Determinants of multi-site phosphorylation of peptide analogues of ribosomal protein S6 by novel protease-activated protein kinases

The substrate specificity determinants of a protease-activated protein kinase from rat liver, termined PAK-1, have been investigated using peptide analogues of the ribosomal protein S6 sequence: Ala229-Lys-Arg-Arg-Arg-Leu-Ser-Ser-Leu-Arg-Ala-Ser-Thr-Ser-Lys- Ser244. Low peptide substrate Km's and a preference for Ser236 were attributed to a combination of sequence determinants located in the vicinity of this site. Thus, Km's are increased appreciably with analogues in which the N-terminal cluster of basic residues is reduced or where alanine is substituted for Arg238. Even more dramatic effects are elicited by alanine substitution of one of the adjacent serine residues, resulting in 20-fold to 800-fold increases in the Km's for the [Ala235] and [Ala236] S6(229-239) variants, respectively. Arg238 is the major specificity determinant of the Ser236 site, with little detectable phosphorylation of Ser236 occurring in the [Ala238] S6(229-239) substrate. Ser235 phosphorylation is also selectively enhanced by the addition of N-terminal basic residues to the Arg-Arg-Leu-Ser-Ser-Leu-Arg-Ala analogue. Finally, multiple phosphorylation events are influenced by negative cooperativity between the Ser235 and Ser236 sites and positive cooperativity between the Ser236 and Ser240 sites. The general S6 peptide substrate determinants for liver PAK-1 resembled those for brain protein kinase C and another major liver PAK, termed PAK-2. However, subtle differences observed between the kinetic properties with individual S6 peptide substrates distinguished PAK-1 from the other enzymes. More striking differences were observed between the liver PAKs and cyclic AMP-dependent protein kinase (cAK), particularly with respect to the cAK's relatively poor S6 peptide substrate kinetics, its preference for Ser235 and its ability to more extensively phosphorylate multiple sites in the S6 peptides