Structure and function of ribonuclease A binding subsites

Ribonuclease A binds nucleic acids through multiple electrostatic interactions between the phosphates of the polynucleotide and the positive groups (side chains of lysines and arginines) of the protein subsites. The bases only play a significant role in the binding at the active site. The active centre p1R1B1 sites determine the specificity of the catalytic cleavage. The phosphate-binding subsites p2 (Lys-7 and Arg-10), p1 (Lys-41, His-12 and His-119) and p0 (Lys-66) are essential for an effective catalysis and are conserved in all mammalian pancreatic ribonucleases. Additional phosphate-binding subsites confer further catalytic efficiency, probably by avoiding non-productive binding. The minimum chain size for optimum catalysis is probably longer than six or seven nucleotides. The full occupancy of binding sites by the long chain polynucleotides would explain the preference of the enzyme for these substrates. The multiplicity of binding subsites is responsible for the helix-destabilizing activity of ribonuclease A. Its capacity for destroying the secondary structure of single-stranded nucleic acids may be of importance for the complete hydrolysis of RNA in the digestive tract. A large variety of proteins, with very different structures and functions, interact with nucleic acids. An analysis of their binding properties shows that there is no general model for protein-nucleic acid interaction. However, the vast amount of work on the ribonuclease A binding subsites should serve as a model for the study of the binding properties of many other proteins that recognize nucleic acids.