N cap

The term N cap (N-cap, Ncap) describes an amino acid in a particular position within a protein or polypeptide. [1] [2] [3] [4] [5] [6] The N cap residue of an alpha helix is the first amino acid residue at the N terminus of the helix. More precisely, it is defined as the first residue (i) whose CO group is hydrogen-bonded to the NH group of residue i+4 (or sometimes residue i+3). Because of this it is sometimes also described as the residue prior to the helix.

Capping motifs are those often found at the N cap. Asx turns, ST turns, and asx motifs are often found at such situations, with the asx or serine or threonine residue at the N cap.

The C cap is the corresponding amino acid residue at the other end of the helix

References
  1. Richardson, JM; Richardson DC (1988). "Amino acid preferences for specific locations at the ends of alpha-helices". Science. 240 (4859): 1648–1652. Bibcode:1988Sci...240.1648R. doi:10.1126/science.3381086. PMID 3381086. S2CID 38467101.
  2. Presta, LG; Rose GD (1988). "Helix Caps". Science. 240 (4859): 1632–1641. Bibcode:1988Sci...240.1632P. doi:10.1126/science.2837824. PMID 2837824.
  3. Doig, AJ; MacArthur MW (1997). "Structures of N-termini of helices in proteins". Protein Science. 6 (1): 147–155. doi:10.1002/pro.5560060117. PMC 2143508. PMID 9007987.
  4. Aurora, R; Rose GD (1998). "Helix Capping". Protein Science. 7 (1): 21–38. doi:10.1002/pro.5560070103. PMC 2143812. PMID 9514257.
  5. Gunasekaran, K; Nagarajam HA (1998). "Sterochemical punctuation marks in protein structure" (PDF). Journal of Molecular Biology. 275 (5): 917–932. doi:10.1006/jmbi.1997.1505. PMID 9480777.
  6. Leader, DP; Milner-White EJ (2011). "The structure of the ends of helices in globular proteins". Proteins. 79 (3): 1010–1019. doi:10.1002/prot.22942. PMID 21287629. S2CID 22240314.
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