Lasso Proteins-Unifying Cysteine Knots and Miniproteins.

Complex lasso proteins are a recently identified class of biological compounds that are present in considerable fraction of proteins with disulfide bridges. In this work, we look at complex lasso proteins as a generalization of well-known cysteine knots and miniproteins (lasso peptides). In particular, we show that complex lasso proteins with the same crucial topological features-cysteine knots and lasso peptides-are antimicrobial proteins, which suggests that they act as a molecular plug.

Topoly: Python package to analyze topology of polymers.

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.

On folding of entangled proteins: knots, lassos, links and θ-curves.

Around 6% of protein structures deposited in the PDB are entangled, forming knots, slipknots, lassos, links, and θ-curves. In each of these cases, the protein backbone weaves through itself in a complex way, and at some point passes through a closed loop, formed by other regions of the protein structure. Such a passing can be interpreted as crossing a topological barrier.