Integrated NMR and MD structure and dynamics of the stem–loop-II motif (s2m) from the Omicron variant of SARS-CoV-2

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FIGURE 5.
FIGURE 5.

NOE contacts and dihedral angles of the s2m_omicron loop nucleotides. (A) Interresidual NOEs within the loop of s2m_omicron. All atoms within 1 nt are shown in a dashed box, and each NOE is represented by a line between two atoms. (B) Dipole(H1′,C1′)-dipole(H6/8,C6/8)-CCRs determined via the Γ-HCN experiment plotted against the glycosidic angle (χ) based on the theoretical parametrization. Separate plots are shown for the purines (violet) and the pyrimidines (black, gray). Experimentally determined rates were fitted to the theoretical curves (solid lines) and are shown as dots. Nucleotide names are annotated. (C) 3J H-P couplings determined via the PFIDS experiment. Formula couplings are shown in orange, Formula couplings are shown in magenta, and Formula couplings are shown in red. A 10% error was estimated. (D) 3J C-P couplings determined via the qHCP experiment. Formula couplings are shown in blue, and Formula couplings are shown in green. A 5% error was estimated. (E) Determination of the backbone angle β for nucleotide U9 based on Formula couplings (magenta), Formula couplings (red), and Formula couplings (blue). (F) Determination of the backbone angle ε for nucleotide U9 based on Formula couplings (orange) and Formula couplings (green). Each curve corresponds to the experimentally determined coupling minus the theoretical value of the Karplus parametrization plotted against the angle. The sum of these curves is shown in black. The minimum is annotated and gives the angle that best fits all used couplings.

This Article

  1. RNA 31: 1766-1787