Aleksandra M Gierut1,2, Pawel Dabrowski-Tumanski1,3, Wanda Niemyska1, Kenneth C Millett4, Joanna I Sulkowska1,3. 1. Centre of New Technologies, University of Warsaw, Warsaw, Poland. 2. Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Cracow, Poland. 3. Faculty of Chemistry, University of Warsaw, Warsaw, Poland. 4. Department of Mathematics, University of California, Santa Barbara, CA, USA.
Abstract
SUMMARY: Links are generalization of knots, that consist of several components. They appear in proteins, peptides and other biopolymers with disulfide bonds or ions interactions giving rise to the exceptional stability. Moreover because of this stability such biopolymers are the target of commercial and medical use (including anti-bacterial and insecticidal activity). Therefore, topological characterization of such biopolymers, not only provides explanation of their thermodynamical or mechanical properties, but paves the way to design templates in pharmaceutical applications. However, distinction between links and trivial topology is not an easy task. Here, we present PyLink-a PyMOL plugin suited to identify three types of links and perform comprehensive topological analysis of proteins rich in disulfide or ion bonds. PyLink can scan for the links automatically, or the user may specify their own components, including closed loops with several bridges and ion interactions. This creates the possibility of designing new biopolymers with desired properties. AVAILABILITY AND IMPLEMENTATION: The PyLink plugin, manual and tutorial videos are available at http://pylink.cent.uw.edu.pl.
SUMMARY: Links are generalization of knots, that consist of several components. They appear in proteins, peptides and other biopolymers with disulfide bonds or ions interactions giving rise to the exceptional stability. Moreover because of this stability such biopolymers are the target of commercial and medical use (including anti-bacterial and insecticidal activity). Therefore, topological characterization of such biopolymers, not only provides explanation of their thermodynamical or mechanical properties, but paves the way to design templates in pharmaceutical applications. However, distinction between links and trivial topology is not an easy task. Here, we present PyLink-a PyMOL plugin suited to identify three types of links and perform comprehensive topological analysis of proteins rich in disulfide or ion bonds. PyLink can scan for the links automatically, or the user may specify their own components, including closed loops with several bridges and ion interactions. This creates the possibility of designing new biopolymers with desired properties. AVAILABILITY AND IMPLEMENTATION: The PyLink plugin, manual and tutorial videos are available at http://pylink.cent.uw.edu.pl.
Authors: Ives Charlie-Silva; Natália M Feitosa; Leticia G Pontes; Bianca H Fernandes; Rafael H Nóbrega; Juliana M M Gomes; Mariana N L Prata; Fausto K Ferraris; Daniela C Melo; Gabriel Conde; Letícia F Rodrigues; Mayumi F Aracati; José D Corrêa-Junior; Wilson G Manrique; Joshua Superio; Aguinaldo S Garcez; Katia Conceição; Tania M Yoshimura; Silvia C Núñez; Silas F Eto; Dayanne C Fernandes; Anderson Z Freitas; Martha S Ribeiro; Artem Nedoluzhko; Mônica Lopes-Ferreira; Ricardo C Borra; Leonardo J G Barcellos; Andrea C Perez; Guilheme Malafaia; Thiago M Cunha; Marco A A Belo; Jorge Galindo-Villegas Journal: Front Immunol Date: 2022-09-29 Impact factor: 8.786