Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch

Eichhorn, Catherine D.; Feng, Jun; Suddala, Krishna C.; Walter, Nils G.; Brooks, Charles L.; Al-Hashimi, Hashim M.

where P 2 is the second order Legendre polynomial and * is the unit vector along the C-H dipole. Additionally, from the atomic coordinates we constructed the RDC values by first orienting an idealized A-form ssRNA helix into the principal axis system determined from the order tensor analysis of the experimental RDCs. Each frame of the trajectory was superimposed with this ideal helix followed by calculating the average of , 3 cos 2 À1 D E , where is the angle between a given bond vector (e.g. C1 0 H1 0 ) and the z-axis. The RDC values were then scaled by À82/r 3 , in which r is the C-H bond length and a factor of À82 is applied to shift the computed RDCs to the same scale as the NMR values. The average structure of the ssRNA was calculated as the structure with the minimal root-mean-square deviations from all RNA conformations in the 5 ns REMD trajectory.