uses a double mechanism to adapt its structure to the protein: it moves along the easiest deformation modes to approach the bioactive conformation, while final adjustments require localized rearrangements at the base-pair step and backbone level. Our study highlights the large impact of B-DNA dynamics in modulating DNA-protein binding.
Note: Versió postprint del document publicat a:
It is part of: Journal of Molecular Biology, 2019, vol. 431, p. 3845-3859
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ISSN: 0022-2836
Appears in Collections:Articles publicats en revistes (Bioquímica i Biomedicina Molecular)

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