title: Intricate knots in proteins: Function and evolution.
abstract: Our investigation of knotted structures in the Protein Data Bank reveals the most complicated knot discovered to date. We suggest that the occurrence of this knot in a human ubiquitin hydrolase might be related to the role of the enzyme in protein degradation. While knots are usually preserved among homologues, we also identify an exception in a transcarbamylase. This allows us to exemplify the function of knots in proteins and to suggest how they may have been created.
authors.affiliation: Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America. virnau@mit.edu
authors.forename: Peter
authors.initials: P
authors.lastname: Virnau
authors.forename: Leonid A
authors.initials: LA
authors.lastname: Mirny
authors.forename: Mehran
authors.initials: M
authors.lastname: Kardar
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D003546:Cysteine Endopeptidases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D006801:Humans; D008958:Models, Molecular; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D043222:Ubiquitin Thiolesterase
chemical_list: D001426:Bacterial Proteins; C509806:UCHL3 protein, human; D043222:Ubiquitin Thiolesterase; D003546:Cysteine Endopeptidases