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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.

SUBMITTER: Benitex Y 

PROVIDER: S-EPMC3095225 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature

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

Benitex Yulia Y   Baranger Anne M AM  

Journal of the American Chemical Society 20110301 11

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 si  ...[more]