Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

0435963 - BFÚ 2015 RIV FR eng J - Článek v odborném periodiku
Stadlbauer, Petr - Trantírek, L. - Cheatham III, T. E. - Koča, J. - Šponer, Jiří
Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations.
Biochimie. 105C, OCT2014 (2014), s. 22-35. ISSN 0300-9084. E-ISSN 1638-6183
Grant CEP: GA ČR(CZ) GAP208/12/1822; GA ČR(CZ) GA13-28310S
Institucionální podpora: RVO:68081707
Klíčová slova: G-DNA folding * Quadruplex * Triplex
Kód oboru RIV: BO - Biofyzika
Impakt faktor: 2.963, rok: 2014

We have carried out extended set of mu s-scale explicit solvent MD simulations of all possible G-triplexes which can participate in folding pathways of the human telomeric quadruplex. Our study accumulates almost 60 mu s of simulation data, which is by about three orders of magnitude larger sampling compared to the earlier simulations of human telomeric G-DNA triplexes. Starting structures were obtained from experimental quadruplex structures by deleting either the first or the last strand. The life-times of antiparallel triplexes with lateral and diagonal loops are at least on mu s-scale, which should be sufficient to contribute to the folding pathways. However, the triplex states may involve structures with various local deviations from the ideal triplexes, such as strand tilting and various alternative and incomplete triads. The simulations reveal easy rearrangements between lateral and diagonal loop triplex topologies.
Trvalý link: http://hdl.handle.net/11104/0239810