NDLI: Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study.

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Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study.

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Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Lu, Benzhuo Wong, Chung F. McCammon, J. Andrew
Description	Country affiliation: United States Author Affiliation: Lu B ( Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0365, USA.)
Abstract	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.
ISSN	09618368
e-ISSN	1469896X
Journal	Protein Science
Issue Number	1
Volume Number	14
Language	English
Publisher	Wiley-Blackwell (on behalf of The Protein Society)
Publisher Date	2005-01-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Adenosine Diphosphate Chemistry Computer Simulation Cyclic Amp-dependent Protein Kinases Models, Chemical Catalysis Evolution, Molecular Hydrogen Bonding Kinetics Ligands Models, Molecular Protein Conformation Protein Structure, Tertiary Protein Subunits Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s. Research Support, U.s. Gov't, P.h.s. Discipline Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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