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Published online before print March 7, 2006, 10.1110/ps.051852306
Protein Science (2006), 15:672-683. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: A theoretical study

Yuhui Cheng1, Yingkai Zhang2 and J. Andrew McCammon1

1 Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365, USA
2 Department of Chemistry, New York University, New York, New York 10003, USA

(RECEIVED September 15, 2005; FINAL REVISION November 20, 2005; ACCEPTED December 26, 2005)

Phosphorylation mediates the function of many proteins and enzymes. In the catalytic subunit of cAMP-dependent protein kinase, phosphorylation of Thr 197 in the activation loop strongly influences its catalytic activity. In order to provide theoretical understanding about this important regulatory process, classical molecular dynamics simulations and ab initio QM/MM calculations have been carried out on the wild-type PKA–Mg2 ATP–substrate complex and its dephosphorylated mutant, T197A. It was found that pThr 197 not only facilitates the phosphoryl transfer reaction by stabilizing the transition state through electrostatic interactions but also strongly affects its essential protein dynamics as well as the active site conformation.

Keywords: protein kinase A (PKA); phosphorylation of Thr 197; molecular dynamics; QM/MM calculations; collective motion


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