ArticleProtein science : a publication of the Protein Society2005
Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study.
Article in Protein science : a publication of the Protein Society, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
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- Dynamic allostery-based molecular workings of kinase:peptide complexes.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases.PLoS computational biology · 2016Article
- Synchronous opening and closing motions are essential for cAMP-dependent protein kinase A signaling.Structure (London, England : 1993) · 2014Article
- Dynamic architecture of a protein kinase.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Extracellular-regulated kinase 2 is activated by the enhancement of hinge flexibility.Journal of molecular biology · 2014Article
- Transitions to catalytically inactive conformations in EGFR kinase.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2.The journal of physical chemistry. B · 2011Article
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- A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase A.Biochemistry · 2009Article
- Ligand-induced global transitions in the catalytic domain of protein kinase A.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation.Protein science : a publication of the Protein Society · 2008Article
- Crystal Structures of the p21-activated kinases PAK4, PAK5, and PAK6 reveal catalytic domain plasticity of active group II PAKs.Structure (London, England : 1993) · 2007Article
- Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study.Protein science : a publication of the Protein Society · 2006Article
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3 authors.
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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.
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