Knot theory for proteins: Gauss codes, quandles and bondles

DOI10.1007/S10910-020-01151-0MaRDI QIDQ2201029zbMATH OpenOpenAlexFDO

Authors Judah Devadoss, Mohamed Elhamdadi, Alireza Mashaghi, Colin Adams

Publication date 24 September 2020

Published in Journal of Mathematical Chemistry (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://arxiv.org/abs/1912.09353

zbMATH Keywords

topologyknotproteinquandleGauss codesbondle

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Knot theory (57K10)

Abstract: Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that 97% of proteins are, however, classified as unknots when intra-chain interactions are ignored. This raises the question as to whether knot theory can be extended to include intra-chain interactions and thus be able to categorize topology of the proteins that are otherwise classified as unknotted. Here, we develop knot theory for folded linear molecular chains and apply it to proteins. For this purpose, proteins will be thought of as an embedding of a linear segment into three dimensions, with additional structure coming from self-bonding. We then project to a two-dimensional diagram and consider the basic rules of equivalence between two diagrams. We further consider the representation of projections of proteins using Gauss codes, or strings of numbers and letters, and how we can equate these codes with changes allowed in the diagrams. Finally, we explore the possibility of applying the algebraic structure of quandles to distinguish the topologies of proteins. Because of the presence of bonds, we extend the theory to define bondles, a type of quandle particularly adapted to distinguishing the topological types of proteins.

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Cited in

(10)

• Knot theory in understanding proteins
• Protein folding invariants
• The Chern-Simons current in time series of knots and links in proteins
• Invariants of multi-linkoids
• Topological complexity in protein structures
• A knot polynomial invariant for analysis of topology of RNA stems and protein disulfide bonds
• Knotoids and protein structure
• Enhancement of the coloring invariant for folded molecular chains
• A relation between the crossing number and the height of a knotoid
• On the minimum number of Fox colorings of knots

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