title: Conformational equilibrium of N-myristoylated cAMP-dependent protein kinase A by molecular dynamics simulations.
abstract: The catalytic subunit of protein kinase A (PKA-C) is subject to several post- or cotranslational modifications that regulate its activity both spatially and temporally. Among those, N-myristoylation increases the kinase affinity for membranes and might also be implicated in substrate recognition and allosteric regulation. Here, we investigated the effects of N-myristoylation on the structure, dynamics, and conformational equilibrium of PKA-C using atomistic molecular dynamics simulations. We found that the myristoyl group inserts into the hydrophobic pocket and leads to a tighter packing of the A-helix against the core of the enzyme. As a result, the conformational dynamics of the A-helix are reduced and its motions are more coupled with the active site. Our simulations suggest that cation-π interactions among W30, R190, and R93 are responsible for coupling these motions. Two major conformations of the myristoylated N-terminus are the most populated: a long loop (LL conformation), similar to Protein Data Bank (PDB) entry  1CMK , and a helix-turn-helix structure (HTH conformation), similar to PDB entry  4DFX , which shows stronger coupling between the conformational dynamics observed at the A-helix and active site. The HTH conformation is stabilized by S10 phosphorylation of the kinase via ionic interactions between the protonated amine of K7 and the phosphate group on S10, further enhancing the dynamic coupling to the active site. These results support a role of N-myristoylation in the allosteric regulation of PKA-C.
authors.affiliation: Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cembran
authors.forename: Larry R
authors.initials: LR
authors.lastname: Masterson
authors.forename: Christopher L
authors.initials: CL
authors.lastname: McClendon
authors.forename: Susan S
authors.initials: SS
authors.lastname: Taylor
authors.forename: Jiali
authors.initials: J
authors.lastname: Gao
authors.forename: Gianluigi
authors.initials: G
authors.lastname: Veglia
mesh_terms: D020134:Catalytic Domain; D017868:Cyclic AMP-Dependent Protein Kinases / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D019814:Myristic Acid / Q000378:metabolism*; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D019814:Myristic Acid; D017868:Cyclic AMP-Dependent Protein Kinases