ArticleProceedings of the National Academy of Sciences of the United States of America2009
Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed, 195 citations in OpenAlex.
- Ubiquitin's Conformational Heterogeneity as Discerned by Nuclear Magnetic Resonance Spectroscopy.Chembiochem : a European journal of chemical biology · 2024Review
- Article
- Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics.International journal of molecular sciences · 2024Review
- Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics.Structural dynamics (Melville, N.Y.) · 2023Article
- Atomic resolution protein allostery from the multi-state structure of a PDZ domain.Nature communications · 2022Article
- Kinetic Constraints in the Specific Interaction between Phosphorylated Ubiquitin and Proteasomal Shuttle Factors.Biomolecules · 2021Article
- Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding.Journal of chemical theory and computation · 2021Article
- Understanding the Binding Transition State After the Conformational Selection Step: The Second Half of the Molecular Recognition Process Between NS1 of the 1918 Influenza Virus and Host p85β.Frontiers in molecular biosciences · 2021Article
- Homodimerization of a glycoside hydrolase family GH1 β-glucosidase suggests distinct activity of enzyme different states.Protein science : a publication of the Protein Society · 2020Article
- Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin.Biophysical journal · 2020Article
- Capturing transient antibody conformations with DNA origami epitopes.Nature communications · 2020Article
- CUBAN, a Case Study of Selective Binding: Structural Details of the Discrimination between Ubiquitin and NEDD8.International journal of molecular sciences · 2019Article
- Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors.PloS one · 2019Article
- Structural Consideration of the Working Mechanism of Fold Type I Transaminases From Eubacteria: Overt and Covert Movement.Computational and structural biotechnology journal · 2019Review
- Unified understanding of folding and binding mechanisms of globular and intrinsically disordered proteins.Biophysical reviews · 2018Review
- Conformational Dynamics Modulate Activation of the Ubiquitin Conjugating Enzyme Ube2g2.ACS omega · 2017Article
- Article
- Article
- Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study.Biophysical journal · 2016Article
- Molecular Mechanism and Energy Basis of Conformational Diversity of Antibody SPE7 Revealed by Molecular Dynamics Simulation and Principal Component Analysis.Scientific reports · 2016Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Noncovalent binding interactions between proteins are the central physicochemical phenomenon underlying biological signaling and functional control on the molecular level. Here, we perform an extensive structural analysis of a large set of bound and unbound ubiquitin conformers and study the level of residual induced fit after conformational selection in the binding process. We show that the region surrounding the binding site in ubiquitin undergoes conformational changes that are significantly more pronounced compared with the whole molecule on average. We demonstrate that these induced-fit structural adjustments are comparable in magnitude to conformational selection. Our final model of ubiquitin binding blends conformational selection with the subsequent induced fit and provides a quantitative measure of their respective contributions.
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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.