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@article{1382658, author = {Stadlbauer, Petr and Mazzanti, L and Cragnolini, T and Wales, DJ and Derreumaux, P and Pasquali, S and Šponer, Jiří}, article_location = {Washington DC}, article_number = {12}, doi = {http://dx.doi.org/10.1021/acs.jctc.6b00667}, language = {eng}, issn = {1549-9618}, journal = {Journal of Chemical Theory and Computation}, title = {Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes}, url = {http://dx.doi.org/10.1021/acs.jctc.6b00667}, volume = {12}, year = {2016} }
TY - JOUR ID - 1382658 AU - Stadlbauer, Petr - Mazzanti, L - Cragnolini, T - Wales, DJ - Derreumaux, P - Pasquali, S - Šponer, Jiří PY - 2016 TI - Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes JF - Journal of Chemical Theory and Computation VL - 12 IS - 12 SP - 6077-6097 EP - 6077-6097 PB - American Chemical Society SN - 15499618 UR - http://dx.doi.org/10.1021/acs.jctc.6b00667 L2 - http://dx.doi.org/10.1021/acs.jctc.6b00667 N2 - G-quadruplexes are the most important non canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)(n), have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite the availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradictory models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach thermodynamic equilibrium. Based on atomistic simulations of diverse classes of intermediates in G-quadruplex folding, we have suggested that the folding is an extremely multipathway process combining a kinetic partitioning mechanism with conformational diffusion. However, complete G-quadruplex folding is far beyond the time scale of atomistic simulations. Here we use high-resolution coarse-grained simulations to investigate potential unfolding intermediates, whose structural dynamics are then further explored with all-atom simulations. This multiscale approach indicates how various pathways are interconnected in a complex network. Spontaneous conversions between different folds are observed. We demonstrate the inability of simple order parameters, such as radius of gyration or the number of native H-bonds, to describe the folding landscape of the G-quadruplexes. Our study also provides information relevant to further development of the coarse grained force field. ER -
STADLBAUER, Petr, L MAZZANTI, T CRAGNOLINI, DJ WALES, P DERREUMAUX, S PASQUALI a Jiří ŠPONER. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. \textit{Journal of Chemical Theory and Computation}. Washington DC: American Chemical Society, 2016, roč.~12, č.~12, s.~6077-6097. ISSN~1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.6b00667.
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