ArticleJournal of computational chemistry2016
Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.
Article in Journal of computational chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Umbrella Sampling Workflows for Fast-Converging PMF Calculations without Artificial WHAM Constraints.Journal of chemical theory and computation · 2026Article
- Combined prediction and design reveals the target recognition mechanism of an intrinsically disordered protein interaction domain.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Local Ion Densities can Influence Transition Paths of Molecular Binding.Frontiers in molecular biosciences · 2022Article
- Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.Biomolecules · 2021Review
- Detection of key sites of dimer dissociation and unfolding initiation during activation of acid-stress chaperone HdeA at low pH.Biochimica et biophysica acta. Proteins and proteomics · 2021Article
- Structural basis and mechanism of the unfolding-induced activation of HdeA, a bacterial acid response chaperone.The Journal of biological chemistry · 2019Article
- The Mechanism of HdeA Unfolding and Chaperone Activation.Journal of molecular biology · 2018Article
- Flexibility vs Preorganization: Direct Comparison of Binding Kinetics for a Disordered Peptide and Its Exact Preorganized Analogues.The journal of physical chemistry. B · 2017Article
- Optimal allosteric stabilization sites using contact stabilization analysis.Journal of computational chemistry · 2017Article
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Roles of structural plasticity in chaperone HdeA activity are revealed byChemical science · 2016Article
- Accelerating physical simulations of proteins by leveraging external knowledge.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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3 authors.
Funding
Abstract
Intrinsically disordered regions of proteins can gain structure by binding to a partner. This process, of coupled folding and binding (CFaB), is a fundamental part of many important biological processes. Structure-based models have proven themselves capable of revealing fundamental aspects of how CFaB occurs, however, typical methods to enhance the sampling of these transitions, such as replica exchange, do not adequately sample the transition state region of this extremely rare process. Here, we use a variant of Umbrella Sampling to enforce sampling of the transition states of CFaB of HdeA monomers at neutral pH, an extremely rare process that occurs over timescales ranging from seconds to hours. Using high resolution sampling in the transition state region, we cluster states along the principal transition path to obtain a detailed description of coupled binding and folding for the HdeA dimer, revealing new insight into the ensemble of states that are accessible to client recognition. We then demonstrate that exchanges between umbrella sampling windows, as done in previous work, significantly improve relaxation in variables orthogonal to the restraints used. Altogether, these results show that Window-Exchange Umbrella Sampling is a promising approach for systems that exhibit flexible binding, and can reveal transition state ensembles of these systems in high detail. © 2015 Wiley Periodicals, Inc.
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