Specificity of arginine binding by the Tetrahymena intron.

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 inhibitors can 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 charge of the alpha-amino group is the third feature essential to effective inhibition. The negative carboxyl charge of arginine inhibits binding, and the substituents 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 observations 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.

[1]  H. E. Shiver,et al.  THE EQUILIBRIUM BETWEEN CREATINE AND CREATININE, IN AQUEOUS SOLUTION. THE EFFECT OF HYDROGEN ION , 1925 .

[2]  R. K. Cannan,et al.  The creatine-creatinine equilibrium. The apparent dissociation constants of creatine and creatinine. , 1928, The Biochemical journal.

[3]  Allende Cc,et al.  PURIFICATION AND SUBSTRATE SPECIFICITY OF ARGINYL-RIBONUCLEIC ACID SYNTHETASE FROM RAT LIVER. , 1964 .

[4]  G. L. Kenyon,et al.  Tautomeric preferences among glycocyamidines , 1971 .

[5]  T. Cech,et al.  Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena , 1982, Cell.

[6]  T. Cech,et al.  The intervening sequence excised from the ribosomal RNA precursor of Tetrahymena contains a 5-terminal guanosine residue not encoded by the DNA. , 1982, Nucleic acids research.

[7]  T. Cech,et al.  Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage–ligation reaction , 1983, Nature.

[8]  T. Cech,et al.  Specific interaction between the self-splicing RNA of Tetrahymena and its guanosine substrate: implications for biological catalysis by RNA , 1984, Nature.

[9]  T. Cech,et al.  Ribozyme inhibitors: deoxyguanosine and dideoxyguanosine are competitive inhibitors of self-splicing of the Tetrahymena ribosomal ribonucleic acid precursor. , 1986, Biochemistry.

[10]  A. Weiner,et al.  tRNA-like structures tag the 3' ends of genomic RNA molecules for replication: implications for the origin of protein synthesis. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[11]  R. Cedergren,et al.  A mechanism for the RNA‐catalyzed formation of 5′‐phosphates The origin of nucleases , 1987, FEBS letters.

[12]  J. Ponder,et al.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.

[13]  M Yarus,et al.  A specific amino acid binding site composed of RNA. , 1988, Science.