ArticlePLoS computational biology2012
Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study.
Article in PLoS computational biology, 2012. 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, 44 citations in OpenAlex.
- Prediction of MoRFs based on sequence properties and convolutional neural networks.BioData mining · 2021Article
- Computational Prediction of Intrinsically Disordered Proteins Based on Protein Sequences and Convolutional Neural Networks.Computational intelligence and neuroscience · 2021Article
- Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding.Protein science : a publication of the Protein Society · 2019Review
- Intrinsically Disordered Transactivation Domains Bind to TAZ1 Domain of CBP via Diverse Mechanisms.Biophysical journal · 2019Article
- Roles of computational modelling in understanding p53 structure, biology, and its therapeutic targeting.Journal of molecular cell biology · 2019Review
- Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review.Computational and structural biotechnology journal · 2019Review
- Femtosecond Hydration Map of Intrinsically Disordered α-Synuclein.Biophysical journal · 2018Article
- Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling.Journal of computational chemistry · 2016Article
- Long range recognition and selection in IDPs: the interactions of the C-terminus of p53.Scientific reports · 2016Article
- Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2016Review
- Article
- Intrinsically disordered energy landscapes.Scientific reports · 2015Article
- Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model.The Journal of chemical physics · 2014Article
- Advantages of proteins being disordered.Protein science : a publication of the Protein Society · 2014Review
- Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening.PLoS computational biology · 2013Article
- Novel interactions of the TRTK12 peptide with S100 protein family members: specificity and thermodynamic characterization.Biochemistry · 2013Article
- Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins.PLoS computational biology · 2013Article
- Polycation-π interactions are a driving force for molecular recognition by an intrinsically disordered oncoprotein family.PLoS computational biology · 2013Article
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
No grant is acknowledged in the PubMed record.
Abstract
The unique ability of intrinsically disordered proteins (IDPs) to fold upon binding to partner molecules makes them functionally well-suited for cellular communication networks. For example, the folding-binding of different IDP sequences onto the same surface of an ordered protein provides a mechanism for signaling in a many-to-one manner. Here, we study the molecular details of this signaling mechanism by applying both Molecular Dynamics and Monte Carlo methods to S100B, a calcium-modulated homodimeric protein, and two of its IDP targets, p53 and TRTK-12. Despite adopting somewhat different conformations in complex with S100B and showing no apparent sequence similarity, the two IDP targets associate in virtually the same manner. As free chains, both target sequences remain flexible and sample their respective bound, natively [Formula: see text]-helical states to a small extent. Association occurs through an intermediate state in the periphery of the S100B binding pocket, stabilized by nonnative interactions which are either hydrophobic or electrostatic in nature. Our results highlight the importance of overall physical properties of IDP segments, such as net charge or presence of strongly hydrophobic amino acids, for molecular recognition via coupled folding-binding.
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.