Specificity of arginine binding by the Tetrahymena intron

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Abstract
L-Arginine competitively inhibits the reaction of GTP with the Tetrahymena ribosomal self-splicing intron. In order to define this RNA binding site for arginine, Ki''s have now been measured for numerous arginine-like competitive inhibitors. Detailed consideration of the Ki''s suggests a tripartite binding model. The dissociation constants of the inhibitor scan be consistently interpreted if the guanidino group of arginine binds in the GTP site by utilizing the H-bonds otherwise made to the N1-H and 2-NH2 of the guanine pyrimidine ring. The positive charge of the arginine guanidino group also enhances binding. A second requirement is for the precise length of the aliphatic arm connecting the guanidino with the .alpha.-carbon. The positive change of the .alpha.-amino group is the third feature essential to effective inhibition. The negative carboxyl charge of arginine inhibits binding, and the substitution on the .alpha.-carbon are probably oriented, with the .alpha.-amino group near the phosphate backbone of the RNA. This orientation contributes strongly to the L stereoselectivity of the amino acid site on the RNA. When spaced optimally, net contribution to the free energy of binding is of the same order for the guanidino group and for the arginine .alpha.-carbon substituents, but the guanidino apparently contributes more to binding free energy. Taken together, these obesrvations extend the previous binding model [Yarus, M. (1988) Science (Washington, D.C.) 240, 1751-1758]. The observed dependence of binding on universal characteristics of amino acids suggests that RNA binding sites with other amino acid specificities could exist.