Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study.
Substrate phosphorylation by cAMP-dependent-protein kinase A (protein kinase A, PKA) has been studied extensively. Phosphoryl transfer was found to be fast, whereas ADP release was found to be the slow, rate-limiting step. There is also evidence that ADP release may be preceded by a partially rate-limiting conformational change. However, the atomic details of the conformational change and the mode of ADP release are difficult to obtain experimentally. In this work, we studied ADP release from PKA by carrying out molecular dynamics simulations with different pulling forces applied to the ligand. The detailed ADP release pathway and the associated conformational changes were analyzed. The ADP release process was found to involve a swinging motion with the phosphate of ADP anchored to the Gly-rich loop, so that the more buried adenine base and ribose ring came out before the phosphate. In contrast to the common belief that a hinge-bending motion was responsible for the opening of the ligand-binding cleft, our simulations showed that the small lobe exhibited a large amplitude "rocking" motion when the ligand came out. The largest conformational change of the protein was observed at about the first quarter time point along the release pathway. Two prominent intermediate states were observed in the release process.
Lu
Benzhuo
B
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0365, USA.
Wong
Chung F
CF
McCammon
J Andrew
JA
D000244:Adenosine Diphosphate / Q000737:chemistry*; D002384:Catalysis; D003198:Computer Simulation; D017868:Cyclic AMP-Dependent Protein Kinases / Q000737:chemistry*; D019143:Evolution, Molecular; D006860:Hydrogen Bonding; D007700:Kinetics; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry
D008024:Ligands; D021122:Protein Subunits; D000244:Adenosine Diphosphate; D017868:Cyclic AMP-Dependent Protein Kinases