ArticleeLife2015
Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis.
Article in eLife, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 43 citations in OpenAlex.
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- Understanding the physiological role and cross-interaction network of VapBC35 toxin-antitoxin system from Mycobacterium tuberculosis.Communications biology · 2025Article
- Multiplexed Epitope Mapping of HIV-1 Neutralizing Antibodies by Coupling Chemical Labeling of Cysteines to Deep Sequencing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Rapid Mapping of Protein Binding Sites and Conformational Epitopes by Coupling Yeast Surface Display to Chemical Labeling and Deep Sequencing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Data-driven design of orthogonal protein-protein interactions.Science signaling · 2023Article
- Mechanistic insights into global suppressors of protein folding defects.PLoS genetics · 2022Article
- Structural and functional determinants inferred from deep mutational scans.Protein science : a publication of the Protein Society · 2022Article
- Interpreting protein variant effects with computational predictors and deep mutational scanning.Disease models & mechanisms · 2022Review
- From systems to structure - using genetic data to model protein structures.Nature reviews. Genetics · 2022Review
- Functional and Biochemical Characterization of the MazEF6 Toxin-Antitoxin System of Mycobacterium tuberculosis.Journal of bacteriology · 2022Article
- Identification of stabilizing point mutations through mutagenesis of destabilized protein libraries.The Journal of biological chemistry · 2022Article
- Combining cysteine scanning with chemical labeling to map protein-protein interactions and infer bound structure in an intrinsically disordered region.Frontiers in molecular biosciences · 2022Article
- Prediction of Residue-specific Contributions to Binding and Thermal Stability Using Yeast Surface Display.Frontiers in molecular biosciences · 2021Article
- A Stabilized, Monomeric, Receptor Binding Domain Elicits High-Titer Neutralizing Antibodies Against All SARS-CoV-2 Variants of Concern.Frontiers in immunology · 2021Article
- A facile method of mapping HIV-1 neutralizing epitopes using chemically masked cysteines and deep sequencing.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding.ACS chemical biology · 2020Article
- MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect.Genome biology · 2019Article
- Determining protein structures using deep mutagenesis.Nature genetics · 2019Article
- Inferring protein 3D structure from deep mutation scans.Nature genetics · 2019Article
- Mutagenesis-based protein structure determination.Nature genetics · 2019Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification of residue-residue contacts from primary sequence can be used to guide protein structure prediction. Using Escherichia coli CcdB as the test case, we describe an experimental method termed saturation-suppressor mutagenesis to acquire residue contact information. In this methodology, for each of five inactive CcdB mutants, exhaustive screens for suppressors were performed. Proximal suppressors were accurately discriminated from distal suppressors based on their phenotypes when present as single mutants. Experimentally identified putative proximal pairs formed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset. Suppressor methodology was also applied to the integral membrane protein, diacylglycerol kinase A where the structures determined by X-ray crystallography and NMR were significantly different. Suppressor as well as sequence co-variation data clearly point to the X-ray structure being the functional one adopted in vivo. The methodology is applicable to any macromolecular system for which a convenient phenotypic assay exists.
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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.