ArticleJournal of chemical theory and computation2014
Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 29 citations in OpenAlex.
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- Multiplexed molecular profiling of lung cancer with malignant pleural effusion using next generation sequencing in Chinese patients.Oncology letters · 2020Article
- Structural Characterization of the Aurora Kinase B "DFG-flip" Using Metadynamics.The AAPS journal · 2019Article
- Review
- Probing the Druggablility on the Interface of the Protein-Protein Interaction and Its Allosteric Regulation Mechanism on the Drug Screening for the CXCR4 Homodimer.Frontiers in pharmacology · 2019Article
- Altered conformational landscape and dimerization dependency underpins the activation of EGFR byProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Redefining the Protein Kinase Conformational Space with Machine Learning.Cell chemical biology · 2018Article
- Conformational landscape of the epidermal growth factor receptor kinase reveals a mutant specific allosteric pocket.Chemical science · 2018Article
- Structural Features and Ligand Selectivity for 10 Intermediates in the Activation Process of βACS omega · 2017Article
- Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins.Science signaling · 2017Article
- Dynamic, structural and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation.Chemical science · 2017Article
- Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4-protein interaction.Physical chemistry chemical physics : PCCP · 2015Article
- Statistical analysis of EGFR structures' performance in virtual screening.Journal of computer-aided molecular design · 2015Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
The epidermal growth factor receptor (EGFR) is aberrantly activated in various cancer cells and an important target for cancer treatment. Deep understanding of EGFR conformational changes between the active and inactive states is of pharmaceutical interest. Here we present a strategy combining multiply targeted molecular dynamics simulations, unbiased molecular dynamics simulations, and Bayesian clustering to investigate transition pathways during the activation/inactivation process of EGFR kinase domain. Two distinct pathways between the active and inactive forms are designed, explored, and compared. Based on Bayesian clustering and rough two-dimensional free energy surfaces, the energy-favorable pathway is recognized, though DFG-flip happens in both pathways. In addition, another pathway with different intermediate states appears in our simulations. Comparison of distinct pathways also indicates that disruption of the Lys745-Glu762 interaction is critically important in DFG-flip while movement of the A-loop significantly facilitates the conformational change. Our simulations yield new insights into EGFR conformational transitions. Moreover, our results verify that this approach is valid and efficient in sampling of protein conformational changes and comparison of distinct pathways.
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Registered trials
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