相关论文: How knots influence properties of proteins

Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a…

A number of recently discovered protein structures incorporate a rather unexpected structural feature: a knot in the polypeptide backbone. These knots are extremely rare, but their occurrence is likely connected to protein function in as…

Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…

Proteins can sometimes be knotted, and for many reasons the study of knotted proteins is rapidly becoming very important. For example, it has been proposed that a knot increases the stability of a protein. Knots may also alter enzymatic…

Many experiments have been done to determine the relative strength of different knots, and these show that the break in a knotted rope almost invariably occurs at a point just outside the `entrance' to the knot. The influence of knots on…

An increasing number of proteins are being discovered with a remarkable and somewhat surprising feature, a knot in their native structures. How the polypeptide chain is able to knot itself during the folding process to form these highly…

Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…

Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…

Although rare, an increasing number of proteins have been observed to contain entanglements in their native structures. To gain more insight into the significance of protein knotting, researchers have been investigating protein knot…

Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and…

Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…

The computer artificial intelligence system AlphaFold has recently predicted previously unknown three-dimensional structures of thousands of proteins. Focusing on the subset with high-confidence scores, we algorithmically analyze these…

Protein MJ0366 is a hypothetical protein from Methanocaldococcus jannaschii that has a rare and complex knot in its structure. The knot is a right-handed trefoil knot that involves about half of the protein's residues. In this article, we…

Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport,…

We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they…

Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…

Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…

Apart from the knots formed by the main-chain, the proteins can form numerous topological structures, when included the covalent and ion-mediated interactions. In this work, we define the protein non-trivial $\theta$-curves and identify 7…

The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…

The mechanical resistance of a polyethylene strand subject to tension and the way its properties are affected by the presence of a knot is studied using first-principles molecular dynamics calculations. The distribution of strain energy for…