ArticleBiophysical journal2009
Sequence-specific size, structure, and stability of tight protein knots.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Properties Governing Native State Entanglements and Relationships to Protein Function.Journal of molecular biology · 2025Article
- Folding a Molecular Strand into a Trefoil Knot of Single Handedness with Co(II)/Co(III) Chaperones.Journal of the American Chemical Society · 2024Article
- Effect of temperature and nucleotide on the binding of BiP chaperone to a protein substrate.Protein science : a publication of the Protein Society · 2023Article
- Temperature dependent mechanical unfolding and refolding of a protein studied by thermo-regulated optical tweezers.Biophysical journal · 2023Article
- Effects of turn-structure on folding and entanglement in artificial molecular overhand knots.Chemical science · 2020Article
- Mechanical unfolding of a knotted protein unveils the kinetic and thermodynamic consequences of threading a polypeptide chain.Scientific reports · 2020Article
- The AAA+ protease ClpXP can easily degrade a 3Scientific reports · 2019Article
- Effects of knot tightness at the molecular level.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Stereoselective synthesis of a composite knot with nine crossings.Nature chemistry · 2018Article
- The Pathways of the iRFP713 Unfolding Induced by Different Denaturants.International journal of molecular sciences · 2018Article
- The energy cost of polypeptide knot formation and its folding consequences.Nature communications · 2017Article
- To Tie or Not to Tie? That Is the Question.Polymers · 2017Review
- Knots can impair protein degradation by ATP-dependent proteases.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Knotting and unknotting of a protein in single molecule experiments.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Periodic forces trigger knot untying during translocation of knotted proteins.Scientific reports · 2016Article
- A knot in the protein structure - probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochrome.The FEBS journal · 2014Article
- The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations.Biomolecules · 2013Review
- Knot theory in understanding proteins.Journal of mathematical biology · 2012Review
- Conservation of complex knotting and slipknotting patterns in proteins.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Experimental detection of knotted conformations in denatured proteins.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
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Abstract
Approximately 1% of known protein structures display knotted configurations in their native fold, but the function of these configurations is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport, e.g., as in cellular threading or translocation processes through narrow biological pores. Protein knot manipulation, e.g., knot tightening and localization, has become possible in single-molecule experiments. Here, we investigate tight peptide knot (TPK) characteristics in detail by pulling selected 3(1) and 4(1)-knotted peptides using all-atom molecular dynamics computer simulations. We find that the 3(1)- and 4(1)-TPK lengths are typically Deltal approximately 47+/- 4 A and 69 +/- 4 A, respectively, for a wide range of tensions (0.1 nN less, similarF less, similar 1.5 nN). The 4(1)-knot length is in agreement with recent atomic force microscopy pulling experiments. Calculated TPK radii of gyration point to a pore diameter of approximately 20 A, below which a translocated knotted protein might get stuck. TPK characteristics, however, may be sequence-specific: we find a different size and structural behavior in polyglycines, and, strikingly, a strong hydrogen bonding and water trapping capability of hydrophobic TPKs. Water capture and release is found to be controllable by the tightening force in a few cases. These mechanisms result in a sequence-specific "locking" and metastability of TPKs, which might lead to a blocking of knotted peptide transport at designated sequence positions. We observe that macroscopic tight 4(1)-knot structures are reproduced microscopically ("figure of eight" versus the "pretzel") and can be tuned by sequence, in contrast to mathematical predictions. Our findings may explain a function of knots in native proteins, challenge previous studies on macromolecular knots, and prove useful in bio- and nanotechnology.
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