ArticleThe Journal of biological chemistry2012
Trimming down a protein structure to its bare foldons: spatial organization of the cooperative unit.
Article in The Journal of biological chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 27 citations in OpenAlex.
- Likely Overstabilization of Charge-Charge Interactions in CHARMM36m(w): A Case for a99SB-disp Water.The journal of physical chemistry. B · 2024Article
- Design and characterization of a protein fold switching network.Nature communications · 2023Article
- Exposing the distinctive modular behavior of β-strands and α-helices in folded proteins.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Modeling, Mutagenesis andIranian journal of biotechnology · 2020Article
- StructureDistiller: Structural relevance scoring identifies the most informative entries of a contact map.Scientific reports · 2019Article
- Application of an interpretable classification model on Early Folding Residues during protein folding.BioData mining · 2019Article
- Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- Force Field for Peptides and Proteins based on the Classical Drude Oscillator.Journal of chemical theory and computation · 2013Article
- Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture.BMC structural biology · 2013Article
- Article
- Deletional protein engineering based on stable fold.PloS one · 2012Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Folding of the ribosomal protein S6 is a malleable process controlled by two competing, and partly overlapping, folding nuclei. Together, these nuclei extend over most of the S6 structure, except the edge strand β2, which is consistently missing in the folding transition states; despite being part of the S6 four-stranded sheet, β2 seems not to be part of the cooperative unit of the protein. The question is then whether β2 can be removed from the S6 structure without compromising folding cooperativity or native state integrity. To investigate this, we constructed a truncated variant of S6 lacking β2, reducing the size of the protein from 96 to 76 residues (S6(Δβ2)). The new S6 variant expresses well in Escherichia coli and has a well dispersed heteronuclear single quantum correlation spectrum and a perfectly wild-type-like crystal structure, but with a smaller three-stranded β-sheet. Moreover, S6(Δβ2) displays an archetypical v-shaped chevron plot with decreased slope of the unfolding limb, as expected from a protein with maintained folding cooperativity and reduced size. The results support the notion that foldons, as defined by the structural distribution of the folding nuclei, represent a property-based level of hierarchy in the build-up of larger protein structures and suggest that the role of β2 in S6 is mainly in intermolecular binding, consistent with the position of this strand in the ribosomal assembly.
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