Protein topology: Difference between revisions
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{{Short description|Invariant property of protein molecules}} |
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[[Image:Anthrax toxin protein key motif.svg|right|thumb|100px|Topology of beta-strands in "Greek-key" [[protein motif]].]] |
[[Image:Anthrax toxin protein key motif.svg|right|thumb|100px|Topology of beta-strands in "Greek-key" [[protein motif]].]] |
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'''Protein topology''' is a property of protein molecule that does not change under deformation (without cutting or breaking a bond). |
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==Frameworks== |
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Two main topology frameworks have been developed and applied to protein molecules. |
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===Knot Theory=== |
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[[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. |
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===Circuit topology=== |
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[[Circuit topology]] categorises intra-chain contacts based on their arrangements. Circuit topology is a determinant of protein folding kinetics<ref>B. Scalvini et al., Topological principles of protein folding. Physical Chemistry Chemical Physics 23, 21316-21328 (2021)</ref> and stability.<ref>J. Woodard et al., Chain topology predicts pathogenicity of missense mutations. Proteins: Structure, Function, and Bioinformatics 90(9) 1634-1644 (2022)</ref> |
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==Other Uses== |
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| ⚫ | In biology literature, the term topology is also used to refer to mutual orientation of regular [[Protein secondary structure|secondary structures]], such as [[alpha-helices]] and [[beta strand]]s in [[protein structure]]<ref>{{cite journal| doi=10.1016/0263-7855(85)80027-8 | volume=3 | issue=4 | title=Reasoning about protein topology using the logic programming language PROLOG | year=1985 | journal=Journal of Molecular Graphics | pages=151–157 | last1 = Rawlings | first1 = C J | last2 = Taylor | first2 = W R | last3 = Nyakairu | first3 = J | last4 = Fox | first4 = J | last5 = Sternberg | first5 = M J.E.}}</ref> [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]] ([http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1qjp&template=protein.html&r=wiring&l=1&chain=A an example]). |
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==See also== |
==See also== |
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*[[ |
* [[Circuit topology]] |
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*[[ |
* [[Membrane topology]] |
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* [[Protein folding]] |
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==References== |
==References== |
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*[http://ptgl.uni-frankfurt.de/ PTGL] |
*[http://ptgl.uni-frankfurt.de/ PTGL] |
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*[http://www.ccp4.ac.uk/html/topdraw.html TOPDRAW] |
*[http://www.ccp4.ac.uk/html/topdraw.html TOPDRAW] |
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{{Protein quaternary structure}} |
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[[Category:Protein structure]] |
[[Category:Protein structure]] |
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[[Category:Molecular topology]] |
[[Category:Molecular topology]] |
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{{Protein-stub}} |
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Latest revision as of 03:31, 24 April 2023
Protein topology is a property of protein molecule that does not change under deformation (without cutting or breaking a bond).
Frameworks
[edit]Two main topology frameworks have been developed and applied to protein molecules.
Knot Theory
[edit]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
[edit]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
[edit]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] [1]. 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
[edit]References
[edit]- ^ B. Scalvini et al., Topological principles of protein folding. Physical Chemistry Chemical Physics 23, 21316-21328 (2021)
- ^ J. Woodard et al., Chain topology predicts pathogenicity of missense mutations. Proteins: Structure, Function, and Bioinformatics 90(9) 1634-1644 (2022)
- ^ 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
[edit]
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