Publication details

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non- Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding


CSASZAR Kristina ŠPAČKOVÁ Naděžda ŠTEFL Richard ŠPONER Jiří LEONTIS Neocles B.

Year of publication 2001
Type Article in Periodical
Magazine / Source Journal of Molecular Biology
MU Faculty or unit

Faculty of Science

Field Biophysics
Keywords molecular dynamics simulation; pseudoknot; non-Watson-Crick; base-pairs; beet western yellows virus
Description Molecular dynamics simulations of the frame-shifting pseudoknot from beet western yellows virus (BWYV, NDB file UR0004) were performed with explicit inclusion of solvent and counterions. In all, 33 ns of simulation were carried out, including 10 ns of the native structure with protonation of the crucial cytosine residue, C8(N3+). The native structure exhibited stable trajectories retaining all Watson-Crick and tertiary base-pairs, except for fluctuations or transient disruptions at spec most significant fluctuations involved the change or disruption of hydrogen-bonding between C8(N3+) and bases G12, A25, and C26, as well as disruption of the water bridges linking C8(N3+) with A25 and C26. The simulations revealed several critical, highly ordered hydration sites with close to 100% occupancies and residency times of individual water molecules of up to 5 ns. Sodium cation coordination sites with occupancies above 50% were also observed.
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