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 kineticsB. Scalvini et al., Topological principles of protein folding. Physical Chemistry Chemical Physics 23, 21316-21328 (2021) and stability.J. Woodard et al., Chain topology predicts pathogenicity of missense mutations. Proteins: Structure, Function, and Bioinformatics 90(9) 1634-1644 (2022)
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
External links Pro-origami: Protein structure cartoons TOPS services at Glasgow University PTGL TOPDRAW