Protein crosslinks
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.
- Example: Bacterial pilus adhesin 2xi9 has 2 isopeptide bonds (and 2 thioester bonds).
- Visualization: View 2xi9 in FirstGlance. If you see "➤➤Show more details" in the Molecule Information Tab, click on that.
- Thioester bonds:
- Example: Bacterial pilus adhesin 2xi9 has 2 isopeptide bonds (and 2 thioester bonds).
- Visualization: View 2xi9 in FirstGlance. If you see "➤➤Show more details" in the Molecule Information Tab, click on that.
Artificial CrosslinksArtificial Crosslinks
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%.