Chemistry:Molecular knot

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Short description: Molecule whose structure resembles a knot

In chemistry, a molecular knot is a mechanically interlocked molecular architecture that is analogous to a macroscopic knot.[1] Naturally-forming molecular knots are found in organic molecules like DNA, RNA, and proteins. It is not certain that naturally occurring knots are evolutionarily advantageous to nucleic acids or proteins, though knotting is thought to play a role in the structure, stability, and function of knotted biological molecules.[2] The mechanism by which knots naturally form in molecules, and the mechanism by which a molecule is stabilized or improved by knotting, is ambiguous.[3] The study of molecular knots involves the formation and applications of both naturally occurring and chemically synthesized molecular knots. Applying chemical topology and knot theory to molecular knots allows biologists to better understand the structures and synthesis of knotted organic molecules.[1]

The term knotane was coined by Vögtle et al. in 2000 to describe molecular knots by analogy with rotaxanes and catenanes, which are other mechanically interlocked molecular architectures.[1][4] The term has not been broadly adopted by chemists and has not been adopted by IUPAC.

Crystal structure of a molecular trefoil knot with two copper(I) templating ions bound within it reported by Jean Pierre Sauvage and coworkers [5]
Crystal structure of a molecular trefoil knot reported by Vögtle and coworkers in the Angew. Chem. Int. Ed., 2000, 1616–1618.

Naturally occurring molecular knots

Organic molecules containing knots may fall into the categories of slipknots or pseudo-knots.[2] They are not considered mathematical knots because they are not a closed curve, but rather a knot that exists within an otherwise linear chain, with termini at each end. Knotted proteins are thought to form molecular knots during their tertiary structure folding process, and knotted nucleic acids generally form molecular knots during genomic replication and transcription,[6] though details of knotting mechanism continue to be disputed and ambiguous. Molecular simulations are fundamental to the research on molecular knotting mechanisms.

Knotted DNA was found first by Liu et al. in 1981, in single-stranded, circular, bacterial DNA, though double-stranded circular DNA has been found to also form knots. Naturally knotted RNA has not yet been reported.[7]

A number of proteins containing naturally occurring molecular knots have been identified. The knot types found to be naturally occurring in proteins are the [math]\displaystyle{ +3_1, -3_1, 4_1, -5_2, }[/math] and [math]\displaystyle{ +6_1 }[/math]knots, as identified in the KnotProt database of known knotted proteins.[8]

Chemically synthesized molecular knots

Several synthetic molecular knots have been reported.[9][10][11][12][13][14][15]

Crystal structure of a contra-helical trefoil knot reported by Zhichang Liu and coworkers in Nat. Synth. 2023, 2, 17–25[15]

Knot types that have been successfully synthesized in molecules are [math]\displaystyle{ 3_1, 4_1, 5_1 }[/math]and 819 knots. Though the [math]\displaystyle{ -5_2 }[/math] and [math]\displaystyle{ +6_1 }[/math] knots have been found to naturally occur in knotted molecules, they have not been successfully synthesized. Small-molecule composite knots have also not yet been synthesized.[7]

Artificial DNA, RNA, and protein knots have been successfully synthesized. DNA is a particularly useful model of synthetic knot synthesis, as the structure naturally forms interlocked structures and can be easily manipulated into forming knots[16] control precisely the raveling necessary to form knots. Molecular knots are often synthesized with the help of crucial metal ion ligands.[7]

Knot Year Reference
31 1989 [17][18]
41 2014 [19][18]
51 2012 [20][18][21]
52 2020 [22][18][23]
71 2020 [24][18]
74 2021 [25][26]
818 2018 [27][18]
819 2017 [28][18][29]

History

The first researcher to suggest the existence of a molecular knot in a protein was Jane Richardson in 1977, who reported that carbonic anhydrase B (CAB) exhibited apparent knotting during her survey of various proteins' topological behavior.[30] However, the researcher generally attributed with the discovery of the first knotted protein is Marc. L. Mansfield in 1994, as he was the first to specifically investigate the occurrence of knots in proteins and confirm the existence of the trefoil knot in CAB. Knotted DNA was found first by Liu et al. in 1981, in single-stranded, circular, bacterial DNA, though double-stranded circular DNA has been found to also form knots.[31]

In 1989, Sauvage and coworkers reported the first synthetic knotted molecule: a trefoil synthesized via a double-helix complex with the aid of Cu+ ions.[17]

Vogtle et al. was the first to describe molecular knots as knotanes in 2000.[1] Also in 2000 was William Taylor's creation of an alternative computational method to analyze protein knotting that set the termini at a fixed point far enough away from the knotted component of the molecule that the knot type could be well-defined. In this study, Taylor discovered a deep [math]\displaystyle{ 4_1 }[/math] knot in a protein.[32] With this study, Taylor confirmed the existence of deeply knotted proteins.

