ArticleBiophysical chemistry2011
In vivo tests of thermodynamic models of transcription repressor function.
Article in Biophysical chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 30 citations in OpenAlex.
- Rheostats, toggles, and neutrals, Oh my! A new framework for understanding how amino acid changes modulate protein function.The Journal of biological chemistry · 2024Review
- The strengths and limitations of using biolayer interferometry to monitor equilibrium titrations of biomolecules.Protein science : a publication of the Protein Society · 2020Article
- Homolog comparisons further reconcile in vitro and in vivo correlations of protein activities by revealing over-looked physiological factors.Protein science : a publication of the Protein Society · 2019Article
- RheoScale: A tool to aggregate and quantify experimentally determined substitution outcomes for multiple variants at individual protein positions.Human mutation · 2018Article
- Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs.PLoS computational biology · 2018Article
- Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction.Cell systems · 2018Article
- Computational predictors fail to identify amino acid substitution effects at rheostat positions.Scientific reports · 2017Article
- Using Evolution to Guide Protein Engineering: The Devil IS in the Details.Biophysical journal · 2016Review
- In vitro transcription accurately predicts lac repressor phenotype in vivo in Escherichia coli.PeerJ · 2014Article
- Steroid receptor-DNA interactions: toward a quantitative connection between energetics and transcriptional regulation.Nucleic acids research · 2014Review
- Protein:protein interactions in control of a transcriptional switch.Journal of molecular biology · 2013Article
- Article
- Novel insights from hybrid LacI/GalR proteins: family-wide functional attributes and biologically significant variation in transcription repression.Nucleic acids research · 2012Article
- Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations.The journal of physical chemistry. B · 2012Article
- Functional versatility of a single protein surface in two protein:protein interactions.Journal of molecular biology · 2012Article
- Substitutions at rheostat position 52 of LacI have long-range effects on the LacI conformational landscape.Biophysical chemistryArticle
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
One emphasis of the Gibbs Conference on Biothermodynamics is the value of thermodynamic measurements for understanding behaviors of biological systems. In this study, the correlation between thermodynamic measurements of in vitro DNA binding affinity with in vivo transcription repression was investigated for two transcription repressors. In the first system, which comprised an engineered LacI/GalR homolog, mutational changes altered the equilibrium constant for binding DNA. Changes correlated with altered repression, but estimates of in vivo repressor concentration suggest a ≥25-fold discrepancy with in vitro conditions. In the second system, changes in ligand binding to BirA altered dimerization and subsequent DNA occupancy. Again, these changes correlate with altered in vivo repression, but comparison with in vitro measurements reveals a ~10-fold discrepancy. Further analysis of each system suggests that the observed discrepancies between in vitro and in vivo results reflect the contributions of additional equilibria to the transcription repression process.
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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.