Paper Citing NAMD - Abstract
Lu, B.Z.; Wong, C.F.; Mccammon, J.A.
Release of ADP from the catalytic subunit of protein kinase A: A molecular dynamics simulation study
PROTEIN SCIENCE, 14:159-168, JAN 2005
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.