In 2007, Eric Yeates reported the identification of a molecular slipknot, which is when the molecule contains knotted subchains even though their backbone chain as a whole is unknotted and does not contain completely knotted structures that are easily detectable by computational models.[33] Mathematically, slipknots are difficult to analyze because they are not recognized in the examination of the complete structure.

A pentafoil knot prepared using dynamic covalent chemistry was synthesized by Ayme et al. in 2012, which at the time was the most complex non-DNA molecular knot prepared to date.[20] Later in 2016, a fully organic pentafoil knot was also reported, including the very first use of a molecular knot to allosterically regulate catalysis.[34] In January 2017, an 819 knot was synthesized by David Leigh's group, making the 819 knot the most complex molecular knot synthesized.[28]

An important development in knot theory is allowing for intra-chain contacts within an entangled molecular chain. Circuit topology has emerged as a topology framework that formalises the arrangement of contacts as well as chain crossings in a folded linear chain. As a complementary approach, Colin Adams. et al., developed a singular knot theory that is applicable to folded linear chains with intramolecular interactions.[35]

Applications

Many synthetic molecular knots have a distinct globular shape and dimensions that make them potential building blocks in nanotechnology.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 Lukin, Oleg; Vögtle, Fritz (25 February 2005). "Knotting and Threading of Molecules: Chemistry and Chirality of Molecular Knots and Their Assemblies". Angewandte Chemie International Edition 44 (10): 1456–1477. doi:10.1002/anie.200460312. PMID 15704147. 
  2. ↑ 2.0 2.1 Lim, Nicole C. H.; Jackson, Sophie E. (20 August 2015). "Molecular knots in biology and chemistry". Journal of Physics: Condensed Matter 27 (35): 354101. doi:10.1088/0953-8984/27/35/354101. ISSN 0953-8984. PMID 26291690. Bibcode: 2015JPCM...27I4101L. 
  3. ↑ Xu, Yan; Li, Shixin; Yan, Zengshuai; Luo, Zhen; Ren, Hao; Ge, Baosheng; Huang, Fang; Yue, Tongtao (2018-11-06). "Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations". Biophysical Journal 115 (9): 1681–1689. doi:10.1016/j.bpj.2018.09.015. ISSN 0006-3495. PMID 30314655. Bibcode: 2018BpJ...115.1681X. 
  4. ↑ "A Molecular Knot with Twelve Amide Groups - One-Step Synthesis, Crystal Structure, Chirality". Angewandte Chemie International Edition 39 (9): 1616–1618. 2000. doi:10.1002/(SICI)1521-3773(20000502)39:9<1616::AID-ANIE1616>3.0.CO;2-Y. PMID 10820452. 
  5. ↑ Albrecht-Gary, A. M.; Meyer, M.; Dietrich-Buchecker, C. O.; Sauvage, J. P.; Guilhem, J.; Pascard, C. (2 September 2010). "Dicopper (I) trefoil knots: Demetallation kinetic studies and molecular structures". Recueil des Travaux Chimiques des Pays-Bas 112 (6): 427–428. doi:10.1002/recl.19931120622. 
  6. ↑ Qi, Xiaodong; Zhang, Fei; Su, Zhaoming; Jiang, Shuoxing; Han, Dongran; Ding, Baoquan; Liu, Yan; Chiu, Wah et al. (2018-11-02). "Programming molecular topologies from single-stranded nucleic acids". Nature Communications 9 (1): 4579. doi:10.1038/s41467-018-07039-7. ISSN 2041-1723. PMID 30389935. Bibcode: 2018NatCo...9.4579Q. 
  7. ↑ 7.0 7.1 7.2 Fielden, Stephen D. P.; Leigh, David A.; Woltering, Steffen L. (2017-09-04). "Molecular Knots". Angewandte Chemie International Edition 56 (37): 11166–11194. doi:10.1002/anie.201702531. ISSN 1433-7851. PMID 28477423. 
  8. ↑ Jamroz, Michal; Niemyska, Wanda; Rawdon, Eric J.; Stasiak, Andrzej; Millett, Kenneth C.; Sułkowski, Piotr; Sulkowska, Joanna I. (2015-01-28). "KnotProt: a database of proteins with knots and slipknots". Nucleic Acids Research 43 (Database issue): D306–D314. doi:10.1093/nar/gku1059. ISSN 0305-1048. PMID 25361973. 
