Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

0485734 - BFÚ 2018 RIV US eng J - Článek v odborném periodiku
Islam, Barira - Stadlbauer, Petr - Gil-Ley, A. - Perez-Hernandez, J. A. - Haider, S.M. - Neidle, S. - Bussi, G. - Banáš, P. - Otyepka, Michal - Šponer, Jiří
Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.
Journal of Chemical Theory and Computation. Roč. 13, č. 6 (2017), s. 2458-2480. ISSN 1549-9618. E-ISSN 1549-9626
Grant CEP: GA ČR(CZ) GA16-13721S
Institucionální podpora: RVO:68081707
Klíčová slova: amber force-field * particle mesh ewald
Obor OECD: Physical chemistry
Impakt faktor: 5.399, rok: 2017

We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 its long, similar to 162 mu s in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few,us, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQtopologies and for all force field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical gamma-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 alpha/gamma dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory.
Trvalý link: http://hdl.handle.net/11104/0280681