ArticlePLoS computational biology2011
Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members.
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 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed, 56 citations in OpenAlex.
- Negative allosteric regulation of protein arginine methyltransferase 1 (PRMT1) through half-of-sites reactivity.The Journal of biological chemistry · 2026Article
- Global comparative structural analysis of responses to protein phosphorylation.Nature communications · 2025Article
- An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1.NPJ systems biology and applications · 2025Article
- The crystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor.PloS one · 2025Article
- Article
- Biophysical Insight into the SARS-CoV2 Spike-ACE2 Interaction and Its Modulation by Hepcidin through a Multifaceted Computational Approach.ACS omega · 2022Article
- Structural dynamics in the evolution of a bilobed protein scaffold.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions.Molecules (Basel, Switzerland) · 2021Article
- Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.Biophysical journal · 2020Article
- Structural Analysis of the Glycoprotein Complex Avidin by Tandem-Trapped Ion Mobility Spectrometry-Mass Spectrometry (Tandem-TIMS/MS).Analytical chemistry · 2020Article
- Both intra and inter-domain interactions define the intrinsic dynamics and allosteric mechanism in DNMT1s.Computational and structural biotechnology journal · 2020Article
- Dynamic properties of oligomers that characterize low-frequency normal modes.Biophysics and physicobiology · 2019Article
- Dissecting conformational changes in APP's transmembrane domain linked to ε-efficiency in familial Alzheimer's disease.PloS one · 2018Article
- Gaussian network model can be enhanced by combining solvent accessibility in proteins.Scientific reports · 2017Article
- Article
- Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS.Journal of chemical theory and computation · 2017Article
- Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case.BioMed research international · 2017Article
- Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes.PLoS computational biology · 2016Article
- Identification of Hot Spots in Protein Structures Using Gaussian Network Model and Gaussian Naive Bayes.BioMed research international · 2016Article
- Collisional unfolding of multiprotein complexes reveals cooperative stabilization upon ligand binding.Protein science : a publication of the Protein Society · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Oligomerization is a functional requirement for many proteins. The interfacial interactions and the overall packing geometry of the individual monomers are viewed as important determinants of the thermodynamic stability and allosteric regulation of oligomers. The present study focuses on the role of the interfacial interactions and overall contact topology in the dynamic features acquired in the oligomeric state. To this aim, the collective dynamics of enzymes belonging to the amino acid kinase family both in dimeric and hexameric forms are examined by means of an elastic network model, and the softest collective motions (i.e., lowest frequency or global modes of motions) favored by the overall architecture are analyzed. Notably, the lowest-frequency modes accessible to the individual subunits in the absence of multimerization are conserved to a large extent in the oligomer, suggesting that the oligomer takes advantage of the intrinsic dynamics of the individual monomers. At the same time, oligomerization stiffens the interfacial regions of the monomers and confers new cooperative modes that exploit the rigid-body translational and rotational degrees of freedom of the intact monomers. The present study sheds light on the mechanism of cooperative inhibition of hexameric N-acetyl-L-glutamate kinase by arginine and on the allosteric regulation of UMP kinases. It also highlights the significance of the particular quaternary design in selectively determining the oligomer dynamics congruent with required ligand-binding and allosteric activities.
Indexed as
Identifiers
What OpenQuestion holds
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.