ArticlePLoS computational biology2011
Nucleotide binding switches the information flow in ras GTPases.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 40 citations in OpenAlex.
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- Insight into structural dynamics involved in activation mechanism of full length KRAS wild type and P-loop mutants.Heliyon · 2024Article
- The potential therapeutic roles of Rho GTPases in substance dependence.Frontiers in molecular neuroscience · 2023Article
- Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles.Computational and structural biotechnology journal · 2023Article
- Structural communication between the GTPase Sec4p and its activator Sec2p: Determinants of GEF activity and early deformations to nucleotide release.Computational and structural biotechnology journal · 2022Article
- Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics.The journal of physical chemistry. B · 2021Article
- Comparative MD simulations and advanced analytics based studies on wild-type and hot-spot mutant A59G HRas.PloS one · 2020Article
- Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.PLoS computational biology · 2019Review
- Evolutionary-Conserved Allosteric Properties of Three Neuronal Calcium Sensor Proteins.Frontiers in molecular neuroscience · 2019Article
- Comparative structural dynamic analysis of GTPases.PLoS computational biology · 2018Article
- The K-Ras, N-Ras, and H-Ras Isoforms: Unique Conformational Preferences and Implications for Targeting Oncogenic Mutants.Cold Spring Harbor perspectives in medicine · 2018Review
- The Evolutionary Landscape of Dbl-Like RhoGEF Families: Adapting Eukaryotic Cells to Environmental Signals.Genome biology and evolution · 2017Article
- Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions.Scientific reports · 2016Article
- Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view.Chemical Society reviews · 2016Review
- The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B.Scientific reports · 2016Article
- Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteins.Bioinformatics (Oxford, England) · 2015Article
- Probing the wild-type HRas activation mechanism using steered molecular dynamics, understanding the energy barrier and role of water in the activation.European biophysics journal : EBJ · 2014Article
- Lessons from computer simulations of Ras proteins in solution and in membrane.Biochimica et biophysica acta · 2013Review
- Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases.PLoS computational biology · 2013Article
- The role of conserved waters in conformational transitions of Q61H K-ras.PLoS computational biology · 2012Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
The Ras superfamily comprises many guanine nucleotide-binding proteins (G proteins) that are essential to intracellular signal transduction. The guanine nucleotide-dependent intrinsic flexibility patterns of five G proteins were investigated in atomic detail through Molecular Dynamics simulations of the GDP- and GTP-bound states (S(GDP) and S(GTP), respectively). For all the considered systems, the intrinsic flexibility of S(GDP) was higher than that of S(GTP), suggesting that Guanine Exchange Factor (GEF) recognition and nucleotide switch require higher amplitude motions than effector recognition or GTP hydrolysis. Functional mode, dynamic domain, and interaction energy correlation analyses highlighted significant differences in the dynamics of small G proteins and Gα proteins, especially in the inactive state. Indeed, S(GDP) of Gα(t), is characterized by a more extensive energy coupling between nucleotide binding site and distal regions involved in GEF recognition compared to small G proteins, which attenuates in the active state. Moreover, mechanically distinct domains implicated in nucleotide switch could be detected in the presence of GDP but not in the presence of GTP. Finally, in small G proteins, functional modes are more detectable in the inactive state than in the active one and involve changes in solvent exposure of two highly conserved amino acids in switches I and II involved in GEF recognition. The average solvent exposure of these amino acids correlates in turn with the rate of GDP release, suggesting for them either direct or indirect roles in the process of nucleotide switch. Collectively, nucleotide binding changes the information flow through the conserved Ras-like domain, where GDP enhances the flexibility of mechanically distinct portions involved in nucleotide switch, and favors long distance allosteric communication (in Gα proteins), compared to GTP.
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