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
In topology, knot theory is the study of knot (mathematics), mathematical knots. While inspired by knots which appear in daily life, such as those in shoelaces and rope, a mathematical knot differs in that the ends are joined so it cannot be und ...
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
The circuit topology of a folded linear polymer refers to the arrangement of its intra-molecular contacts. Examples of linear polymers with intra-molecular contacts are nucleic acids and proteins. Proteins fold via the formation of contacts of v ...
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 strand
The beta sheet (β-sheet, also β-pleated sheet) is a common structural motif, motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone chain, backbon ...
s in
protein structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid ...
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
The circuit topology of a folded linear polymer refers to the arrangement of its intra-molecular contacts. Examples of linear polymers with intra-molecular contacts are nucleic acids and proteins. Proteins fold via the formation of contacts of v ...
* Membrane topology Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect to the inner or outer sides of the biological membrane occupied by the protein.
Several databases provide experimental ...
* Protein folding
Protein folding is the physical process by which a protein, after Protein biosynthesis, synthesis by a ribosome as a linear chain of Amino acid, amino acids, changes from an unstable random coil into a more ordered protein tertiary structure, t ...
References
External links
Pro-origami: Protein structure cartoonsTOPS services at Glasgow UniversityPTGL
Protein structure
Molecular topology
{{Protein-stub