ArticlePLoS computational biology2012
Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection.
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 31 papers.
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Who cites it
31 citing papers in PubMed.
- The structural influence of the oncogenic driver mutation N642H in the STAT5B SH2 domain.Protein science : a publication of the Protein Society · 2025Article
- Article
- An Updated Review on Developing Small Molecule Kinase Inhibitors Using Computer-Aided Drug Design Approaches.International journal of molecular sciences · 2023Review
- Kinetic Constraints in the Specific Interaction between Phosphorylated Ubiquitin and Proteasomal Shuttle Factors.Biomolecules · 2021Article
- Data-Driven Molecular Dynamics: A Multifaceted Challenge.Pharmaceuticals (Basel, Switzerland) · 2020Review
- Local frustration determines loop opening during the catalytic cycle of an oxidoreductase.eLife · 2020Article
- Enhancing NMR derived ensembles with kinetics on multiple timescales.Journal of biomolecular NMR · 2020Article
- CUBAN, a Case Study of Selective Binding: Structural Details of the Discrimination between Ubiquitin and NEDD8.International journal of molecular sciences · 2019Article
- Conformational Dynamics Modulate Activation of the Ubiquitin Conjugating Enzyme Ube2g2.ACS omega · 2017Article
- Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.Biophysical journal · 2016Article
- A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions.BMC bioinformatics · 2016Article
- Allosteric switch regulates protein-protein binding through collective motion.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Revealing an outward-facing open conformational state in a CLC Cl(-)/H(+) exchange transporter.eLife · 2016Article
- Population shuffling between ground and high energy excited states.Protein science : a publication of the Protein Society · 2015Article
- 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
- Binding affinities controlled by shifting conformational equilibria: opportunities and limitations.Biophysical journal · 2015Article
- Article
- A designed conformational shift to control protein binding specificity.Angewandte Chemie (International ed. in English) · 2014Article
- Structural basis of valmerins as dual inhibitors of GSK3β/CDK5.Journal of molecular modeling · 2014Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Protein-protein interactions play an important role in all biological processes. However, the principles underlying these interactions are only beginning to be understood. Ubiquitin is a small signalling protein that is covalently attached to different proteins to mark them for degradation, regulate transport and other functions. As such, it interacts with and is recognised by a multitude of other proteins. We have conducted molecular dynamics simulations of ubiquitin in complex with 11 different binding partners on a microsecond timescale and compared them with ensembles of unbound ubiquitin to investigate the principles of their interaction and determine the influence of complex formation on the dynamic properties of this protein. Along the main mode of fluctuation of ubiquitin, binding in most cases reduces the conformational space available to ubiquitin to a subspace of that covered by unbound ubiquitin. This behaviour can be well explained using the model of conformational selection. For lower amplitude collective modes, a spectrum of zero to almost complete coverage of bound by unbound ensembles was observed. The significant differences between bound and unbound structures are exclusively situated at the binding interface. Overall, the findings correspond neither to a complete conformational selection nor induced fit scenario. Instead, we introduce a model of conformational restriction, extension and shift, which describes the full range of observed effects.
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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.