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• W2171153313 abstract "One of the most striking topological features to be found in a protein is that of a distinct knot formed by the path of the polypeptide backbone. Such knotted structures represent some of the smallest “self-tying” knots observed in Nature. Proteins containing a knot deep within their structure add an extra complication to the already challenging protein-folding problem; it is not obvious how, during the process of folding, a substantial length of polypeptide chain manages to spontaneously thread itself through a loop. Here, we probe the folding mechanism of YibK, a homodimeric α/β-knot protein containing a deep trefoil knot at its carboxy terminus. By analyzing the effect of mutations made in the knotted region of the protein we show that the native structure in this area remains undeveloped until very late in the folding reaction. Single-site destabilizing mutations made in the knot structure significantly affect only the folding kinetics of a late-forming intermediate and the slow dimerization step. Furthermore, we find evidence to suggest that the heterogeneity observed in the denatured state is not caused by isomerization of the single cis proline bond as previously thought, but instead could be a result of the knotting mechanism. These results allow us to propose a folding model for YibK where the threading of the polypeptide chain and the formation of native structure in the knotted region of the protein occur independently as successive events." @default.
• W2171153313 created "2016-06-24" @default.
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• W2171153313 date "2008-12-02" @default.
• W2171153313 modified "2023-09-27" @default.
• W2171153313 title "Exploring knotting mechanisms in protein folding" @default.
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• W2171153313 doi "https://doi.org/10.1073/pnas.0806697105" @default.
• W2171153313 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2596204" @default.
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• W2171153313 hasPublicationYear "2008" @default.
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