title: Complex lasso: new entangled motifs in proteins.
abstract: We identify new entangled motifs in proteins that we call complex lassos. Lassos arise in proteins with disulfide bridges (or in proteins with amide linkages), when termini of a protein backbone pierce through an auxiliary surface of minimal area, spanned on a covalent loop. We find that as much as 18% of all proteins with disulfide bridges in a non-redundant subset of PDB form complex lassos, and classify them into six distinct geometric classes, one of which resembles supercoiling known from DNA. Based on biological classification of proteins we find that lassos are much more common in viruses, plants and fungi than in other kingdoms of life. We also discuss how changes in the oxidation/reduction potential may affect the function of proteins with lassos. Lassos and associated surfaces of minimal area provide new, interesting and possessing many potential applications geometric characteristics not only of proteins, but also of other biomolecules.
authors.affiliation: Institute of Mathematics, University of Silesia, Bankowa 14, 40-007 Katowice, Poland.|Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
authors.forename: Wanda
authors.initials: W
authors.lastname: Niemyska
authors.affiliation: Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.|Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland.
authors.forename: Pawel
authors.initials: P
authors.lastname: Dabrowski-Tumanski
authors.affiliation: Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Kadlof
authors.affiliation: Center for Theoretical Biological Physics and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, USA.
authors.forename: Ellinor
authors.initials: E
authors.lastname: Haglund
authors.affiliation: Faculty of Physics, University of Warsaw, ul. Pasteura 5, 02-093 Warsaw, Poland.|Walter Burke Institute for Theoretical Physics, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Piotr
authors.initials: P
authors.lastname: Sułkowski
authors.affiliation: Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.|Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland.
authors.forename: Joanna I
authors.initials: JI
authors.lastname: Sulkowska
mesh_terms: D000818:Animals; D030562:Databases, Protein; D004220:Disulfides / Q000737:chemistry; D005658:Fungi / Q000378:metabolism; D010088:Oxidoreductases / Q000737:chemistry / Q000378:metabolism; D010944:Plants / Q000378:metabolism; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D004220:Disulfides; D011506:Proteins; D010088:Oxidoreductases