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

These crosslinks are formed either spontaneously during protein folding, or as a result of natural enzymatic processes.

Disulfide BondsDisulfide Bonds

Disulfide bonds are the most common protein crosslinks. About 23% of protein structures in the PDB have disulfide bonds (July, 2021).

• Example: Insulin 9ins has 2 interchain and one intrachain disulfide bonds. Additional examples will be found in the lower left panel of FirstGlance when this example is viewed.

• Visualization: View 9ins in FirstGlance. In FirstGlance, in the Tools Tab, click Disulfides/S/Se.

Isopeptide BondsIsopeptide Bonds

Isopeptide bonds: An estimate of the frequency of isopeptide crosslinks in the PDB may not be available.

• A text search for "isopeptide" at RCSB.Org gives ~400 hits (July, 2021).

• A text search at PDBe gives ~12,000 hits (July, 2021). 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 (for example, 5jqf).

• Example: Bacterial pilus adhesin 2xi9 has 2 isopeptide bonds (and 2 thioester bonds). Additional examples will be found in the lower left panel of FirstGlance when this example is viewed.

• Visualization: View 2xi9 in FirstGlance. If you see "➤➤Show more details" in the Molecule Information Tab, click on that.

Thioester BondsThioester Bonds

Thioester bonds: An estimate of the frequency of thioester crosslinks in the PDB may not be available.

• A text search for "thioester" at RCSB.Org gives ~2,000 hits (out of ~180,000 total, July, 2021).

• A text search at PDBe gives ~1,400 hits (July, 2021). Among a sample of 5 of the PDBe hits (the first of every 100 in a listing sorted with best resolution at the top), none had thioester bonds, but most contained terms such as "thioesterase" or "thioester".

• Adding "and not thioesterase" to the PDBe search reduced the hits to ~500. Five hits were tested (the first of every 100 in a listing sorted with best resolution at the top) but none had thioester bonds.

• Example: Bacterial pilus adhesin 2xi9 has 2 thioester bonds (and 2 isopeptide bonds). Additional examples will be found in the lower left panel of FirstGlance when this example is viewed.

• Visualization: View 2xi9 in FirstGlance. If you see "➤➤Show more details" in the Molecule Information Tab, click on that.

Ester BondsEster Bonds

• Ester bonds: An estimate of the frequency of ester crosslinks in the PDB may not be available. Thr-Gln ester crosslinks were first reported in 2013.

• Example: Bacterial pilus repeat domains 4mkm has 2 interchain Thr-Gln ester bonds. Additional examples will be found in the lower left panel of FirstGlance when this example is viewed.

• Visualization: View 4mkm in FirstGlance. If you see "➤➤Show more details" in the Molecule Information Tab, click on that.

Lysine-Cysteine NOS BondsLysine-Cysteine NOS Bonds

• Lysine-cysteine NOS bonds as protein crosslinks were first reported in 2021 by Wensien et al.. They reported that following a search of the entire PDB, they "identified a number of proteins from all domains of life that are highly likely to possess one or more NOS bridges", to be detailed in a manuscript in preparation. However, because such bonds were not recognized before 2021, those that occur in published structures would have been overlooked.

• Example: 6zx4 was analyzed in depth and provided the first documented case. Additional examples will be found in the lower left panel of FirstGlance when this example is viewed.

• Visualization: View 6zx4 in FirstGlance. If you see "➤➤Show more details" in the Molecule Information Tab, click on that.