ArticleNature communications2018
Ultrahigh specificity in a network of computationally designed protein-interaction pairs.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- Bacteriocin biophysics: From protein-protein interaction models to navigators of the bacterial cell envelope.The Journal of biological chemistry · 2026Article
- Graph attention with structural features improves the generalizability of identifying functional sequences at a protein interface.bioRxiv : the preprint server for biology · 2025Article
- Evolutionary paths that link orthogonal pairs of binding proteins.Cell systems · 2025Article
- Addressing epistasis in the design of protein function.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Designed Loop Extension Followed by Combinatorial Screening Confers High Specificity to a Broad Matrix MetalloproteinaseInhibitor.Journal of molecular biology · 2023Article
- Allosteric regulation of the 20S proteasome by the Catalytic Core Regulators (CCRs) family.Nature communications · 2023Article
- Marginal specificity in protein interactions constrains evolution of a paralogous family.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Computational design of BclxL inhibitors that target transmembrane domain interactions.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Data-driven design of orthogonal protein-protein interactions.Science signaling · 2023Article
- A genetically encoded system for oxygen generation in living cells.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- How gene duplication diversifies the landscape of protein oligomeric state and function.Current opinion in genetics & development · 2022Review
- Assessing and enhancing foldability in designed proteins.Protein science : a publication of the Protein Society · 2022Article
- Affinity of disordered protein complexes is modulated by entropy-energy reinforcement.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Stabilization of the SARS-CoV-2 receptor binding domain by protein core redesign and deep mutational scanning.Protein engineering, design & selection : PEDS · 2022Article
- What Have We Learned from Design of Function in Large Proteins?Biodesign research · 2022Review
- Computer-aided engineering of staphylokinase toward enhanced affinity and selectivity for plasmin.Computational and structural biotechnology journal · 2022Article
- Protein Engineering in the Design of Protein-Protein Interactions: SARS-CoV-2 Inhibitors as a Test Case.Biochemistry · 2021Article
- Biomolecular Recognition of the Glycan Neoantigen CA19-9 by Distinct Antibodies.Journal of molecular biology · 2021Article
- Programmable protein circuit design.Cell · 2021Review
- Computationally designed pyocyanin demethylase acts synergistically with tobramycin to kill recalcitrantProceedings of the National Academy of Sciences of the United States of America · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Protein networks in all organisms comprise homologous interacting pairs. In these networks, some proteins are specific, interacting with one or a few binding partners, whereas others are multispecific and bind a range of targets. We describe an algorithm that starts from an interacting pair and designs dozens of new pairs with diverse backbone conformations at the binding site as well as new binding orientations and sequences. Applied to a high-affinity bacterial pair, the algorithm results in 18 new ones, with cognate affinities from pico- to micromolar. Three pairs exhibit 3-5 orders of magnitude switch in specificity relative to the wild type, whereas others are multispecific, collectively forming a protein-interaction network. Crystallographic analysis confirms design accuracy, including in new backbones and polar interactions. Preorganized polar interaction networks are responsible for high specificity, thus defining design principles that can be applied to program synthetic cellular interaction networks of desired affinity and specificity.
Indexed as
Identifiers
What OpenQuestion holds
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.