ArticleThe Journal of chemical physics2014
Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model.
Article in The Journal of chemical physics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Beyond the structure-function paradigm: A comprehensive review of intrinsically disordered proteins.Biochemistry and biophysics reports · 2026Review
- Multi-Journal of chemical theory and computation · 2024Article
- Structural basis of protein condensation on microtubules underlying branching microtubule nucleation.Nature communications · 2023Article
- More is simpler: Decomposition of ligand-binding affinity for proteins being disordered.Protein science : a publication of the Protein Society · 2022Article
- Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes.Biomolecules · 2021Review
- The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective.Computational and structural biotechnology journal · 2021Review
- A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway.PLoS computational biology · 2020Article
- Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model.The journal of physical chemistry. B · 2020Article
- Biomolecular Phase Separation: From Molecular Driving Forces to Macroscopic Properties.Annual review of physical chemistry · 2020Review
- Intrinsically Disordered Transactivation Domains Bind to TAZ1 Domain of CBP via Diverse Mechanisms.Biophysical journal · 2019Article
- Coupled Binding and Helix Formation Monitored by Synchrotron-Radiation Circular Dichroism.Biophysical journal · 2019Article
- Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins.Biomolecules · 2019Review
- A structurally heterogeneous transition state underlies coupled binding and folding of disordered proteins.The Journal of biological chemistry · 2019Article
- AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins.The journal of physical chemistry. B · 2018Article
- Advances in coarse-grained modeling of macromolecular complexes.Current opinion in structural biology · 2018Review
- Quarterly intrinsic disorder digest (April-May-June, 2014).Intrinsically disordered proteins · 2017Article
- Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.PLoS computational biology · 2016Article
- Expanding the Range of Protein Function at the Far End of the Order-Structure Continuum.The Journal of biological chemistry · 2016Review
- Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation.The Journal of chemical physics · 2015Article
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2 authors.
Funding
Abstract
Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an "induced fit" or "conformational selection" mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.
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