title: Kinase conformations: a computational study of the effect of ligand binding.
abstract: Protein function is often controlled by ligand-induced conformational transitions. Yet, in spite of the increasing number of three-dimensional crystal structures of proteins in different conformations, not much is known about the driving forces of these transitions. As an initial step toward exploring the conformational and energetic landscape of protein kinases by computational methods, intramolecular energies and hydration free energies were calculated for different conformations of the catalytic domain of cAMP-dependent protein kinase (cAPK) with a continuum (Poisson) model for the electrostatics. Three protein kinase crystal structures for ternary complexes of cAPK with the peptide inhibitor PKI(5-24) and ATP or AMP-PNP were modeled into idealized intermediate and open conformations. Concordant with experimental observation, we find that the binding of PKI(5-24) is more effective in stabilizing the closed and intermediate forms of cAPK than ATP. PKI(5-24) seems to drive the final closure of the active site cleft from intermediate to closed state because ATP does not distinguish between these two states. Binding of PKI(5-24) and ATP is energetically additive.
authors.affiliation: Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0365, USA. vhelms@ucsd.edu
authors.forename: V
authors.initials: V
authors.lastname: Helms
authors.forename: J A
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D000255:Adenosine Triphosphate / Q000494:pharmacology; D003198:Computer Simulation; D017868:Cyclic AMP-Dependent Protein Kinases / Q000037:antagonists & inhibitors / Q000737:chemistry*; D004791:Enzyme Inhibitors / Q000494:pharmacology; D008024:Ligands; D008958:Models, Molecular; D010446:Peptide Fragments / Q000494:pharmacology; D011487:Protein Conformation / Q000187:drug effects
chemical_list: D004791:Enzyme Inhibitors; D008024:Ligands; D010446:Peptide Fragments; C518603:protein kinase inhibitor peptide (5-24); D000255:Adenosine Triphosphate; D017868:Cyclic AMP-Dependent Protein Kinases