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- W2010121434 abstract "Backbone sugar groups are central components of nucleic acids. The conformations of the ribose/deoxyribose can be elegantly described using the concept of pseudorotation (Altona and Sundaralingam, 1972), and are dominated by the C2′- and C3′-endo conformers. The free energy barrier of the transition between these two major puckering modes can be probed by NMR relaxation experiments (Johnson and Hoogstraten, 2008), but an atomic picture of the transition path per se is only available for several truncated nucleoside analogues (Brameld & Goddard III, 1999). Here, we implemented a new free energy simulation method for Molecular Dynamics simulations using pseudorotation as the reaction coordinate (Cremer and Pople, 1975). This allowed us to compute the free energy landscape of a complete pseudorotation cycle. The free energy landscape revealed not only the relative stability of C2′- and C3′-endo conformers, but also the main transition path and its free energy barrier. As a validation of our new approach, we ..." @default.
- W2010121434 created "2016-06-24" @default.
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- W2010121434 date "2013-01-01" @default.
- W2010121434 modified "2023-09-25" @default.
- W2010121434 title "8 Using pseudorotation as a reaction coordinate in free energy simulations of nucleic acids" @default.
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- W2010121434 doi "https://doi.org/10.1080/07391102.2013.786334" @default.
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