“…In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. …”
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“…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 knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. …”
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“…A new class of proteins, involving cystein slipknots, is identified as one that is expected to lead to the strongest force clamps known. …”
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“…These proteins are structurally distinct from Class I TEDs due to a β‐sandwich domain that is inserted into the conserved TED fold to form a slipknot structure. Further, the B. anthracis TED domain is presented in the context of a full‐length sortase‐anchored protein structure (BaTIE). …”
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“…While the slipknot topology in proteins has been known for over a decade, its evolutionary origin is still a mystery. …”
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“…Using multiple sequence alignments (MSA), a unique insert was identified in loop 1 that exacerbates the appearance of the atypical fold-giving it a slipknot-like topology. However, PfDHFR has not been deposited in the knotted proteins database, and processing its structure failed to identify any knots within its folds. …”
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“…We observe that the final slipknot causes a slight swelling of the folded AFV3-109 structure. …”
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“…Molecular modeling predicts that CRPs contain a cystine slipknot motif, but experimental evidence to support this assertion remains to be reported. …”
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“…METHODS: Thirty rabbits were divided into three groups: group A) Fundus-first technique by Hook dissecting instrument and Roeder Slipknot applied for cystic duct (CD) ligation; group B) conventional technique by Maryland dissecting forceps and electrothermal bipolar vessel sealing (EBVS) for CD seal; group C) conventional technique by EBVS for gallbladder (GB) dissection and CD seal. …”
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“…In the stylet group, the NGT was inserted with the assistance of a “Rusch” intubation stylet tied together at the tips by a slipknot. The success rates of the two methods, the durations of the insertions, and the occurrences of complications were recorded. …”
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“…The KnotProt database did not predict any knot or slipknot in the protein structure of CLDN16. Seven putative miRNA binding sites within the 3’-UTR region of CLDN16 were identified. …”
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“…We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. …”
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“…Male C57BL/6J mice (8‐10‐week‐old) were administered adenovirus MITOL shRNA through intracardiac injection followed by MI/R surgery through ligation and release the slipknot of cardiac left anterior descending coronary artery. …”
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“…The ProGlide’s knot-pushers are used to push down the pledget and the hand-made slipknot to seal the femoral artery leak. This technique was used as a bailout strategy in patients undergoing TF-TAVR with a systematic double pre-closure technique. …”
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“…By analyzing a small set of two-state and multi-state proteins with no knots or slipknots, our results show that 95.4% of the analyzed proteins have non-trivial topological characteristics, as reflected by the second Vassiliev measure, and that the logarithm of the experimental protein folding rate depends on both the local geometry and the topology of the protein’s native state.…”
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“…Around 6% of protein structures deposited in the PBD are entangled, forming knots, slipknots, lassos and links. We present theoretical methods and tools that enabled discovering and classifying such structures. …”
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“…Protein chains are known to fold into topologically complex shapes, such as knots, slipknots or complex lassos. This complex topology of the chain can be considered as an additional feature of a protein, separate from secondary and tertiary structures. …”
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“…This package enables the distinguishing of knots, slipknots, links and spatial graphs through the calculation of different topological polynomial invariants. …”
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“…Knot_pull is a command line utility designed to simplify this process—it presents the user with a smoothing trajectory for provided structures (any number and length of protein, RNA or chromatin chains in PDB, CIF or XYZ format), and calculates the knot type (including presence of any links, and slipknots when a subchain is specified). AVAILABILITY AND IMPLEMENTATION: Knot_pull works under Python >=2.7 and is system independent. …”
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