ArticleThe journal of physical chemistry. B2011
Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 42 citations in OpenAlex.
- Interplay of Ser273 Phosphorylation and K268 and K293 Acetylation in PPARγ: Implications for PPARγ Activation.Proteins · 2026Article
- The priming phosphorylation of KaiC is activated by the release of its autokinase autoinhibition.PNAS nexus · 2025Article
- Decoding Drug Discovery: Exploring A-to-Z In Silico Methods for Beginners.Applied biochemistry and biotechnology · 2025Review
- CDK9: A Comprehensive Review of Its Biology, and Its Role as a Potential Target for Anti-Cancer Agents.Frontiers in oncology · 2021Review
- Review
- Kinase Activation by Small Conformational Changes.Journal of chemical information and modeling · 2020Article
- Studying the phosphoryl transfer mechanism of theChemical science · 2019Article
- Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: A QM/MM study.PloS one · 2019Article
- Article
- DNA cytosine methylation: structural and thermodynamic characterization of the epigenetic marking mechanism.Biochemistry · 2013Article
- Why nature really chose phosphate.Quarterly reviews of biophysics · 2013Review
- Revelation of a catalytic calcium-binding site elucidates unusual metal dependence of a human apyrase.Journal of the American Chemical Society · 2012Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensible role in cellular signaling, and their malfunctioning is implicated in many diseases. A better understanding of the catalytic mechanism will help design novel and effective mechanism-based inhibitors of these enzymes. In this work, ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a dissociative, metaphosphate-like structure, stabilized by the Mg(2+) ion and several hydrogen bonds. The calculated free-energy barrier is consistent with experimental values. Implications of our results in this and other protein kinases are discussed.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.