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Title: | Long-timescale dynamics of the Drew-Dickerson dodecamer |
Author: | Dans, Pablo D. Danilāne, Linda Ivani, Ivan Dršata, Tomáš Lankaš, Filip Hospital Gasch, Adam Walther, Jürgen Illa Pujagut, Ricard Battistini, Federica Gelpí Buchaca, Josep Lluís Lavery, Richard Orozco López, Modesto |
Keywords: | Duplicació de l'ADN Biologia computacional DNA replication Computational biology |
Issue Date: | 15-Apr-2016 |
Publisher: | Oxford University Press |
Abstract: | We present a systematic study of the long-timescale dynamics of the Drew-Dickerson dodecamer (DDD: d(CGCGAATTGCGC)2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na(+)Cl(-) or K(+)Cl(-) The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 μs) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 μs of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex. |
Note: | Reproducció del document publicat a: http://dx.doi.org/10.1093/nar/gkw264 |
It is part of: | Nucleic Acids Research, 2016, vol. 44, num. 9, p. 4052-4066 |
URI: | http://hdl.handle.net/2445/102469 |
Related resource: | http://dx.doi.org/10.1093/nar/gkw264 |
ISSN: | 0305-1048 |
Appears in Collections: | Articles publicats en revistes (Bioquímica i Biomedicina Molecular) Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona)) Publicacions de projectes de recerca finançats per la UE |
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