ArticleThe journal of physical chemistry. B2012
αC helix as a switch in the conformational transition of Src/CDK-like kinase domains.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Nicotinonitriles-based therapeutics as versatile pharmacophores in rational anticancer drug design.RSC advances · 2026Review
- Article
- The stress-activated kinase p38 mediates non-canonical activation of Src and tyrosine phosphorylation of the adapter protein TAB1.The Journal of biological chemistry · 2026Article
- Elucidating the Molecular Mechanism of 3D1 Antibody Binding to a Swine Enteric Coronavirus Antigen.Viruses · 2026Article
- Structure-Based Design of Potent and Selective MerTK Inhibitors by Modulating the Conformation of αC Helix.Journal of medicinal chemistry · 2025Article
- Dimerization Promotes PKR Activation by Modulating Energetics of αC Helix Conversion between Active and Inactive Conformations.The journal of physical chemistry. B · 2024Article
- Inhibitor Trapping in Kinases.International journal of molecular sciences · 2024Article
- Structure and regulation of full-length human leucine-rich repeat kinase 1.Nature communications · 2023Article
- Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation Pathway.The journal of physical chemistry. B · 2023Article
- Validation of an Allosteric Binding Site of Src Kinase Identified by Unbiased Ligand Binding Simulations.Journal of molecular biology · 2022Article
- A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.Journal of chemical theory and computation · 2022Article
- TYROSINE KINASES: COMPLEX MOLECULAR SYSTEMS CHALLENGING COMPUTATIONAL METHODOLOGIES.The European physical journal. B · 2021Article
- Evolution of CDK1 Paralog Specializations in a Lineage With Fast Developing Planktonic Embryos.Frontiers in cell and developmental biology · 2021Article
- All-atom adaptively biased path optimization of Src kinase conformational inactivation: Switched electrostatic network in the concerted motion of αC helix and the activation loop.The Journal of chemical physics · 2020Article
- Substrate binding to Src: A new perspective on tyrosine kinase substrate recognition from NMR and molecular dynamics.Protein science : a publication of the Protein Society · 2020Article
- How Electrostatic Coupling Enables Conformational Plasticity in a Tyrosine Kinase.Journal of the American Chemical Society · 2019Article
- MARK4 protein can explore the active-like conformations in its non-phosphorylated state.Scientific reports · 2019Article
- Protein Conformational Transitions from All-Atom Adaptively Biased Path Optimization.Journal of chemical theory and computation · 2018Article
- Towards simple kinetic models of functional dynamics for a kinase subfamily.Nature chemistry · 2018Article
- Redefining the Protein Kinase Conformational Space with Machine Learning.Cell chemical biology · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
One mechanism of regulating the catalytic activity of protein kinases is through conformational transitions. Despite great diversity in the structural changes involved in the transitions, a certain set of changes within the kinase domain (KD) has been observed for many kinases including Src and CDK2. We investigated this conformational transition computationally to identify the topological features that are energetically critical to the transition. Results from both molecular dynamics sampling and transition path optimization highlight the displacement of the αC helix as the major energy barrier, mediating the switch of the KD between the active and down-regulated states. The critical role of the αC helix is noteworthy by providing a rationale for a number of activation and deactivation mechanisms known to occur in cells. We find that kinases with the αC helix displacement exist throughout the kinome, suggesting that this feature may have emerged early in evolution.
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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.