Slipknotting upon native-like loop formation in a trefoil knot protein.

ABSTRACT: Protein knots and slipknots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Recent experimental results show that knotting, starting from a fully extended polypeptide, has not yet been observed. Understanding the nucleation process of folding knots is thus a natural challenge for both experimental and theoretical investigation. In this study, we employ energy landscape theory and molecular dynamics to elucidate the entire folding mechanism. The full free energy landscape of a knotted protein is mapped using an all-atom structure-based protein model. Results show that, due to the topological constraint, the protein folds through a three-state mechanism that contains (i) a precise nucleation site that creates a correctly twisted nativ

SUBMITTER: Noel JK 

PROVIDER: S-EPMC2932594 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature