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Complex lasso: new entangled motifs in proteins

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. https://resolver.caltech.edu/CaltechAUTHORS:20161128-153056394

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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:
URLURL TypeDescription
http://dx.doi.org/10.1038/srep36895DOIArticle
http://www.nature.com/articles/srep36895PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118788/PubMed CentralArticle
ORCID:
AuthorORCID
Dabrowski-Tumanski, Pawel0000-0001-9412-1716
Sułkowski, Piotr0000-0002-6176-6240
Sulkowska, Joanna I.0000-0003-2452-0724
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:
Funding AgencyGrant Number
National Science Centre (Poland)2012/07/E/NZ1/01900
European Molecular Biology Organization (EMBO)2057
University of Warsaw120000-501/86-DSM-112 700
European Research Council (ERC)335739
Foundation for Polish ScienceUNSPECIFIED
NSFPHY-1308264
NSFMCB-1214457
NSFPHY-1212312
PubMed Central ID:PMC5118788
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:11 Feb 2020 19:16

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