ArticleJournal of molecular biology2011
Side-chain conformational changes upon Protein-Protein Association.
Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 31 citations in OpenAlex.
- Quantification of Conformational Changes of Kinase Regulators, Kinases, and Regulator-Kinase Complexes Using the TSR Algorithm.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Understanding the Impacts of Conformational Dynamics on the Regulation of Protein-Protein Association by a Multiscale Simulation Method.Journal of chemical theory and computation · 2020Article
- How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking.Proteins · 2020Article
- Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking.Journal of computer-aided molecular design · 2018Article
- Pushing the Backbone in Protein-Protein Docking.Structure (London, England : 1993) · 2016Article
- Side-Chain Conformational Preferences Govern Protein-Protein Interactions.Journal of the American Chemical Society · 2016Article
- Article
- Article
- Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource.BMC bioinformatics · 2015Article
- Protein-protein docking: from interaction to interactome.Biophysical journal · 2014Review
- Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs).Chemical reviews · 2014Review
- A functional feature analysis on diverse protein-protein interactions: application for the prediction of binding affinity.Journal of computer-aided molecular design · 2014Article
- Ensemble-based characterization of unbound and bound states on protein energy landscape.Protein science : a publication of the Protein Society · 2013Article
- Low-resolution structural modeling of protein interactome.Current opinion in structural biology · 2013Review
- Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.PLoS computational biology · 2013Article
- Correlation analysis of the side-chains conformational distribution in bound and unbound proteins.BMC bioinformatics · 2012Article
- Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding.Proteins · 2012Article
- Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins.BMC structural biology · 2012Article
- Structure fluctuations and conformational changes in protein binding.Journal of bioinformatics and computational biology · 2012Article
- Minimal ensembles of side chain conformers for modeling protein-protein interactions.Proteins · 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
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short and long side chains have different propensities for the conformational changes. Long side chains with three or more dihedral angles are often subject to large conformational transition. Shorter residues with one or two dihedral angles typically undergo local conformational changes not leading to a conformational transition. A relationship between the local readjustments and the equilibrium fluctuations of a side chain around its unbound conformation is suggested. Most of the side chains undergo larger changes in the dihedral angle most distant from the backbone. The frequencies of the core-to-surface interface transitions of six nonpolar residues and Tyr are larger than the frequencies of the opposite surface-to-core transitions. The binding increases both polar and nonpolar interface areas. However, the increase of the nonpolar area is larger for all considered classes of protein complexes, suggesting that the protein association perturbs the unbound interfaces to increase the hydrophobic contribution to the binding free energy. To test modeling approaches to side-chain flexibility in protein docking, conformational changes in the X-ray set were compared with those in the docking decoy sets. The results lead to a better understanding of the conformational changes in proteins and suggest directions for efficient conformational sampling in docking protocols.
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.