  9. ↑ Ashton, Peter R.; Matthews, Owen A.; Menzer, Stephan; Raymo, Françisco M.; Spencer, Neil; Stoddart, J. Fraser; Williams, David J. (December 1997). "Molecular Meccano, 27. A Template-directed Synthesis of a Molecular Trefoil Knot". Liebigs Annalen 1997 (12): 2485–2494. doi:10.1002/jlac.199719971210. 
  10. ↑ Rapenne, Gwénaël; Dietrich-Buchecker, and Jean-Pierre Sauvage *, Christiane; Sauvage, Jean-Pierre (February 1999). "Copper(I)- or Iron(II)-Templated Synthesis of Molecular Knots Containing Two Tetrahedral or Octahedral Coordination Sites". Journal of the American Chemical Society 121 (5): 1002–1015. doi:10.1021/ja982239+. 
  11. ↑ Feigel, Martin; Ladberg, Rüdiger; Engels, Simon; Herbst-Irmer, Regine; Fröhlich, Roland (25 August 2006). "A Trefoil Knot Made of Amino Acids and Steroids". Angewandte Chemie International Edition 45 (34): 5698–5702. doi:10.1002/anie.200601111. PMID 16856201. 
  12. ↑ Guo, Jun; Mayers, Paul C.; Breault, Gloria A.; Hunter, Christopher A. (7 February 2010). "Synthesis of a molecular trefoil knot by folding and closing on an octahedral coordination template". Nature Chemistry 2 (3): 218–222. doi:10.1038/nchem.544. PMID 21124480. Bibcode: 2010NatCh...2..218G. 
  13. ↑ Barran, Perdita E.; Cole, Harriet L.; Goldup, Stephen M.; Leigh, David A.; McGonigal, Paul R.; Symes, Mark D.; Wu, Jhenyi; Zengerle, Michael (16 December 2011). "Active-Metal Template Synthesis of a Molecular Trefoil Knot". Angewandte Chemie International Edition 50 (51): 12280–12284. doi:10.1002/anie.201105012. PMID 21919173. 
  14. ↑ Carina, Riccardo F.; Dietrich-Buchecker, Christiane; Sauvage, Jean-Pierre (January 1996). "Molecular Composite Knots". Journal of the American Chemical Society 118 (38): 9110–9116. doi:10.1021/ja961459p. 
  15. ↑ 15.0 15.1 Wu, L; Tang, M; Jiang, L; Chen, Y; Bian, L; Liu, J; Wang, S; Liang, Y et al. (2023). "Synthesis of contra-helical trefoil knots with mechanically tuneable spin-crossover properties". Nature Synthesis 2: 17–25. doi:10.1038/s44160-022-00173-7. ISSN 2468-5194. 
  16. ↑ Sauvage, Jean-Pierre; Amabilino, David B. (2012), "Templated Synthesis of Knots and Ravels", Supramolecular Chemistry (American Cancer Society), doi:10.1002/9780470661345.smc085, ISBN 978-0-470-66134-5 
  17. ↑ 17.0 17.1 Dietrich‐Buchecker, Christiane O.; Sauvage, Jean-Pierre (1989). "A Synthetic Molecular Trefoil Knot". Angewandte Chemie International Edition in English 28 (2): 189–192. doi:10.1002/anie.198901891. ISSN 1521-3773. 
  18. ↑ 18.0 18.1 18.2 18.3 18.4 18.5 18.6 Schaufelberger, Fredrik (2020-12-04). "Open questions in functional molecular topology" (in en). Communications Chemistry 3 (1): 182. doi:10.1038/s42004-020-00433-7. ISSN 2399-3669. PMID 36703419. 
  19. ↑ Ponnuswamy, Nandhini; Cougnon, Fabien B. L.; Pantoş, G. Dan; Sanders, Jeremy K. M. (2014-06-11). "Homochiral and meso Figure Eight Knots and a Solomon Link" (in en). Journal of the American Chemical Society 136 (23): 8243–8251. doi:10.1021/ja4125884. ISSN 0002-7863. PMID 24831779. https://pubs.acs.org/doi/10.1021/ja4125884. 
  20. ↑ 20.0 20.1 Ayme, Jean-François; Beves, Jonathon E.; Leigh, David A.; McBurney, Roy T.; Rissanen, Kari; Schultz, David (6 November 2011). "A synthetic molecular pentafoil knot". Nature Chemistry 4 (1): 15–20. doi:10.1038/nchem.1193. PMID 22169866. Bibcode: 2012NatCh...4...15A. 
  21. ↑ "Tying Molecules in Knots". https://www.catenane.net/pages/2012knot.html. 
  22. ↑ Leigh, David A.; Schaufelberger, Fredrik; Pirvu, Lucian; Stenlid, Joakim Halldin; August, David P.; Segard, Julien (2020-08-27). "Tying different knots in a molecular strand" (in en). Nature 584 (7822): 562–568. doi:10.1038/s41586-020-2614-0. ISSN 0028-0836. PMID 32848222. https://www.nature.com/articles/s41586-020-2614-0. 
