ArticleProteins2010
Thermodynamics of the Trp-cage miniprotein unfolding in urea.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed, 39 citations in OpenAlex.
- The order of PDZ3 and TrpCage in fusion chimeras determines their properties-a biophysical characterization.Protein science : a publication of the Protein Society · 2021Article
- Unperturbed Detection of the Dynamic Structure in the Hydrophobic Core of Trp-Cage via Two-Dimensional Infrared Spectroscopy.The journal of physical chemistry letters · 2020Article
- Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations.Journal of chemical theory and computation · 2015Article
- Structural and thermodynamic characterization of the recognition of the S100-binding peptides TRTK12 and p53 by calmodulin.Protein science : a publication of the Protein Society · 2014Article
- Circular Permutation of the Trp-cage: Fold Rescue upon Addition of a Hydrophobic Staple.RSC advances · 2013Article
- Novel interactions of the TRTK12 peptide with S100 protein family members: specificity and thermodynamic characterization.Biochemistry · 2013Article
- Generating reservoir conformations for replica exchange through the use of the conformational space annealing method.Journal of chemical theory and computation · 2013Article
- Effect of surfactant hydrophobicity on the pathway for unfolding of ubiquitin.Journal of the American Chemical Society · 2012Article
- Molecular mechanism for the preferential exclusion of TMAO from protein surfaces.The journal of physical chemistry. B · 2012Article
- Thermodynamic and kinetic analysis of peptides derived from CapZ, NDR, p53, HDM2, and HDM4 binding to human S100B.Biochemistry · 2012Article
- Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Computational design of thermostabilizing D-amino acid substitutions.Journal of the American Chemical Society · 2011Article
- Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Backbone and side-chain contributions in protein denaturation by urea.Biophysical journal · 2011Article
- Optimal salt bridge for Trp-cage stabilization.Biochemistry · 2011Article
- An effective solvent theory connecting the underlying mechanisms of osmolytes and denaturants for protein stability.Biophysical journal · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The thermodynamic properties of unfolding of the Trp-cage mini protein in the presence of various concentrations of urea have been characterized using temperature-induced unfolding monitored by far-UV circular dichroism spectroscopy. Analysis of the data using a two-state model allowed the calculation of the Gibbs energy of unfolding at 25 degrees C as a function of urea concentration. This in turn was analyzed by the linear extrapolation model that yielded the dependence of Gibbs energy on urea concentration, i.e. the m-value for Trp-cage unfolding. The m-value obtained from the experimental data, as well as the experimental heat capacity change upon unfolding, were correlated with the structural parameters derived from the three dimensional structure of Trp-cage. It is shown that the m-value can be predicted well using a transfer model, while the heat capacity changes are in very good agreement with the empirical models based on model compounds studies. These results provide direct evidence that Trp-cage, despite its small size, is an excellent model for studies of protein unfolding and provide thermodynamic data that can be used to compare with atomistic computer simulations.
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.