Amide ring

Amide Rings are small motifs in proteins and polypeptides. They consist of 9-atom or 11-atom rings formed by two CO...HN hydrogen bonds between a side chain amide group and the main chain atoms of a short polypeptide.[1] They are observed with glutamine or asparagine side chains within proteins and polypeptides. Structurally similar rings occur in the binding of purine, pyrimidine and nicotinamide bases to the main chain atoms of proteins. About 4% of asparagines and glutamines form amide rings; in databases of protein domain structures, one is present, on average, every other protein.

In such rings the polypeptide has the conformation of beta sheet or of type II polyproline helix (PPII). A number of glutamines and asparagines help bind short peptides (with the PPII conformation) in the groove of class II MHC (Major Histocompatibility Complex) proteins [2] by forming these motifs. Another amide ring occurs at the interior of the variable domains of some Immunoglobulin G antibodies and assists in linking the two beta-sheets.

References

  1. ↑ Le Questel, JY; Morris DG (1993). "Common ring motifs in proteins involving asparagine or glutamine groups hydrogen-bonded to main-chain atoms". Journal of Molecular Biology 231: 888–896. doi:10.1006/jmbi.1993.1335.
  2. ↑ Painter, CA; Negroni MP (2011). "Conformational Liability in Class II MHC 3/10-Helix". Proc Natl Acad Sci USA 108: 19329–19338.


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