title: Mapping the Hydrogen Bond Networks in the Catalytic Subunit of Protein Kinase A Using H/D Fractionation Factors.
abstract: Protein kinase A is a prototypical phosphoryl transferase, sharing its catalytic core (PKA-C) with the entire kinase family. PKA-C substrate recognition, active site organization, and product release depend on the enzyme's conformational transitions from the open to the closed state, which regulate its allosteric cooperativity. Here, we used equilibrium nuclear magnetic resonance hydrogen/deuterium (H/D) fractionation factors (φ) to probe the changes in the strength of hydrogen bonds within the kinase upon binding the nucleotide and a pseudosubstrate peptide (PKI5-24). We found that the φ values decrease upon binding both ligands, suggesting that the overall hydrogen bond networks in both the small and large lobes of PKA-C become stronger. However, we observed several important exceptions, with residues displaying higher φ values upon ligand binding. Notably, the changes in φ values are not localized near the ligand binding pockets; rather, they are radiated throughout the entire enzyme. We conclude that, upon ligand and pseudosubstrate binding, the hydrogen bond networks undergo extensive reorganization, revealing that the open-to-closed transitions require global rearrangements of the internal forces that stabilize the enzyme's fold.
authors.affiliation: †Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.
authors.forename: Geoffrey C
authors.initials: GC
authors.lastname: Li
authors.affiliation: ‡Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States.
authors.forename: Atul K
authors.initials: AK
authors.lastname: Srivastava
authors.affiliation: †Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.
authors.forename: Jonggul
authors.initials: J
authors.lastname: Kim
authors.affiliation: §Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States.
authors.forename: Susan S
authors.initials: SS
authors.lastname: Taylor
authors.affiliation: †Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.|‡Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States.
authors.forename: Gianluigi
authors.initials: G
authors.lastname: Veglia
mesh_terms: D000244:Adenosine Diphosphate / Q000378:metabolism; D000818:Animals; D020134:Catalytic Domain; D017868:Cyclic AMP-Dependent Protein Kinases / Q000737:chemistry* / Q000378:metabolism; D003903:Deuterium / Q000032:analysis; D006859:Hydrogen / Q000032:analysis; D006860:Hydrogen Bonding; D051379:Mice; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D000244:Adenosine Diphosphate; D006859:Hydrogen; D003903:Deuterium; D017868:Cyclic AMP-Dependent Protein Kinases