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.

摘要: Molecular dynamics simulations of the frame-shifting pseudoknot from beet western yellows virus (BWYV, NDB file UR0004) were performed with explicit inclusion solvent and counterions. In all, 33 ns simulation carried out, including 10 native structure protonation crucial cytosine residue, C8(N3+). The exhibited stable trajectories retaining all Watson-Crick tertiary base-pairs, except for fluctuations or transient disruptions at specific sites. most significant involved change disruption hydrogen-bonding between C8(N3+) bases G12, A25, C26, as well water bridges linking A25 C26. To increase sampling rare events, was continued 400 K. A partial, irreversible unfolding molecule initiated by slippage relative to G12 sudden concerted changes in involving A23, A24, A25. These events followed a gradual loss stacking interactions loop 2. Of only 5'-terminal pair stem 1 dissociated K, while trans sugar-edge/sugar-edge A20.G4 interaction remained surprisingly stable. Four additional room-temperature out obtain insights into structural dynamic effects selected mutations. two these, C8 left unprotonated. Considerable local rearrangements occurred that not observed crystal structure, thus confirming N3-protonation molecule. We also investigated effect mutating U8, correlate experimental phylogenetic studies, changing G4 x C17 base-pair A4 U17 weaken sugar-edge positions 4 20 test models unfolding. indicate C26 base-triple junction is labile region pseudoknot. They provide roles other non-Watson-Crick base-pairs early stages pseudoknot, which must occur allow readthrough message ribosome. revealed several critical, highly ordered hydration sites close 100 % occupancies residency times individual molecules up 5 ns. Sodium cation coordination above 50 observed.