Pełnotekstowe zasoby PLDML oraz innych baz dziedzinowych są już dostępne w nowej Bibliotece Nauki.
Zapraszamy na https://bibliotekanauki.pl

PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2015 | 3 | 1 |

Tytuł artykułu

Topological Complexity in Protein Structures

Treść / Zawartość

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
For DNA molecules, topological complexity occurs exclusively as the result of knotting or linking of the polynucleotide backbone. By contrast, while a few knots and links have been found within the polypeptide backbones of some protein structures, non-planarity can also result from the connectivity between a polypeptide chain and inter- and intra-chain linking via cofactors and disulfide bonds. In this article, we survey the known types of knots, links, and non-planar graphs in protein structures with and without including such bonds and cofactors. Then we present new examples of protein structures containing Möbius ladders and other non-planar graphs as a result of these cofactors. Finally, we propose hypothetical structures illustrating specific disulfide connectivities that would result in the key ring link, the Whitehead link and the 51 knot, the latter two of which have thus far not been identified within protein structures.

Wydawca

Rocznik

Tom

3

Numer

1

Opis fizyczny

Daty

otrzymano
2014-02-08
zaakceptowano
2015-01-16
online
2015-05-04

Twórcy

autor
  • Department of Mathematics, Pomona College, 640 North College Avenue, Claremont, CA 91711 USA
  • Department of Mathematics, Pomona College, 640 North College Avenue, Claremont, CA 91711 USA

