ArticlePLoS computational biology2011
Coherent conformational degrees of freedom as a structural basis for allosteric communication.
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 18 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
18 citing papers in PubMed.
- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Back in time to the Gly-rich prototype of the phosphate binding elementary function.Current research in structural biology · 2024Review
- A strategy for Cas13 miniaturization based on the structure and AlphaFold.Nature communications · 2023Article
- Explicit versus implicit consideration of binding partners in protein-protein complex to elucidate intrinsic dynamics.Biophysical reviews · 2022Review
- Allosteric perspective on the mutability and druggability of the SARS-CoV-2 Spike protein.Structure (London, England : 1993) · 2022Article
- Zinc-mediated conformational preselection mechanism in the allosteric control of DNA binding to the zinc transcriptional regulator (ZitR).Scientific reports · 2020Article
- AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations.Nucleic acids research · 2020Article
- Disorder driven allosteric control of protein activity.Current research in structural biology · 2020Article
- AlloMAPS: allosteric mutation analysis and polymorphism of signaling database.Nucleic acids research · 2019Article
- Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response.PLoS computational biology · 2018Article
- Nonlinear backbone torsional pair correlations in proteins.Scientific reports · 2016Article
- Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication.PLoS computational biology · 2016Article
- Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access.Proteomics · 2015Article
- A unified view of "how allostery works".PLoS computational biology · 2014Article
- Physicochemical mechanisms of protein regulation by phosphorylation.Frontiers in genetics · 2014Review
- SPACER: Server for predicting allosteric communication and effects of regulation.Nucleic acids research · 2013Article
- A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein.PLoS computational biology · 2013Article
- Direct observation of T4 lysozyme hinge-bending motion by fluorescence correlation spectroscopy.Biophysical journal · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are visited by the protein also in the absence of effector ligands. Previously, we developed the measure binding leverage to find sites where ligand binding can shift the conformational equilibrium of a protein. Binding leverage is calculated for a set of motion vectors representing independent conformational degrees of freedom. In this paper, to analyze allosteric communication between binding sites, we introduce the concept of leverage coupling, based on the assumption that only pairs of sites that couple to the same conformational degrees of freedom can be allosterically connected. We demonstrate how leverage coupling can be used to analyze allosteric communication in a range of enzymes (regulated by both ligand binding and post-translational modifications) and huge molecular machines such as chaperones. Leverage coupling can be calculated for any protein structure to analyze both biological and latent catalytic and regulatory sites.
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.