ArticlePLoS computational biology2015
Data-driven prediction and design of bZIP coiled-coil interactions.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 48 citations in OpenAlex.
- InsiliCoil: An Integrated Software Suite for Coiled Coil Design, Prediction, and Therapeutic Engineering.ACS synthetic biology · 2026Article
- Massively parallel measurement of protein-protein interactions by sequencing using MP3-seq.Nature chemical biology · 2024Article
- The genetic architecture of protein interaction affinity and specificity.Nature communications · 2024Article
- The Damietta Server: a comprehensive protein design toolkit.Nucleic acids research · 2024Article
- Nitrogen-doped carbon quantum dot regulates cell proliferation and differentiation by endoplasmic reticulum stress.Animal cells and systems · 2024Article
- A multiplexed bacterial two-hybrid for rapid characterization of protein-protein interactions and iterative protein design.Nature communications · 2023Article
- Anticancer Activity of ST101, A Novel Antagonist of CCAAT/Enhancer Binding Protein β.Molecular cancer therapeutics · 2022Article
- Data-driven computational protein design.Current opinion in structural biology · 2021Review
- Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion.Scientific reports · 2021Article
- Physiologic Responses to Dietary Sulfur Amino Acid Restriction in Mice Are Influenced by Atf4 Status and Biological Sex.The Journal of nutrition · 2021Article
- Prediction of Protein-Protein Binding Interactions in Dimeric Coiled Coils by Information Contained in Folding Energy Landscapes.International journal of molecular sciences · 2021Article
- Selective antagonism of cJun for cancer therapy.Journal of experimental & clinical cancer research : CR · 2020Review
- A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Dominant-negative ATF5 rapidly depletes survivin in tumor cells.Cell death & disease · 2019Article
- Molecular mechanisms of the protein-protein interaction-regulated binding specificity of basic-region leucine zipper transcription factors.Journal of molecular modeling · 2019Article
- Peptide design by optimization on a data-parameterized protein interaction landscape.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- A conserved leucine zipper-like motif accounts for strong tetramerization capabilities of SEPALLATA-like MADS-domain transcription factors.Journal of experimental botany · 2018Article
- CCBuilder 2.0: Powerful and accessible coiled-coil modeling.Protein science : a publication of the Protein Society · 2018Article
- Designing helical peptide inhibitors of protein-protein interactions.Current opinion in structural biology · 2016Review
- A quantitative model for oxygen uptake and release in a family of hemeproteins.Bioinformatics (Oxford, England) · 2016Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Selective dimerization of the basic-region leucine-zipper (bZIP) transcription factors presents a vivid example of how a high degree of interaction specificity can be achieved within a family of structurally similar proteins. The coiled-coil motif that mediates homo- or hetero-dimerization of the bZIP proteins has been intensively studied, and a variety of methods have been proposed to predict these interactions from sequence data. In this work, we used a large quantitative set of 4,549 bZIP coiled-coil interactions to develop a predictive model that exploits knowledge of structurally conserved residue-residue interactions in the coiled-coil motif. Our model, which expresses interaction energies as a sum of interpretable residue-pair and triplet terms, achieves a correlation with experimental binding free energies of R = 0.68 and significantly out-performs other scoring functions. To use our model in protein design applications, we devised a strategy in which synthetic peptides are built by assembling 7-residue native-protein heptad modules into new combinations. An integer linear program was used to find the optimal combination of heptads to bind selectively to a target human bZIP coiled coil, but not to target paralogs. Using this approach, we designed peptides to interact with the bZIP domains from human JUN, XBP1, ATF4 and ATF5. Testing more than 132 candidate protein complexes using a fluorescence resonance energy transfer assay confirmed the formation of tight and selective heterodimers between the designed peptides and their targets. This approach can be used to make inhibitors of native proteins, or to develop novel peptides for applications in synthetic biology or nanotechnology.
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Registered trials
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.