In this review, we provide an organized summary of the theoretical and computational results that are available for polymers subject to spatial or topological constraints. Because …
The protein topology database KnotProt, http://knotprot. cent. uw. edu. pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots …
The last decade has shown that there are an increasing numbers of known proteins that contain linear open knots or slipknots in their native folded structure. In general, knots in …
NCH Lim, SE Jackson - Journal of Physics: Condensed Matter, 2015 - iopscience.iop.org
Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance …
MA Brems, R Runkel, TO Yeates, P Virnau - Protein Science, 2022 - Wiley Online Library
The computer artificial intelligence system AlphaFold has recently predicted previously unknown three‐dimensional structures of thousands of proteins. Focusing on the subset with …
JI Sulkowska - Current opinion in structural biology, 2020 - Elsevier
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 …
STD Hsu - Current Opinion in Structural Biology, 2023 - Elsevier
Topologically knotted proteins have entangled structural elements within their native structures that cannot be disentangled simply by pulling from the N-and C-termini …
The interplay between the topological and geometrical properties of a polymer ring can be clarified by establishing the entanglement trapped in any portion (arc) of the ring. The task …
Highlights•Knotted proteins span diverse biological functions and cover∼ 1% of all PDB entries.•Reaching their knotted native states requires a concerted series of folding …