Protein topology

Protein topology is a property of protein molecule that does not change under deformation (without cutting or breaking a bond).

Topology of beta-strands in "Greek-key" protein motif.

Frameworks

Two main topology frameworks have been developed and applied to protein molecules.

Knot Theory

Knot theory which categorises chain entanglements. The usage of knot theory is limited to a small percentage of proteins as most of them are unknot.

Circuit topology

Circuit topology categorises intra-chain contacts based on their arrangements. Circuit topology is a determinant of protein folding kinetics[1] and stability.[2]

Other Uses

In biology literature, the term topology is also used to refer to mutual orientation of regular secondary structures, such as alpha-helices and beta strands in protein structure[3] . For example, two adjacent interacting alpha-helices or beta-strands can go in the same or in opposite directions. Topology diagrams of different proteins with known three-dimensional structure are provided by PDBsum (an example).

See also

References
  1. B. Scalvini et al., Topological principles of protein folding. Physical Chemistry Chemical Physics 23, 21316-21328 (2021)
  2. J. Woodard et al., Chain topology predicts pathogenicity of missense mutations. Proteins: Structure, Function, and Bioinformatics 90(9) 1634-1644 (2022)
  3. Rawlings, C J; Taylor, W R; Nyakairu, J; Fox, J; Sternberg, M J.E. (1985). "Reasoning about protein topology using the logic programming language PROLOG". Journal of Molecular Graphics. 3 (4): 151–157. doi:10.1016/0263-7855(85)80027-8.


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