ArticleProceedings of the National Academy of Sciences of the United States of America2019
Predictive shifts in free energy couple mutations to their phenotypic consequences.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 46 citations in OpenAlex.
- The genetic architecture of an allosteric hormone receptor.Nature communications · 2026Article
- Tuning evolvability via plasmid copy number and regulatory architecture.Nature communications · 2025Article
- Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses.Journal of molecular biology · 2025Review
- The Environment-Dependent Regulatory Landscape of thebioRxiv : the preprint server for biology · 2025Article
- Article
- Machine learning in molecular biophysics: Protein allostery, multi-level free energy simulations, and lipid phase transitions.Biophysics reviews · 2025Review
- A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators.Nucleic acids research · 2025Article
- A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery.eLife · 2024Article
- A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery.bioRxiv : the preprint server for biology · 2024Article
- Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR.Journal of the American Chemical Society · 2024Article
- Precision engineering of biological function with large-scale measurements and machine learning.PloS one · 2023Article
- Interpretable modeling of genotype-phenotype landscapes with state-of-the-art predictive power.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Molecular Dynamics Simulations Establish the Molecular Basis for the Broad Allostery Hotspot Distributions in the Tetracycline Repressor.Journal of the American Chemical Society · 2022Article
- The genotype-phenotype landscape of an allosteric protein.Molecular systems biology · 2021Article
- Reconciling kinetic and thermodynamic models of bacterial transcription.PLoS computational biology · 2021Article
- Article
- Functional plasticity and evolutionary adaptation of allosteric regulation.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Biophysical ambiguities prevent accurate genetic prediction.Nature communications · 2020Article
- Deciphering the regulatory genome ofeLife · 2020Article
- Predictive shifts in free energy couple mutations to their phenotypic consequences.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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 at 2 institutions in 1 country.
Funding
Abstract
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level responses. Here, we present a framework centered on measuring changes in the free energy of the system to link individual mutations in an allosteric transcriptional repressor to the parameters which govern its response. We find that the energetic effects of the mutations can be categorized into several classes which have characteristic curves as a function of the inducer concentration. We experimentally test these diagnostic predictions using the well-characterized LacI repressor of
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.