Topological knots and links in proteins
Pawel Dabrowski-Tumanski a,b and Joanna I. Sulkowska a,b,1
Author Affiliations
aFaculty of Chemistry, University of Warsaw, 02-093, Warsaw, Poland;
bCentre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
Edited by George H. Lorimer, University of Maryland, College Park, MD, and approved February 1, 2017 (received for review September 23, 2016)
Significance
Twenty years after a discovery of knotted proteins, we found that some single-protein chains can form links, which have even more complex structures than knots. We derive conditions that proteins need to meet to form links. We search through the entire Protein Data Bank and identify several chains that form a Hopf link and a Solomon link. The link motif has not been recognized before; however, it is clearly of important functional significance in proteins. In this article, we relate topological properties of proteins with links to their function and stability and show that the link topology is characteristic of eukaryotes only.
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.
folding catenanes slipknot lasso disulphide bridge
Footnotes
1To whom correspondence should be addressed. Email: jsulkowska@chem.uw.edu.pl.
Author contributions: P.D.-T. and J.I.S. designed research; P.D.-T. performed research; P.D.-T. and J.I.S. analyzed data; and P.D.-T. and J.I.S. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1615862114/-/DCSupplemental.
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