ArticleProtein engineering, design & selection : PEDS2016
GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins.
Article in Protein engineering, design & selection : PEDS, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- Design of intrinsically disordered protein variants with diverse structural properties.Science advances · 2024Article
- Structural biases in disordered proteins are prevalent in the cell.Nature structural & molecular biology · 2024Article
- Sequence-ensemble-function relationships for disordered proteins in live cells.bioRxiv : the preprint server for biology · 2023Article
- Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA.Nature communications · 2021Article
- Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures.APL materials · 2021Article
- DispHred: A Server to Predict pH-Dependent Order-Disorder Transitions in Intrinsically Disordered Proteins.International journal of molecular sciences · 2020Article
- Disorder for Dummies: Functional Mutagenesis of Transient Helical Segments in Disordered Proteins.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Information theoretic measures for quantifying sequence-ensemble relationships of intrinsically disordered proteins.Protein engineering, design & selection : PEDS · 2019Article
- Protein motion in the nucleus: from anomalous diffusion to weak interactions.Biochemical Society transactions · 2018Review
- Folding and binding pathways of BH3-only proteins are encoded within their intrinsically disordered sequence, not templated by partner proteins.The Journal of biological chemistry · 2018Article
- InSiDDe: A Server for Designing Artificial Disordered Proteins.International journal of molecular sciences · 2017Article
- Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the Notch receptor.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins.Biophysical journal · 2017Article
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6 authors.
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Abstract
Many intrinsically disordered proteins (IDPs) participate in coupled folding and binding reactions and form alpha helical structures in their bound complexes. Alanine, glycine, or proline scanning mutagenesis approaches are often used to dissect the contributions of intrinsic helicities to coupled folding and binding. These experiments can yield confounding results because the mutagenesis strategy changes the amino acid compositions of IDPs. Therefore, an important next step in mutagenesis-based approaches to mechanistic studies of coupled folding and binding is the design of sequences that satisfy three major constraints. These are (i) achieving a target intrinsic alpha helicity profile; (ii) fixing the positions of residues corresponding to the binding interface; and (iii) maintaining the native amino acid composition. Here, we report the development of a G: enetic A: lgorithm for D: esign of I: ntrinsic secondary S: tructure (GADIS) for designing sequences that satisfy the specified constraints. We describe the algorithm and present results to demonstrate the applicability of GADIS by designing sequence variants of the intrinsically disordered PUMA system that undergoes coupled folding and binding to Mcl-1. Our sequence designs span a range of intrinsic helicity profiles. The predicted variations in sequence-encoded mean helicities are tested against experimental measurements.
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