  23. ↑ "Molecular 5-2 Knot". https://www.catenane.net/pages/2020_molecular_5_2_knot.html. 
  24. ↑ Inomata, Yuuki; Sawada, Tomohisa; Fujita, Makoto (January 2020). "Metal-Peptide Torus Knots from Flexible Short Peptides" (in en). Chem 6 (1): 294–303. doi:10.1016/j.chempr.2019.12.009. https://linkinghub.elsevier.com/retrieve/pii/S245192941930556X. 
  25. ↑ Leigh, David A.; Danon, Jonathan J.; Fielden, Stephen D. P.; Lemonnier, Jean-François; Whitehead, George F. S.; Woltering, Steffen L. (February 2021). "A molecular endless (74) knot" (in en). Nature Chemistry 13 (2): 117–122. doi:10.1038/s41557-020-00594-x. ISSN 1755-4330. PMID 33318672. https://www.nature.com/articles/s41557-020-00594-x. 
  26. ↑ "Endless Knot". https://www.catenane.net/pages/2020_endless_knot.html. 
  27. ↑ Kim, Dong Hwan; Singh, Nem; Oh, Jihun; Kim, Eun‐Hee; Jung, Jaehoon; Kim, Hyunuk; Chi, Ki‐Whan (2018-05-14). "Coordination‐Driven Self‐Assembly of a Molecular Knot Comprising Sixteen Crossings" (in en). Angewandte Chemie International Edition 57 (20): 5669–5673. doi:10.1002/anie.201800638. ISSN 1433-7851. PMID 29569315. https://onlinelibrary.wiley.com/doi/10.1002/anie.201800638. 
  28. ↑ 28.0 28.1 Danon, Jonathan J.; Krüger, Anneke; Leigh, David A.; Lemonnier, Jean-François; Stephens, Alexander J.; Vitorica-Yrezabal, Iñigo J.; Woltering, Steffen L. (2017-01-13). "Braiding a molecular knot with eight crossings". Science 355 (6321): 159–162. doi:10.1126/science.aal1619. ISSN 0036-8075. PMID 28082585. Bibcode: 2017Sci...355..159D. https://www.research.manchester.ac.uk/portal/en/publications/braiding-a-molecular-knot-with-eight-crossings(678fc632-5cef-4f03-a6b4-cd2c719f5763).html. 
  29. ↑ "A Synthetic Molecular 819 Knot". https://www.catenane.net/pages/2017_819knot.html. 
  30. ↑ Richardson, Jane S. (August 1977). "β-Sheet topology and the relatedness of proteins". Nature 268 (5620): 495–500. doi:10.1038/268495a0. ISSN 1476-4687. PMID 329147. Bibcode: 1977Natur.268..495R. 
  31. ↑ Liu, L F; Davis, J L; Calendar, R (1981-08-25). "Novel topologically knotted DNA from bacteriophage P4 capsids: studies with DNA topoisomerases.". Nucleic Acids Research 9 (16): 3979–3989. doi:10.1093/nar/9.16.3979. ISSN 0305-1048. PMID 6272191. 
  32. ↑ Faísca, Patrícia F. N. (2015-01-01). "Knotted proteins: A tangled tale of Structural Biology". Computational and Structural Biotechnology Journal 13: 459–468. doi:10.1016/j.csbj.2015.08.003. ISSN 2001-0370. PMID 26380658. 
  33. ↑ King, Neil P.; Yeates, Eric O.; Yeates, Todd O. (2007-10-12). "Identification of Rare Slipknots in Proteins and Their Implications for Stability and Folding". Journal of Molecular Biology 373 (1): 153–166. doi:10.1016/j.jmb.2007.07.042. ISSN 0022-2836. PMID 17764691. 
  34. ↑ Marcos, Vanesa; Stephens, Alexander J.; Jaramillo-Garcia, Javier; Nussbaumer, Alina L.; Woltering, Steffen L.; Valero, Alberto; Lemonnier, Jean-François; Vitorica-Yrezabal, Iñigo J. et al. (2016-06-24). "Allosteric initiation and regulation of catalysis with a molecular knot". Science 352 (6293): 1555–1559. doi:10.1126/science.aaf3673. ISSN 0036-8075. PMID 27339983. Bibcode: 2016Sci...352.1555M. https://www.research.manchester.ac.uk/portal/en/publications/allosteric-initiation-and-regulation-of-catalysis-with-a-molecular-knot(24654363-2a06-4fe4-aaa2-2a7b01b7f936).html. 
  35. ↑ Colin Adams, Judah Devadoss, Mohamed Elhamdadi and Alireza Mashaghi, Knot theory for proteins: Gauss codes, quandles and bondles. Journal of Mathematical Chemistry volume 58, pages1711–1736(2020)

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