title: A computational analysis of substrate binding strength by phosphorylase kinase and protein kinase A.
abstract: Protein kinases exhibit various degrees of substrate specificity. The large number of different protein kinases in the eukaryotic proteomes makes it impractical to determine the specificity of each enzyme experimentally. To test if it were possible to discriminate potential substrates from non-substrates by simple computational techniques, we analysed the binding enthalpies of modelled enzyme-substrate complexes and attempted to correlate it with experimental enzyme kinetics measurements. The crystal structures of phosphorylase kinase and cAMP-dependent protein kinase were used to generate models of the enzyme with a series of known peptide substrates and non-substrates, and the approximate enthalpy of binding assessed following energy minimization. We show that the computed enthalpies do not correlate closely with kinetic measurements, but the method can distinguish good substrates from weak substrates and non-substrates.
authors.affiliation: Department of Biochemistry and Molecular Biology/Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.
authors.forename: Ross I
authors.initials: RI
authors.lastname: Brinkworth
authors.forename: James
authors.initials: J
authors.lastname: Horne
authors.forename: Bostjan
authors.initials: B
authors.lastname: Kobe
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D000242:Cyclic AMP / Q000494:pharmacology; D017868:Cyclic AMP-Dependent Protein Kinases / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D010764:Phosphorylase Kinase / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D013379:Substrate Specificity; D013997:Time Factors
chemical_list: D000242:Cyclic AMP; D010764:Phosphorylase Kinase; D017868:Cyclic AMP-Dependent Protein Kinases