Topological Complexity in Protein Structures

Erica Flapan; Gabriella Heller

Molecular Based Mathematical Biology (2015)

  • Volume: 3, Issue: 1
  • ISSN: 2299-3266

Abstract

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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.

How to cite

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Erica Flapan, and Gabriella Heller. "Topological Complexity in Protein Structures." Molecular Based Mathematical Biology 3.1 (2015): null. <http://eudml.org/doc/270849>.

@article{EricaFlapan2015,
abstract = {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.},
author = {Erica Flapan, Gabriella Heller},
journal = {Molecular Based Mathematical Biology},
keywords = {non-planarity; proteins; topology; knots; links; spatial graphs; Möbius ladders},
language = {eng},
number = {1},
pages = {null},
title = {Topological Complexity in Protein Structures},
url = {http://eudml.org/doc/270849},
volume = {3},
year = {2015},
}

TY - JOUR
AU - Erica Flapan
AU - Gabriella Heller
TI - Topological Complexity in Protein Structures
JO - Molecular Based Mathematical Biology
PY - 2015
VL - 3
IS - 1
SP - null
AB - 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.
LA - eng
KW - non-planarity; proteins; topology; knots; links; spatial graphs; Möbius ladders
UR - http://eudml.org/doc/270849
ER -

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