ArticleProceedings of the National Academy of Sciences of the United States of America2012
Structure-based model of allostery predicts coupling between distant sites.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 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
86 citing papers in PubMed, 164 citations in OpenAlex.
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- Article
- Structure and function of the ROR2 cysteine-rich domain in vertebrate noncanonical WNT5A signaling.eLife · 2024Article
- G Protein Activation Occurs via a Largely Universal Mechanism.The journal of physical chemistry. B · 2024Article
- Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.Nature structural & molecular biology · 2024Article
- 14-3-3 protein inhibits CaMKK1 by blocking the kinase active site with its last two C-terminal helices.Protein science : a publication of the Protein Society · 2023Article
- Predicting allosteric sites using fast conformational sampling as guided by coarse-grained normal modes.The Journal of chemical physics · 2023Article
- Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches.Journal of chemical information and modeling · 2023Review
- Comparative Protein Structural Network Analysis Reveals C-Terminal Tail Phosphorylation Structural Communication Fingerprint inThe journal of physical chemistry. B · 2023Article
- Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution.Methods in enzymology · 2023Article
- Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade.eLife · 2022Article
- Strengthening of enterococcal biofilms by Esp.PLoS pathogens · 2022Article
- Conformational buffering underlies functional selection in intrinsically disordered protein regions.Nature structural & molecular biology · 2022Article
- Role of water-bridged interactions in metal ion coupled protein allostery.PLoS computational biology · 2022Article
- Characterization of the High-Affinity Fuzzy Complex between the Disordered Domain of the E7 Oncoprotein from High-Risk HPV and the TAZ2 Domain of CBP.Biochemistry · 2021Article
- Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism.Nature communications · 2021Article
- ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules.Nucleic acids research · 2021Article
- Article
- Heparin-mediated dimerization of follistatin.Experimental biology and medicine (Maywood, N.J.) · 2021Article
- Quantification of the Resilience and Vulnerability of HIV-1 Native Glycan Shield at Atomistic Detail.iScience · 2020Article
26 more citing papers are in PubMed but not listed here.
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 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Allostery is a phenomenon that couples effector ligand binding at an allosteric site to a structural and/or dynamic change at a distant regulated site. To study an allosteric transition, we vary the size of the allosteric site and its interactions to construct a series of energy landscapes with pronounced minima corresponding to both the effector bound and unbound crystal structures. We use molecular dynamics to sample these landscapes. The degree of perturbation by the effector, modeled by the size of the allosteric site, provides an order parameter for allostery that allows us to determine how microscopic motions give rise to commonly discussed macroscopic mechanisms: (i) induced fit, (ii) population shift, and (iii) entropy driven. These mechanisms involve decreasing structural differences between the effector bound and unbound populations. A metric (ligand-induced cooperativity) can measure how cooperatively a given regulated site responds to effector binding and therefore what kind of allosteric mechanism is involved. We apply the model to three proteins with experimentally characterized transitions: (i) calmodulin-GFP Ca(2+) sensor protein, (ii) maltose binding protein, and (iii) CSL transcription factor. Remarkably, the model is able to reproduce allosteric motion and predict coupling in a manner consistent with experiment.
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.