ArticleJournal of chemical theory and computation2013
Specific Conformational States of Ras GTPase upon Effector Binding.
Article in Journal of chemical theory and computation, 2013. 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, 28 citations in OpenAlex.
- KRAS Inhibition in Pancreatic Ductal Adenocarcinoma.Journal of clinical medicine · 2026Review
- Exploring binding and allosteric energy landscapes for the KRAS interactions with effector proteins using Markov state modeling of conformational ensembles and allosteric network modeling.Protein science : a publication of the Protein Society · 2025Review
- Article
- Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics.The journal of physical chemistry. B · 2021Article
- Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain.PLoS computational biology · 2020Article
- Conformational and Dynamical Effects of Tyr32 Phosphorylation in K-Ras: Molecular Dynamics Simulation and Markov State Models Analysis.The journal of physical chemistry. B · 2019Article
- Oncogenic G12D mutation alters local conformations and dynamics of K-Ras.Scientific reports · 2019Article
- Article
- Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions.Scientific reports · 2017Article
- Analysis of correlated mutations in Ras G-domain.Bioinformation · 2017Article
- Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm.PLoS computational biology · 2015Article
- Allosteric effects of the oncogenic RasQ61L mutant on Raf-RBD.Structure (London, England : 1993) · 2015Article
- Src promotes GTPase activity of Ras via tyrosine 32 phosphorylation.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Lessons from computer simulations of Ras proteins in solution and in membrane.Biochimica et biophysica acta · 2013Review
- GSATools: analysis of allosteric communication and functional local motions using a structural alphabet.Bioinformatics (Oxford, England) · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To uncover the structural and dynamical determinants involved in the highly specific binding of Ras GTPase to its effectors, the conformational states of Ras in uncomplexed form and complexed to the downstream effectors Byr2, PI3Kγ, PLCε, and RalGDS were investigated using molecular dynamics and cross-comparison of the trajectories. The subtle changes in the dynamics and conformations of Ras upon effector binding require an analysis that targets local changes independent of global motions. Using a structural alphabet, a computational procedure is proposed to quantify local conformational changes. Positions detected by this approach were characterized as either specific for a particular effector, specific for an effector domain type, or as effector unspecific. A set of nine structurally connected residues (Ras residues 5-8, 32-35, 39-42, 55-59, 73-78, and 161-165), which link the effector binding site to the distant C-terminus, changed dynamics upon effector binding, indicating a potential effector-unspecific signaling route within the Ras structure. Additional conformational changes were detected along the N-terminus of the central β-sheet. Besides the Ras residues at the effector interface (e.g., D33, E37, D38, and Y40), which adopt effector-specific local conformations, the binding signal propagates from the interface to distant hot-spot residues, in particular to Y5 and D57. The results of this study reveal possible conformational mechanisms for the stabilization of the active state of Ras upon downstream effector binding and for the structural determinants responsible for effector specificity.
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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.