![]() ![]() In the present study we consider knots of the simplest type, referred to as a trefoil or 3 1 knot. Simulations are performed for 3 knotted proteins (YibK and YbeA) and 2 proteins with slipknots (AFV3-109 and thymidine kinase) by using structure-based coarse-grained models. ![]() To complement the experimental information, we have devised a theoretical computational strategy. These results alone, however, are not sufficient to explain the folding mechanism. In this model the threading of the polypeptide chain and formation of the native structure in the knotted region can occur independently as successive events. In very recent experimental work ( 13), based on analysis of the effect of mutations in the knotted region of the protein, a folding model for YibK was also proposed. It has been shown experimentally that both these proteins unfold spontaneously and reversibly on addition of chemical denaturant ( 8– 11) and they are able to fold even when additional domains are attached to one or both termini ( 12). A schematic representation of these proteins is shown in Fig. This folding mechanism is explored in the context of the two most experimentally investigated knotted families of proteins, Haemophilus influenzae YibK and Escherichia coli YbeA, which are homodimeric α/β-knot methyltransferases (MTases). The fact that such slipknots have already been observed in some protein final structures ( 7) adds support to this suggestion. We suggest a possible mechanism where the knot formation is preceded by a conformation called a “slipknot.” A slipknot is topologically similar to a knot, except that an internal knot is effectively undone as the pathway of the backbone folds back on itself. Although these “knotted” folding motifs have been observed, we still have to face the challenging question of how the protein overcomes the kinetic barrier associated with the search of the knotted conformation. Most proteins avoid complex topologies, but recent discoveries have shown that some proteins are actually able to fold into nontrivial topologies where the main chain folds into a knotted conformation ( 4– 6). Because proteins have been able to solve the energy problem, the final challenge is the structural complexity of the protein folding motifs. ![]() Most small- and intermediate-size proteins live on a minimally frustrated funnel-like energy landscape, which allows fast and robust folding ( 1– 3). The ropes yield excellent strength from the fibers, and the splices weaken the ropes hardly at all.During the past 2 decades, a joint theoretical and experimental effort has largely advanced the quantitative understanding of the protein folding mechanism. These ropes require suitable splicing techniques such as the Brummel and Long Bury. ![]() These fibers encouraged the development of the loosely woven, hollow braid ropes in which the fiber-alignment maximized strength. Modern, strong, high modulus fibers are often slippery and cannot be secured with customarily trustworthy knots and splices. Some workers installing electricity cables, however, have reported using the same splice to haul cables through buried pipes. We created it to make a Sailor's Rope Belt – for which it is well suited – and was never intended to take a critical load. With tapering, a breaking strain approaching 100% of the rope's rated strength is possible - especially with the Brummel and Long Bury techniques. StrengthĬareful tapering of the strands, or of the buried end, preserves strength it ensures a gradual transition of the fiber-alignment in the strands of the standing end. Undoing a splice and re-making it takes much more time than doing the same with most knots. A Splice is usually significantly stronger than a knot and is intended to be permanent. ![]()
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