STADLBAUER, Petr, Petra KUHROVÁ, Pavel BANÁŠ, Jaroslav KOČA, Giovanni BUSSI, Lukáš TRANTÍREK, Michal OTYEPKA a Jiří ŠPONER. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic Acids Research. Oxford: Oxford University Press, 2015, roč. 43, č. 20, s. 9626-9644. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkv994. |
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@article{1335876, author = {Stadlbauer, Petr and Kuhrová, Petra and Banáš, Pavel and Koča, Jaroslav and Bussi, Giovanni and Trantírek, Lukáš and Otyepka, Michal and Šponer, Jiří}, article_location = {Oxford}, article_number = {20}, doi = {http://dx.doi.org/10.1093/nar/gkv994}, keywords = {MOLECULAR-DYNAMICS SIMULATIONS; INTRAMOLECULAR DNA QUADRUPLEXES; PARTICLE MESH EWALD; AMBER FORCE-FIELD; G-TRACT LENGTH; NUCLEIC-ACIDS; REPLICA-EXCHANGE; K+ SOLUTION; ENERGY LANDSCAPE; STRUCTURAL DYNAMICS}, language = {eng}, issn = {0305-1048}, journal = {Nucleic Acids Research}, title = {Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations}, url = {http://nar.oxfordjournals.org/content/43/20/9626.full.pdf+html}, volume = {43}, year = {2015} }
TY - JOUR ID - 1335876 AU - Stadlbauer, Petr - Kuhrová, Petra - Banáš, Pavel - Koča, Jaroslav - Bussi, Giovanni - Trantírek, Lukáš - Otyepka, Michal - Šponer, Jiří PY - 2015 TI - Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations JF - Nucleic Acids Research VL - 43 IS - 20 SP - 9626-9644 EP - 9626-9644 PB - Oxford University Press SN - 03051048 KW - MOLECULAR-DYNAMICS SIMULATIONS KW - INTRAMOLECULAR DNA QUADRUPLEXES KW - PARTICLE MESH EWALD KW - AMBER FORCE-FIELD KW - G-TRACT LENGTH KW - NUCLEIC-ACIDS KW - REPLICA-EXCHANGE KW - K+ SOLUTION KW - ENERGY LANDSCAPE KW - STRUCTURAL DYNAMICS UR - http://nar.oxfordjournals.org/content/43/20/9626.full.pdf+html L2 - http://nar.oxfordjournals.org/content/43/20/9626.full.pdf+html N2 - DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating similar to 130 mu s of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-mu s scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best understood by the kinetic partitioning mechanism with a set of deep competing minima on the folding landscape, with only a small fraction of molecules directly folding to the native fold. The landscape should further include non-specific collapse processes where the molecules move via diffusion and consecutive random rare transitions, which could, e.g. structure the propeller loops. ER -
STADLBAUER, Petr, Petra KUHROVÁ, Pavel BANÁŠ, Jaroslav KOČA, Giovanni BUSSI, Lukáš TRANTÍREK, Michal OTYEPKA a Jiří ŠPONER. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2015, roč.~43, č.~20, s.~9626-9644. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkv994.
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