Bibliografia

  • [1] Andrew Belmonte, Michael J Shelley, Shaden T Eldakar, and Chris HWiggins. Dynamic patterns and self-knotting of a driven hanging chain. Physical review letters, 87(11):114301, 2001. [Crossref]
  • [2] Daniel Bölinger, Joanna I Sułkowska, Hsiao-Ping Hsu, Leonid A Mirny, Mehran Kardar, José N Onuchic, and Peter Virnau. A stevedore’s protein knot. PLoS computational biology, 6(4):e1000731, 2010. [WoS][Crossref]
  • [3] Zhenbo Cao, Aleksander W Roszak, Louise J Gourlay, J Gordon Lindsay, and Neil W Isaacs. Bovine mitochondrial peroxiredoxin iii forms a two-ring catenane. Structure, 13(11):1661–1664, 2005. [Crossref]
  • [4] Frank B Dean, Andrzej Stasiak, Theo Koller, and Nicolas R Cozzarelli. Duplex dna knots produced by escherichia coli topoisomerase i. structure and requirements for formation. Journal of Biological Chemistry, 260(8):4975–4983, 1985.
  • [5] Harry L Frisch and EdelWasserman. Chemical topology. Journal of the American Chemical Society, 83(18):3789–3795, 1961. [Crossref]
  • [6] Jack D Griflth and Howard A Nash. Genetic rearrangement of dna induces knots with a unique topology: implications for the mechanism of synapsis and crossing-over. Proceedings of the National Academy of Sciences, 82(10):3124–3128, 1985.
  • [7] Vsevolod Katritch, Wilma K Olson, Alexander Vologodskii, Jacques Dubochet, and Andrzej Stasiak. Tightness of random knotting. Physical Review E, 61(5):5545, 2000. [Crossref]
  • [8] Firas Khatib, Matthew T Weirauch, and Carol A Rohl. Rapid knot detection and application to protein structure prediction. Bioinformatics, 22(14):e252–e259, 2006. [Crossref]
  • [9] Chengzhi Liang and Kurt Mislow. Knots in proteins. Journal of the American Chemical Society, 116(24):11189–11190, 1994. [WoS][Crossref]
  • [10] Chengzhi Liang and Kurt Mislow. Topological chirality of proteins. Journal of the American Chemical Society, 116(8):3588– 3592, 1994. [Crossref]
  • [11] Chengzhi Liang and Kurt Mislow. Topological features of protein structures: knots and links. Journal of the American Chemical Society, 117(15):4201–4213, 1995. [Crossref]
  • [12] Rhonald C Lua and Alexander Y Grosberg. Statistics of knots, geometry of conformations, and evolution of proteins. PLoS computational biology, 2(5):e45, 2006. [Crossref]
  • [13] Anna L Mallam and Sophie E Jackson. A comparison of the folding of two knotted proteins: Ybea and yibk. Journal of molecular biology, 366(2):650–665, 2007.
  • [14] Marc L Mansfield. Are there knots in proteins? Nature Structural & Molecular Biology, 1(4):213–214, 1994.
  • [15] Gurvan Michel, Véronique Sauvé, Robert Larocque, Yunge Li, Allan Matte, and Miroslaw Cygler. The structure of the rlmb 23s rrna methyltransferase reveals a new methyltransferase fold with a unique knot. Structure, 10(10):1303–1315, 2002. [Crossref]
  • [16] Kenneth C Millet and Benjamin M Sheldon. Tying down open knots: A statistical method for identifying open knots with applications to proteins. In Jorge A Calvo, Kenneth C Millet, Eric J Rawdon, and Andrzej Stasiak, editors, Physical and numerical models in knot theory. Singapore: World Scientific, pages 203–217. 2005.
  • [17] Kenneth Millett, Akos Dobay, and Andrzej Stasiak. Linear random knots and their scaling behavior. Macromolecules, 38(2):601–606, 2005. [Crossref]
  • [18] Kenneth C Millett. Physical knot theory: an introduction to the study of the influence of knotting on the spatial characteristics of polymers. In Introductory Lectures on Knot Theory: Selected Lectures Presented at the Advanced School and Conference on Knot Theory and Its Applications to Physics and Biology, volume 46, pages 346–378. World Scientific, 2011.
  • [19] Kenneth C Millett, Eric J Rawdon, Andrzej Stasiak, Joanna I Sułkowska, et al. Identifying knots in proteins. Biochemical Society Transactions, 41(part 2):533–537, 2013. [WoS][Crossref]
  • [20] Eleni Panagiotou, Kenneth C Millett, and Sofia Lambropoulou. Quantifying entanglement for collections of chains in models with periodic boundary conditions. Procedia IUTAM, 7:251–260, 2013. [Crossref]
  • [21] Eleni Panagiotou, Christos Tzoumanekas, Sofia Lambropoulou, Kenneth C Millett, and Doros N Theodorou. A study of the entanglement in systems with periodic boundary conditions. Progress of Theoretical Physics Supplement, 191:172–181, 2011.
  • [22] Piotr Pierański, Sylwester Przybył, and Andrzej Stasiak. Tight open knots. The European Physical Journal E, 6(2):123–128, 2001. [Crossref]
  • [23] Elizabeth Pleshe, John Truesdell, and Robert T. Batey. Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus. Acta Crystallographica Section F, 61(8):722–728, Aug 2005. [Crossref]
  • [24] Raffaello Potestio, Cristian Micheletti, and Henri Orland. Knotted vs. unknotted proteins: evidence of knot-promoting loops. PLoS computational biology, 6(7):e1000864, 2010. [WoS][Crossref]
  • [25] Eric J Rawdon, Kenneth C Millett, Joanna I Sułkowska, Andrzej Stasiak, et al. Knot localization in proteins. Biochemical Society Transactions, 41(part 2):538–541, 2013. [WoS][Crossref]
  • [26] Dale Rolfsen. Knots and links. Publish or Perish Inc., Berkeley, Calif., 1976. Mathematics Lecture Series, No. 7.
  • [27] K Johan Rosengren, Norelle L Daly, Manuel R Plan, Clement Waine, and David J Craik. Twists, knots, and rings in proteins structural definition of the cyclotide framework. Journal of Biological Chemistry, 278(10):8606–8616, 2003.
  • [28] Chris Sander and Reinhard Schneider. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Structure, Function, and Bioinformatics, 9(1):56–68, 1991.
  • [29] Jonathan Simon. Topological chirality of certain molecules. Topology, 25(2):229–235, 1986. [Crossref]
  • [30] Jonathan Simon. Long tangled filaments. Applications of Knot Theory:AmericanMathematical Society, Short Course, January 4-5, 2008, San Diego, California, 66:155, 2009.
  • [31] Thomas Spatzal, Müge Aksoyoglu, Limei Zhang, Susana LA Andrade, Erik Schleicher, Stefan Weber, Douglas C Rees, and Oliver Einsle. Evidence for interstitial carbon in nitrogenase femo cofactor. Science, 334(6058):940–940, 2011. [WoS]
  • [32] Fusao Takusagawa and Shigehiro Kamitori. A real knot in protein. Journal of the American Chemical Society, 118(37):8945– 8946, 1996. [WoS][Crossref]
  • [33] William R Taylor. A deeply knotted protein structure and how it might fold. Nature, 406(6798):916–919, 2000.
  • [34] William R Taylor. Protein knots and fold complexity: some new twists. Computational biology and chemistry, 31(3):151–162, 2007.
  • [35] EJ Janse Van Rensburg, DAW Sumners, E Wasserman, and SG Whittington. Entanglement complexity of self-avoiding walks. Journal of Physics A: Mathematical and General, 25(24):6557, 1992.
  • [36] Peter Virnau, Leonid A Mirny, and Mehran Kardar. Intricate knots in proteins: Function and evolution. PLoS computational biology, 2(9):e122, 2006. [Crossref]
  • [37] David M Walba. Topological stereochemistry. Tetrahedron, 41(16):3161–3212, 1985. [Crossref]
  • [38] David M Walba, Rodney M Richards, and R Curtis Haltiwanger. Total synthesis of the first molecular möbius strip. Journal of the American Chemical Society, 104(11):3219–3221, 1982. [Crossref]
  • [39] Edel Wasserman. Chemical topology. Scientific American, 207:94–102, 1962.
  • [40] Steven A Wasserman, Jan M Dungan, and Nicholas R Cozzarelli. Discovery of a predicted dna knot substantiates a model for site-specific recombination. Science, 229(4709):171–174, 1985.
  • [41] William RWikoff, Lars Liljas, Robert L Duda, Hiro Tsuruta, RogerWHendrix, and John E Johnson. Topologically linked protein rings in the bacteriophage hk97 capsid. Science, 289(5487):2129–2133, 2000.
  • [42] Todd O Yeates, Todd S Norcross, and Neil P King. Knotted and topologically complex proteins as models for studying folding and stability. Current opinion in chemical biology, 11(6):595–603, 2007.

Typ dokumentu

Bibliografia

Identyfikatory

Identyfikator YADDA

bwmeta1.element.doi-10_1515_mlbmb-2015-0002
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.