The increasing role of topology in (bio)physical properties of matter creates a need for an efficient method of detecting the topology of a (bio)polymer. However, the existing tools allow one to classify only the simplest knots and cannot be used in automated sample analysis. To answer this need, we created the Topoly Python package. This package enables the distinguishing of knots, slipknots, links and spatial graphs through the calculation of different topological polynomial invariants. It also enables one to create the minimal spanning surface on a given loop, e.g. to detect a lasso motif or to generate random closed polymers. It is capable of reading various file formats, including PDB. The extensive documentation along with test cases and the simplicity of the Python programming language make it a very simple to use yet powerful tool, suitable even for inexperienced users. Topoly can be obtained from https://topoly.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.

Motivation: Over 25% of protein structures possess unresolved fragments. On the other hand, approximately 6% of protein chains have non-trivial topology (and form knots, slipknots, lassos and links). As the topology is fundamental for the proper function of proteins, modeling of topologically correct structures is decisive in various fields, including biophysics, biotechnology and molecular biology. However, none of the currently existing tools take into account the topology of the model and those which could be modified to include topology, demand experience in bioinformatics, protein topology and knot theory. Results: In this work, we present the GapRepairer-the server that fills the gap in the spectrum of structure modeling methods. Its easy and intuitive interface offers the power of Modeller homology modeling to many non-experts in the field. This server determines the topology of templates and predicted structures. Such information when possible is used by the server to suggest the best model, or it can be used by the user to score models or to design artificially (dis)entangled structures. Availability and implementation: GapRepairer server along with tutorials, usage notes, movies and the database of already repaired structures is available at http://gaprepairer.cent.uw.edu.pl. Supplementary information: Supplementary data are available at Bioinformatics online.

The folding of proteins with a complex knot is still an unresolved question. Based on representative members of Ubiquitin C-terminal Hydrolases (UCHs) that contain the 52 knot in the native state, we explain how UCHs are able to unfold and refold in vitro reversibly within the structure-based model. In particular, we identify two, topologically different folding/unfolding pathways and corroborate our results with experiment, recreating the chevron plot. We show that confinement effect of chaperonin or weak crowding greatly facilitates folding, simultaneously slowing down the unfolding process of UCHs, compared with bulk conditions. Finally, we analyze the existence of knots in the denaturated state of UCHs. The results of the work show that the crowded environment of the cell should have a positive effect on the kinetics of complex knotted proteins, especially when proteins with deeper knots are found in this family.

SUMMARY: Entanglement in macromolecules is an important phenomenon and a subject of multidisciplinary research. As recently discovered, around 4% of proteins form new entangled motifs, called lassos. Here we present the PyLasso-a PyMOL plugin to identify and analyse properties of lassos in proteins and other (bio)polymers, as well as in other biological, physical and mathematical systems. The PyLasso is a useful tool for all researchers working on modeling of macromolecules, structure prediction, properties of polymers, entanglement in fluids and fields, etc. AVAILABILITY AND IMPLEMENTATION: The PyLasso and tutorial videos are available at http://pylasso.cent.uw.edu.pl. CONTACT: [email protected].