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http://hdl.handle.net/2445/153994
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 Proteïnes Molecular genetics Proteins |
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: https://doi.org/10.1016/j.jmb.2019.07.021 |
It is part of: | Journal of Molecular Biology, 2019, vol. 431, p. 3845-3859 |
URI: | http://hdl.handle.net/2445/153994 |
Related resource: | https://doi.org/10.1016/j.jmb.2019.07.021 |
ISSN: | 0022-2836 |
Appears in Collections: | Articles publicats en revistes (Bioquímica i Biomedicina Molecular) |
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