ArticleProtein science : a publication of the Protein Society2016
Comprehensive analysis of sequences of a protein switch.
Article in Protein science : a publication of the Protein Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Signatures of protein fold switching in the unfolded state.Biophysical journal · 2026Article
- Aromatic-aromatic interactions drive fold switch of GA95 and GB95 with three residue difference.Chemical science · 2025Article
- A mutagenesis study of autoantigen optimization for potential T1D vaccine design.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A review of visualisations of protein fold networks and their relationship with sequence and function.Biological reviews of the Cambridge Philosophical Society · 2023Review
- Design and characterization of a protein fold switching network.Nature communications · 2023Article
- Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes.Advanced drug delivery reviews · 2022Review
- Exploring the sequence fitness landscape of a bridge between protein folds.PLoS computational biology · 2020Article
- Structure-based enzyme engineering improves donor-substrate recognition of Arabidopsis thaliana glycosyltransferases.The Biochemical journal · 2020Article
- In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Length-Dependent Structural Transformations of Huntingtin PolyQ Domain Upon Binding to 2D-Nanomaterials.Frontiers in chemistry · 2020Article
- Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.PLoS computational biology · 2016Article
- The role of negative selection in protein evolution revealed through the energetics of the native state ensemble.Proteins · 2016Article
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Authors and funding
3 authors.
Funding
Abstract
Switches form a special class of proteins that dramatically change their three-dimensional structures upon a small perturbation. One possible perturbation that we explore is that of a single point mutation. Building on the pioneering experimental work of Alexander et al. (Alexander et al. PNAS, 2007; 104,11963-11968) that determines switch sequences between α and α+β folds we conduct a comprehensive sequence sampling by a Markov Chain with multiple fitness criteria to identify new switches given the experimental folds. We screen for switch sequences using a combination of contact potential, secondary structure prediction, and finally molecular dynamics simulations. Statistical properties of switch sequences are discussed and illustrated to be most sensitive to mutation at the N- and C- termini of the switch protein. Based on this analysis, a particularly stable putative switch pair is identified and proposed for further experimental analysis.
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Registered trials
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