ArticlePloS one2009
Molecular dynamics simulation of phosphorylated KID post-translational modification.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 47 citations in OpenAlex.
- Activation of p53: How phosphorylated Ser15 triggers sequential phosphorylation of p53 at Thr18 by CK1δ.Proteins · 2022Article
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteins.Physical chemistry chemical physics : PCCP · 2022Review
- Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions.PLoS computational biology · 2021Article
- Explicit Characterization of the Free Energy Landscape of pKID-KIX Coupled Folding and Binding.ACS central science · 2019Article
- Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB.The Journal of chemical physics · 2018Article
- pKID Binds to KIX via an Unstructured Transition State with Nonnative Interactions.Biophysical journal · 2017Article
- Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis.Scientific reports · 2016Article
- Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine.Journal of biological physics · 2016Article
- Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications.Nucleic acids research · 2013Article
- Using simulations to provide the framework for experimental protein folding studies.Archives of biochemistry and biophysics · 2013Review
- Computational studies on the substrate interactions of influenza A virus PB2 subunit.PloS one · 2012Article
- Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations.PloS one · 2012Article
- Insight into the stability of cross-β amyloid fibril from VEALYL short peptide with molecular dynamics simulation.PloS one · 2012Article
- Folding of Intrinsically Disordered Protein Phosphatase 1 Regulatory Proteins.Current physical chemistry · 2012Article
- Importance of electrostatic interactions in the association of intrinsically disordered histone chaperone Chz1 and histone H2A.Z-H2B.PLoS computational biology · 2012Article
- Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response.PloS one · 2011Article
- Induced fit or conformational selection for RNA/U1A folding.RNA (New York, N.Y.) · 2010Article
- Intrinsically disordered proteins in a physics-based world.International journal of molecular sciences · 2010Review
- Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundKinase-inducible domain (KID) as transcriptional activator can stimulate target gene expression in signal transduction by associating with KID interacting domain (KIX). NMR spectra suggest that apo-KID is an unstructured protein. After post-translational modification by phosphorylation, KID undergoes a transition from disordered to well folded protein upon binding to KIX. However, the mechanism of folding coupled to binding is poorly understood. METHODOLOGY: To get an insight into the mechanism, we have performed ten trajectories of explicit-solvent molecular dynamics (MD) for both bound and apo phosphorylated KID (pKID). Ten MD simulations are sufficient to capture the average properties in the protein folding and unfolding.
conclusionsRoom-temperature MD simulations suggest that pKID becomes more rigid and stable upon the KIX-binding. Kinetic analysis of high-temperature MD simulations shows that bound pKID and apo-pKID unfold via a three-state and a two-state process, respectively. Both kinetics and free energy landscape analyses indicate that bound pKID folds in the order of KIX access, initiation of pKID tertiary folding, folding of helix alpha(B), folding of helix alpha(A), completion of pKID tertiary folding, and finalization of pKID-KIX binding. Our data show that the folding pathways of apo-pKID are different from the bound state: the foldings of helices alpha(A) and alpha(B) are swapped. Here we also show that Asn139, Asp140 and Leu141 with large Phi-values are key residues in the folding of bound pKID. Our results are in good agreement with NMR experimental observations and provide significant insight into the general mechanisms of binding induced protein folding and other conformational adjustment in post-translational modification.
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.