Protein crosslinks
From Proteopedia
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[[Disulfide bonds]] 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>). | [[Disulfide bonds]] 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>). | ||
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*Example: Insulin [[9ins]] has 2 interchain and one intrachain disulfide bonds. | *Example: Insulin [[9ins]] has 2 interchain and one intrachain disulfide bonds. | ||
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*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. | ||
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[[Isopeptide bonds]] are less common, but an estimate of their frequency may not be available. A text search for "isopeptide" at RCSB.Org gives ~400 hits, while 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. | [[Isopeptide bonds]] are less common, but an estimate of their frequency may not be available. A text search for "isopeptide" at RCSB.Org gives ~400 hits, while 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. | ||
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*Example: Bacterial pilus adhesin [[2xi9]] has 2 isopeptide bonds (and 2 thioester bonds). | *Example: Bacterial pilus adhesin [[2xi9]] has 2 isopeptide bonds (and 2 thioester bonds). | ||
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*Visualization: [https://firstglance.jmol.org/fg.htm?mol=2xi9 View 2xi9 in FirstGlance]. If you see "<span style='color:#00d0a0;'>➤➤</span><u>Show more details</u>" in the [http://firstglance.jmol.org/where.htm#mit Molecule Information Tab], click on that. | *Visualization: [https://firstglance.jmol.org/fg.htm?mol=2xi9 View 2xi9 in FirstGlance]. If you see "<span style='color:#00d0a0;'>➤➤</span><u>Show more details</u>" in the [http://firstglance.jmol.org/where.htm#mit Molecule Information Tab], click on that. | ||
| - | + | ====Thioester Bonds==== | |
| - | **Example: Bacterial pilus adhesin [[2xi9]] has 2 | + | |
| + | [[Thioester protein crosslinks|Thioester bonds]]: Again, an estimate of frequency may not be available. A text search for "thioester" at RCSB.Org gives ~2,000 hits, while a text search at PDBe gives ~1,400 hits (July, 2021). Among a sample of 5 of the PDBe hits (every 100th in the listing), none had thioester bonds, but most contained terms such as "thioesterase" or "thioester". RCSB Advanced Search has "Biologically Interesting Molecules (BIRD): BIRD Type = Thioester", which gives 19 hits (July, 2021). However, only 2% of entries have BIRD annotations. | ||
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| + | **Example: Bacterial pilus adhesin [[2xi9]] has 2 thioester bonds (and 2 isopeptide bonds). | ||
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**Visualization: [https://firstglance.jmol.org/fg.htm?mol=2xi9 View 2xi9 in FirstGlance]. If you see "<span style='color:#00d0a0;'>➤➤</span><u>Show more details</u>" in the [http://firstglance.jmol.org/where.htm#mit Molecule Information Tab], click on that. | **Visualization: [https://firstglance.jmol.org/fg.htm?mol=2xi9 View 2xi9 in FirstGlance]. If you see "<span style='color:#00d0a0;'>➤➤</span><u>Show more details</u>" in the [http://firstglance.jmol.org/where.htm#mit Molecule Information Tab], click on that. | ||
Revision as of 17:15, 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).
Contents |
Natural Crosslinks
These crosslinks are formed either spontaneously during protein folding, or as a result of natural enzymatic processes.
Disulfide Bonds
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
Isopeptide bonds are less common, but an estimate of their frequency may not be available. A text search for "isopeptide" at RCSB.Org gives ~400 hits, while 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.
- 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
Thioester bonds: Again, an estimate of frequency may not be available. A text search for "thioester" at RCSB.Org gives ~2,000 hits, while a text search at PDBe gives ~1,400 hits (July, 2021). Among a sample of 5 of the PDBe hits (every 100th in the listing), none had thioester bonds, but most contained terms such as "thioesterase" or "thioester". RCSB Advanced Search has "Biologically Interesting Molecules (BIRD): BIRD Type = Thioester", which gives 19 hits (July, 2021). However, only 2% of entries have BIRD annotations.
- Example: Bacterial pilus adhesin 2xi9 has 2 thioester bonds (and 2 isopeptide bonds).
- Visualization: View 2xi9 in FirstGlance. If you see "➤➤Show more details" in the Molecule Information Tab, click on that.
Artificial Crosslinks
Notes
- ↑ 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%.
