Long-timescale dynamics of the Drew-Dickerson dodecamer

0462092 - ÚOCHB 2017 RIV GB eng J - Journal Article
Dans, P. D. - Danilane, L. - Ivani, I. - Dršata, Tomáš - Lankaš, Filip - Hospital, A. - Walther, J. - Pujagut, R. I. - Battistini, F. - Gelpí, J. L. - Lavery, R. - Orozco, M.
Long-timescale dynamics of the Drew-Dickerson dodecamer.
Nucleic Acids Research. Roč. 44, č. 9 (2016), s. 4052-4066. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA14-21893S
Institutional support: RVO:61388963
Keywords : microsecond molecular dynamics * B-DNA dodecamer * analyzing ion distributions
Subject RIV: CE - Biochemistry
Impact factor: 10.162, year: 2016
http://nar.oxfordjournals.org/content/44/9/4052.full

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 mu s) 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 mu s of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.
Permanent Link: http://hdl.handle.net/11104/0261617