ArticlePLoS computational biology2011
In silico elucidation of the recognition dynamics of ubiquitin.
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 23 papers.
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Who cites it
23 citing papers in PubMed.
- Article
- Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package.BMC bioinformatics · 2020Article
- Atomistic Insights into the Functional Instability of the Second Helix of Fatty Acid Binding Protein.Biophysical journal · 2019Article
- Conformational Dynamics Modulate Activation of the Ubiquitin Conjugating Enzyme Ube2g2.ACS omega · 2017Article
- Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2016Review
- Using protein motion to read, write, and erase ubiquitin signals.The Journal of biological chemistry · 2015Review
- Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding.Scientific reports · 2015Article
- Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model.The Journal of chemical physics · 2014Article
- Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics.Protein science : a publication of the Protein Society · 2014Article
- Ubiquitin-dependent sorting in endocytosis.Cold Spring Harbor perspectives in biology · 2014Review
- Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry.Journal of the American Chemical Society · 2013Article
- Allosteric conformational barcodes direct signaling in the cell.Structure (London, England : 1993) · 2013Review
- Conformational dynamics control ubiquitin-deubiquitinase interactions and influence in vivo signaling.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.Journal of biomolecular NMR · 2013Article
- Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin.Protein science : a publication of the Protein Society · 2013Article
- Thermal adaptation of conformational dynamics in ribonuclease H.PLoS computational biology · 2013Article
- Bioinformatics and variability in drug response: a protein structural perspective.Journal of the Royal Society, Interface · 2012Review
- Article
- Protein dynamics and conformational selection in bidirectional signal transduction.BMC biology · 2012Article
- Noncovalent dimerization of ubiquitin.Angewandte Chemie (International ed. in English) · 2012Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Elucidation of the mechanism of biomacromolecular recognition events has been a topic of intense interest over the past century. The inherent dynamic nature of both protein and ligand molecules along with the continuous reshaping of the energy landscape during the binding process renders it difficult to characterize this process at atomic detail. Here, we investigate the recognition dynamics of ubiquitin via microsecond all-atom molecular dynamics simulation providing both thermodynamic and kinetic information. The high-level of consistency found with respect to experimental NMR data lends support to the accuracy of the in silico representation of the conformational substates and their interconversions of free ubiquitin. Using an energy-based reweighting approach, the statistical distribution of conformational states of ubiquitin is monitored as a function of the distance between ubiquitin and its binding partner Hrs-UIM. It is found that extensive and dense sampling of conformational space afforded by the µs MD trajectory is essential for the elucidation of the binding mechanism as is Boltzmann sampling, overcoming inherent limitations of sparsely sampled empirical ensembles. The results reveal a population redistribution mechanism that takes effect when the ligand is at intermediate range of 1-2 nm from ubiquitin. This mechanism, which may be depicted as a superposition of the conformational selection and induced fit mechanisms, also applies to other binding partners of ubiquitin, such as the GGA3 GAT domain.
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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.