ArticleScientific reports2016
Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions.
Article in Scientific reports, 2016. 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, 37 citations in OpenAlex.
- Directional information flow as a tool for analyzing protein allostery.bioRxiv : the preprint server for biology · 2026Article
- Identification and characterization of binders to a cryptic and functional pocket in KRAS.Nature communications · 2025Article
- A protein dynamics-based deep learning model enhances predictions of fitness and epistasis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Deciphering allosteric mechanisms in KRAS activation: insights from GTP-induced conformational dynamics and interaction network reorganization.RSC advances · 2025Article
- Tumor-derived RHOA mutants interact with effectors in the GDP-bound state.Nature communications · 2024Article
- Reduced dynamic complexity allows structure elucidation of an excited state of KRASCommunications biology · 2023Article
- Mechanisms of isoform-specific residue influence on GTP-bound HRas, KRas, and NRas.Biophysical journal · 2022Article
- Granger Causality Analysis of Chignolin Folding.Journal of chemical theory and computation · 2022Article
- Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma.Biophysics reviews · 2022Review
- Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics.The journal of physical chemistry. B · 2021Article
- Dynamically encoded reactivity of Ras enzymes: opening new frontiers for drug discovery.Cancer metastasis reviews · 2020Review
- Comparative effects of oncogenic mutations G12C, G12V, G13D, and Q61H on local conformations and dynamics of K-Ras.Computational and structural biotechnology journal · 2020Article
- Phenotypic Switching of Naïve T Cells to Immune-Suppressive Treg-Like Cells by Mutant KRAS.Journal of clinical medicine · 2019Article
- The DNA walk and its demonstration of deterministic chaos-relevance to genomic alterations in lung cancer.Bioinformatics (Oxford, England) · 2019Article
- Oncogenic G12D mutation alters local conformations and dynamics of K-Ras.Scientific reports · 2019Article
- Catalytically Competent Non-transforming H-RASScientific reports · 2019Article
- Allosterism and signal transfer in DNA.Nucleic acids research · 2018Article
- The small GTPases K-Ras, N-Ras, and H-Ras have distinct biochemical properties determined by allosteric effects.The Journal of biological chemistry · 2017Article
- Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.PLoS computational biology · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
K-Ras is the most frequently mutated oncogene in human cancers, but there are still no drugs that directly target it in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting mutant K-Ras. However, despite extensive characterization, the mechanisms by which K-Ras residue fluctuations transfer allosteric regulatory information remain unknown. Understanding the direction of information flow can provide new mechanistic insights for K-Ras targeting. Here, we present a novel approach -conditional time-delayed correlations (CTC) - using the motions of all residue pairs of a protein to predict directionality in the allosteric regulation of the protein fluctuations. Analyzing nucleotide-dependent intrinsic K-Ras motions with the new approach yields predictions that agree with the literature, showing that GTP-binding stabilizes K-Ras motions and leads to residue correlations with relatively long characteristic decay times. Furthermore, our study is the first to identify driver-follower relationships in correlated motions of K-Ras residue pairs, revealing the direction of information flow during allosteric modulation of its nucleotide-dependent intrinsic activity: active K-Ras Switch-II region motions drive Switch-I region motions, while α-helix-3L7 motions control both. Our results provide novel insights for strategies that directly target mutant K-Ras.
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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.