Topological knots and links in proteins
- 9 March 2017
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 114 (13), 3415-3420
- https://doi.org/10.1073/pnas.1615862114
Abstract
Twenty years after their discovery, knots in proteins are now quite well understood. They are believed to be functionally advantageous and provide extra stability to protein chains. In this work, we go one step further and search for links—entangled structures, more complex than knots, which consist of several components. We derive conditions that proteins need to meet to be able to form links. We search through the entire Protein Data Bank and identify several sequentially nonhomologous chains that form a Hopf link and a Solomon link. We relate topological properties of these proteins to their function and stability and show that the link topology is characteristic of eukaryotes only. We also explain how the presence of links affects the folding pathways of proteins. Finally, we define necessary conditions to form Borromean rings in proteins and show that no structure in the Protein Data Bank forms a link of this type.Funding Information
- European Molecular Biology Organization (2057)
- MNiSW (120000-501/86-DSM-112 700)
- National Science Center Poland (2016/21/N/NZ1/02848)
This publication has 36 references indexed in Scilit:
- Driving the Formation of Molecular KnotsScience, 2012
- Energy landscape of knotted protein foldingProceedings of the National Academy of Sciences of the United States of America, 2012
- Conservation of complex knotting and slipknotting patterns in proteinsProceedings of the National Academy of Sciences of the United States of America, 2012
- Oxidative Folding and Structural Analyses of a Kunitz-Related Inhibitor and Its Disulfide Intermediates: Functional ImplicationsJournal of Molecular Biology, 2011
- The Structure of the Elicitor Cerato-platanin (CP), the First Member of the CP Fungal Protein Family, Reveals a Double ψβ-Barrel Fold and Carbohydrate BindingJournal of Biological Chemistry, 2011
- Slipknotting upon native-like loop formation in a trefoil knot proteinProceedings of the National Academy of Sciences of the United States of America, 2010
- A Stevedore's Protein KnotPLoS Computational Biology, 2010
- Dodging the crisis of folding proteins with knotsProceedings of the National Academy of Sciences of the United States of America, 2009
- Discovery of a Thermophilic Protein Complex Stabilized by Topologically Interlinked ChainsJournal of Molecular Biology, 2007
- The Pfam protein families databaseNucleic Acids Research, 2004