Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.
Journal of chemical theory and computation
American Chemical Society (ACS)
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Stadlbauer, P., Mazzanti, L., Cragnolini, T., Wales, D., Derreumaux, P., Pasquali, S., & Šponer, J. (2016). Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.. Journal of chemical theory and computation, 12 (12), 6077-6097. https://doi.org/10.1021/acs.jctc.6b00667
G-quadruplexes are the most important noncanonical 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.
Telomere, Humans, Temperature, Nucleic Acid Conformation, Kinetics, Thermodynamics, G-Quadruplexes, Inverted Repeat Sequences, Molecular Dynamics Simulation
External DOI: https://doi.org/10.1021/acs.jctc.6b00667
This record's URL: https://www.repository.cam.ac.uk/handle/1810/289442