Protein phosphorylation of Thr-197 in the activation loop of the catalytic subunit (C-subunit) of cAMP-dependent protein kinase (PKA) is an essential step for its proper biological function. In order to explore the influences triggered by phosphorylation of Thr197, comparative molecular dynamics (MD) simulation studies with or without phosphate group on Thr-197 and Ser-338 were performed on the complex of C-subunit bound to ATP and two Mg 2+ ions (C/Mg2ATP complex) and on the complex of C-subunit bound to substrate peptide (C/substrate complex). The results present a decreased flexibility of the activation loop in the phosphorylated state, because of several critical interactions formed by the phosphorylated Thr-197 with His-87, Arg-165, Lys-189 and Thr-195. The unphosphorylated activation loop does not block the substrate-binding site, which is in good agreement with experimental result. In unphosphorylated state, the crucial interaction between Thr-197 and His-87 of C-helix does not exist, which eventually makes glycine-rich loop run away from its original position and displaces the phosphates group of ATP. We suggest that the reduction in rate of phosphoryl transfer may be caused by the displacement of c-phosphate group that demolish phosphoryl transfer in-line mechanism. 2006 Elsevier B.V. All rights reserved.