Control of the stability of a protein-RNA complex by the position of fluorine in a base analogue

Abstract

The effects of modifying the electronic characteristics of nonpolar base analogues substituted at positions involved in stacking interactions between SL2 RNA and the U1A protein are described. A surprisingly large difference in the stability between complexes formed with base analogues that differ only in the position of substitution of a single fluorine atom is observed. The results of high-level ab initio calculations of the interactions between the nonpolar base analogue and the amino acid side chain correlate with the experimentally observed trends in complex stability, which suggests that changes in stacking interactions that result from varying the position and degree of fluorine substitution contribute to the effects of fluorine substitution on the stability of the U1A-SL2 RNA complex.

Figure 1

(a) The U1A-SL2 RNA complex from the X-ray cocrystal structure. (b) SL2 RNA. (c) An expanded view of the structure.

Figure 2

Phenyl and fluorinated phenyl base analogs. Below each structure is shown calculated electrostatic surface potentials for each base or base analog. The electrostatic surface potentials were calculated for structures in which R=Me, using MP2 6-31G*(0.25)//B3LYP6-31G(d).