Protein crosslinks: Difference between revisions
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==Natural Crosslinks== | ==Natural Crosslinks== | ||
*<big>[[Disulfide bonds]]</big> are the most common protein crosslinks. About 23% of protein structures in the [[PDB]] have disulfide bonds | *<big>[[Disulfide bonds]]</big> are the most common protein crosslinks. About 23% of protein structures in the [[PDB]] have disulfide bonds (July, 2021<ref>In July, 2021, the PDB had ~180,000 entries. Advanced search at RCSB.Org for "Polymer molecuar features: polymer entity type = protein" and "Deposited entry features: Disulfide bond count per deposited model > 0" gave ~41,000 hits, or about 23%.</ref>). | ||
(July, 2021<ref>In July, 2021, the PDB had ~180,000 entries. Advanced search at RCSB.Org for "Polymer molecuar features: polymer entity type = protein" and "Deposited entry features: Disulfide bond count per deposited model > 0" gave ~41,000 hits, or about 23%.</ref>). | |||
Example: Insulin [[9ins]] has 2 interchain and one intrachain disulfide bonds. | Example: Insulin [[9ins]] has 2 interchain and one intrachain disulfide bonds. | ||
**Visualization: [https://firstglance.jmol.org/fg.htm?mol=9ins View 9ins in FirstGlance]. In [[FirstGlance]], in the Tools tab, click Disulfides/S/Se. | **Visualization: [https://firstglance.jmol.org/fg.htm?mol=9ins View 9ins in FirstGlance]. In [[FirstGlance]], in the Tools tab, click Disulfides/S/Se. | ||
Revision as of 19:10, 2 July 2021
Proteins are linear (unbranched) polypeptide chains of amino acids. The subject of this article is covalent crosslinks between polypeptides, either between protein chains (interchain crosslinks), or within chains (intrachain crosslinks).
Natural CrosslinksNatural Crosslinks
- Disulfide bonds are the most common protein crosslinks. About 23% of protein structures in the PDB have disulfide bonds (July, 2021[1]).
Example: Insulin 9ins has 2 interchain and one intrachain disulfide bonds.
- Visualization: View 9ins in FirstGlance. In FirstGlance, in the Tools tab, click Disulfides/S/Se.
- Isopeptide bonds are less common, but an estimate of their frequency may not be available. A text search for "isopeptide" at RCSB.Org gives 433 hits, while a search at PDBe gives >11,000 hits. In a small sample of the latter hits, none contained the term "isopeptide". Also based on a small sample, some entries that contain verified isopeptide bonds do not contain the term.
- Visualization: View 9ins in FirstGlance. In FirstGlance, in the Tools tab, click Disulfides/S/Se.
NotesNotes
- ↑ In July, 2021, the PDB had ~180,000 entries. Advanced search at RCSB.Org for "Polymer molecuar features: polymer entity type = protein" and "Deposited entry features: Disulfide bond count per deposited model > 0" gave ~41,000 hits, or about 23%.