ArticleThe journal of physical chemistry. B2016
Computational Equilibrium Thermodynamic and Kinetic Analysis of K-Ras Dimerization through an Effector Binding Surface Suggests Limited Functional Role.
Article in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed.
- RAS-membrane interaction and oligomerization: there is more than meets the eye.Biochemical Society transactions · 2025Review
- Membrane-Driven Dimerization of the Peripheral Membrane Protein KRAS: Implications for Downstream Signaling.International journal of molecular sciences · 2024Review
- Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure.Journal of chemical theory and computation · 2023Article
- α4-α5 Helices on Surface of KRAS Can Accommodate Small Compounds That Increase KRAS Signaling While Inducing CRC Cell Death.International journal of molecular sciences · 2023Article
- Review
- Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- First Principles Calculation of Protein-Protein Dimer Affinities of ALS-Associated SOD1 Mutants.Frontiers in molecular biosciences · 2022Article
- Oncogenic KRAS G12D mutation promotes dimerization through a second, phosphatidylserine-dependent interface: a model for KRAS oligomerization.Chemical science · 2021Article
- Review
- Raf promotes dimerization of the Ras G-domain with increased allosteric connections.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- RAS Nanoclusters: Dynamic Signaling Platforms Amenable to Therapeutic Intervention.Biomolecules · 2021Review
- Approaches to inhibiting oncogenic K-Ras.Small GTPases · 2021Review
- Molecular Dynamics Simulation of Lipid-Modified Signaling Proteins.Methods in molecular biology (Clifton, N.J.) · 2021Article
- RAS Nanoclusters Selectively Sort Distinct Lipid Headgroups and Acyl Chains.Frontiers in molecular biosciences · 2021Review
- Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again.Biomolecules · 2020Review
- Two Distinct Structures of Membrane-Associated Homodimers of GTP- and GDP-Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement.Angewandte Chemie (International ed. in English) · 2020Article
- Probing the Conformational and Energy Landscapes of KRAS Membrane Orientation.The journal of physical chemistry. B · 2019Article
- 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
- Ras and the Plasma Membrane: A Complicated Relationship.Cold Spring Harbor perspectives in medicine · 2018Review
- Modeling and subtleties of K-Ras and Calmodulin interaction.PLoS computational biology · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Dimer formation is believed to have a substantial impact on regulating K-Ras function. However, the evidence for dimerization and the molecular details of the process are scant. In this study, we characterize a K-Ras pseudo-C2-symmetric dimerization interface involving the effector interacting β2-strand. We used structure matching and all-atom molecular dynamics (MD) simulations to predict, refine, and investigate the stability of this interface. Our MD simulation suggested that the β2-dimer is potentially stable and remains relatively close to its initial conformation due to the presence of a number of hydrogen bonds, ionic salt bridges, and other favorable interactions. We carried out potential of mean force calculations to determine the relative binding strength of the interface. The results of these calculations indicated that the β2 dimerization interface provides a weak binding free energy in solution and a dissociation constant that is close to 1 mM. Analyses of Brownian dynamics simulations suggested an association rate kon ≈ 10(5)-10(6) M(-1) s(-1). Combining these observations with available literature data, we propose that formation of auto-inhibited β2 K-Ras dimers is possible but its fraction in cells is likely very small under normal physiologic conditions.
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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.