ArticlePLoS computational biology2018
Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- Multiscale Simulation of Phosphofructokinase-1 Assemblies: Capturing the Interplay between Specific and Transient Interactions.The journal of physical chemistry. B · 2025Article
- EncoderMap III: A Dimensionality Reduction Package for Feature Exploration in Molecular Simulations.Journal of chemical information and modeling · 2025Article
- Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution.Nature communications · 2024Article
- An integrated approach of NMR experiments and MD simulations visualizes structural dynamics of a cyclic multi-domain protein.Protein science : a publication of the Protein Society · 2023Article
- Solution structure of the HOIL-1L NZF domain reveals a conformational switch regulating linear ubiquitin affinity.The Journal of biological chemistry · 2023Article
- Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes.PLoS computational biology · 2023Article
- Generating a conformational landscape of ubiquitin chains at atomistic resolution by back-mapping based sampling.Frontiers in chemistry · 2022Article
- CATBOSS: Cluster Analysis of Trajectories Based on Segment Splitting.Journal of chemical information and modeling · 2021Article
- The dynamics of linear polyubiquitin.Science advances · 2020Article
- NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains.International journal of molecular sciences · 2020Article
- The Length of a Ubiquitin Chain: A General Factor for Selective Recognition by Ubiquitin-Binding Proteins.Angewandte Chemie (International ed. in English) · 2020Article
- Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution.PLoS computational biology · 2020Article
- Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers.Scientific reports · 2019Article
- Simulating and analysing configurational landscapes of protein-protein contact formation.Interface focus · 2019Article
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Covalent modification of proteins by ubiquitin or ubiquitin chains is one of the most prevalent post-translational modifications in eukaryotes. Different types of ubiquitin chains are assumed to selectively signal respectively modified proteins for different fates. In support of this hypothesis, structural studies have shown that the eight possible ubiquitin dimers adopt different conformations. However, at least in some cases, these structures cannot sufficiently explain the molecular basis of the selective signaling mechanisms. This indicates that the available structures represent only a few distinct conformations within the entire conformational space adopted by a ubiquitin dimer. Here, molecular simulations on different levels of resolution can complement the structural information. We have combined exhaustive coarse grained and atomistic simulations of all eight possible ubiquitin dimers with a suitable dimensionality reduction technique and a new method to characterize protein-protein interfaces and the conformational landscape of protein conjugates. We found that ubiquitin dimers exhibit characteristic linkage type-dependent properties in solution, such as interface stability and the character of contacts between the subunits, which can be directly correlated with experimentally observed linkage-specific properties.
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.