Protein topology explained

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^[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] http://www.diss.fu-berlin.de/diss/servlets/MCRFileNodeServlet/FUDISS_derivate_000000003407/08_kapitel3.pdf?hosts=. 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

External links

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

Notes and 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. 10.1016/0263-7855(85)80027-8 . 3 . 4 . Reasoning about protein topology using the logic programming language PROLOG . 1985 . Journal of Molecular Graphics . 151–157 . Rawlings . C J . Taylor . W R . Nyakairu . J . Fox . J . Sternberg . M J.E..