ArticleProceedings of the National Academy of Sciences of the United States of America2011
Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 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
57 citing papers in PubMed.
- To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era.Briefings in bioinformatics · 2025Article
- The Iconic α-Helix: From Pauling to the Present.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Beta Sandwich-Like Folds: Sequences, Contacts, Classification of Invariant Substructures and Beta Sandwich Protein Grammar.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The transition state for coupled folding and binding of a disordered DNA binding domain resembles the unbound state.Nucleic acids research · 2024Article
- Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection.Organic letters · 2024Article
- Thioimidates provide general access to thioamide, amidine, and imidazolone peptide-bond isosteres.Methods in enzymology · 2024Article
- Thioamide Analogues of MHC I Antigen Peptides.Journal of the American Chemical Society · 2023Article
- Using azobenzene photocontrol to set proteins in motion.Nature reviews. Chemistry · 2022Review
- Multivalent Interaction of Beta-Catenin With its Intrinsically Disordered Binding Partner Adenomatous Polyposis Coli.Frontiers in molecular biosciences · 2022Article
- Parallel and Sequential Pathways of Molecular Recognition of a Tandem-Repeat Protein and Its Intrinsically Disordered Binding Partner.Biomolecules · 2021Article
- Targeting Beta-Blocker Drug-Drug Interactions with Fibrinogen Blood Plasma Protein: A Computational and Experimental Study.Molecules (Basel, Switzerland) · 2020Article
- Revealing the Dynamical Role of Co-solvents in the Coupled Folding and Dimerization of Insulin.The journal of physical chemistry letters · 2020Article
- Measuring and Analyzing Binding Kinetics of Coupled Folding and Binding Reactions Under Pseudo-First-Order Conditions.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Peptide Folding and Binding Probed by Systematic Non-canonical Mutagenesis.Frontiers in molecular biosciences · 2020Review
- Binding-induced folding under unfolding conditions: Switching between induced fit and conformational selection mechanisms.The Journal of biological chemistry · 2019Article
- Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding.Protein science : a publication of the Protein Society · 2019Review
- Biosynthesis and Chemical Applications of Thioamides.ACS chemical biology · 2019Review
- Adaptation of the bound intrinsically disordered protein YAP to mutations at the YAP:TEAD interface.Protein science : a publication of the Protein Society · 2018Article
- The transition state structure for binding between TAZ1 of CBP and the disordered Hif-1α CAD.Scientific reports · 2018Article
- How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein?Biophysical journal · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association.
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.