Niemyska, Wanda and Dabrowski-Tumanski, Pawel and Kadlof, Michal and Haglund, Ellinor and Sułkowski, Piotr and Sulkowska, Joanna I. (2016) Complex lasso: new entangled motifs in proteins. Scientific Reports, 6 . Art. No. 36895. ISSN 2045-2322. PMCID PMC5118788. doi:10.1038/srep36895. https://resolver.caltech.edu/CaltechAUTHORS:20161128-153056394
![[img]](https://authors.library.caltech.edu/style/images/fileicons/application_pdf.png) |
PDF
- Published Version
Creative Commons Attribution. 725kB |
|
PDF
- Supplemental Material
Creative Commons Attribution. 14MB |
Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20161128-153056394
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.
| Item Type: | Article | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Related URLs: |
| ||||||||||||||||||
| ORCID: |
| ||||||||||||||||||
| Additional Information: | © The Author(s) 2016. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ Received: 13 April 2016. Accepted: 10 October 2016. Published online: 22 November 2016. J.I.S. and M.K. were supported by the National Science Centre [#2012/07/E/NZ1/01900], J.I.S. and P.D.-T. were supported by the European Molecular Biology Organization Installation Grant [#2057]. P.D.-T. was supported by University of Warsaw [#120000-501/86-DSM-112 700]. The work of P.S. was supported by the ERC Starting Grant no. 335739 “Quantum fields and knot homologies” funded by the European Research Council under the European Union’s Seventh Framework Programme, and the Foundation for Polish Science. E.H. was supported by the Center for Theoretical Biological Physics sponsored by the NSF (Grant PHY-1308264, NSF-MCB-1214457 and NSF PHY-1212312). Author Contributions: J.I.S. and P.S. designed the work, W.N., P.D.-T., M.K. and J.I.S. performed the work, W.N., P.D.-T., E.H., P.S. and J.I.S. wrote the paper. The authors declare no competing financial interests. | ||||||||||||||||||
| Group: | Walter Burke Institute for Theoretical Physics | ||||||||||||||||||
| Funders: |
| ||||||||||||||||||
| PubMed Central ID: | PMC5118788 | ||||||||||||||||||
| DOI: | 10.1038/srep36895 | ||||||||||||||||||
| Record Number: | CaltechAUTHORS:20161128-153056394 | ||||||||||||||||||
| Persistent URL: | https://resolver.caltech.edu/CaltechAUTHORS:20161128-153056394 | ||||||||||||||||||
| Official Citation: | Niemyska, W. et al. Complex lasso: new entangled motifs in proteins. Sci. Rep. 6, 36895; doi: 10.1038/srep36895 (2016). | ||||||||||||||||||
| Usage Policy: | No commercial reproduction, distribution, display or performance rights in this work are provided. | ||||||||||||||||||
| ID Code: | 72343 | ||||||||||||||||||
| Collection: | CaltechAUTHORS | ||||||||||||||||||
| Deposited By: | George Porter | ||||||||||||||||||
| Deposited On: | 28 Nov 2016 23:53 | ||||||||||||||||||
| Last Modified: | 07 Apr 2022 16:37 |
Repository Staff Only: item control page
