Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.

Autor: Vasilina Zayats, Agata P Perlinska, Aleksandra I Jarmolinska, Borys Jastrzebski, Stanislaw Dunin-Horkawicz, Joanna I Sulkowska

Publikováno v: PLoS Computational Biology, Vol 17, Iss 10, p e1009502 (2021)

While the slipknot topology in proteins has been known for over a decade, its evolutionary origin is still a mystery. We have identified a previously overlooked slipknot motif in a family of two-domain membrane transporters. Moreover, we found that t

Externí odkaz: https://doaj.org/article/f105ce84f84c4826ad5083eca7f3d2ec

PconsFam: An Interactive Database of Structure Predictions of Pfam Families

Autor: John Lamb, Arne Elofsson, Mirco Michel, Joanna I. Sulkowska, Aleksandra I. Jarmolinska, David Menéndez-Hurtado

Publikováno v: Journal of Molecular Biology. 431:2442-2448

At present, about half of the protein domain families lack a structural representative. However, in the last decade, predicting contact maps and using these to model the tertiary structure for these protein families have become an alternative approac

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3ab921fe5b0dd42ebd07ed45c82dd003
https://doi.org/10.1016/j.jmb.2019.01.047

Knot_pull—python package for biopolymer smoothing and knot detection

Autor: Joanna I. Sulkowska, Anna Gambin, Aleksandra I. Jarmolinska

Publikováno v: Bioinformatics. 36:953-955

Summary The biggest hurdle in studying topology in biopolymers is the steep learning curve for actually seeing the knots in structure visualization. Knot_pull is a command line utility designed to simplify this process—it presents the user with a s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::415c5ad210358875816d17400badda59
https://doi.org/10.1093/bioinformatics/btz644

KnotGenome: a server to analyze entanglements of chromosomes

Autor: Peter Virnau, Wanda Niemyska, Szymon Niewieczerzal, Joanna I. Sulkowska, Aleksandra I. Jarmolinska, Jonathan Tammo Siebert

Publikováno v: Nucleic Acids Research

The KnotGenome server enables the topological analysis of chromosome model data using three-dimensional coordinate files of chromosomes as input. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c6df042a53b99008a195233067cf16fb
https://pubmed.ncbi.nlm.nih.gov/29905836

LinkProt: a database collecting information about biological links

Autor: Aleksandra I. Jarmolinska, Kenneth C. Millett, Wanda Niemyska, Eric J. Rawdon, Joanna I. Sulkowska, Pawel Dabrowski-Tumanski

Publikováno v: Dabrowski-Tumanski, P; Jarmolinska, AI; Niemyska, W; Rawdon, EJ; Millett, KC; & Sulkowska, JI. (2017). LinkProt: a database collecting information about biological links. NUCLEIC ACIDS RESEARCH, 45(D1), D243-D249. doi: 10.1093/nar/gkw976. UC Santa Barbara: Retrieved from: http://www.escholarship.org/uc/item/25q2r8p1
Nucleic acids research, vol 45, iss D1
Nucleic Acids Research

Protein chains are known to fold into topologically complex shapes, such as knots, slipknots or complex lassos. This complex topology of the chain can be considered as an additional feature of a protein, separate from secondary and tertiary structure

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b3f0cda06236a861f9567adb8a9e6102
http://www.escholarship.org/uc/item/25q2r8p1