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

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 and stability.

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 . 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

• Circuit topology
• Membrane topology
• Protein folding

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.

External links

• Pro-origami: Protein structure cartoons
• TOPS services at Glasgow University
• PTGL
• TOPDRAW

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