The term N cap (N-cap, Ncap) describes an
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...
in a particular position within a
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
or
polypeptide
Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty ...
.
[{{cite journal, last=Leader, first=DP, author2=Milner-White EJ , title=The structure of the ends of helices in globular proteins, journal=Proteins, year=2011, volume=79, issue=3, pages=1010–1019, doi= 10.1002/prot.22942, pmid=21287629, s2cid=22240314] The N cap residue of an
alpha helix
An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix).
The alpha helix is the most common structural arrangement in the Protein secondary structure, secondary structure of proteins. It is al ...
is the first
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...
residue at the
N terminus
N, or n, is the fourteenth letter of the Latin alphabet, used in the modern English alphabet, the alphabets of other western European languages, and others worldwide. Its name in English is ''en'' (pronounced ), plural ''ens''.
History
...
of the helix. More precisely, it is defined as the first residue (i) whose CO group is
hydrogen-bond
In chemistry, a hydrogen bond (H-bond) is a specific type of molecular interaction that exhibits partial covalent character and cannot be described as a purely electrostatic force. It occurs when a hydrogen (H) atom, covalently bonded to a mo ...
ed 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 turn
The Asx turn
is a structural feature in proteins and polypeptides. It consists of three amino acid residues (labeled i, i+1 and i+2) in which residue i is an aspartate (Asp) or asparagine (Asn) that forms a hydrogen bond from its sidechain CO grou ...
s,
ST turn The ST turn is a structural feature in proteins and polypeptides. Each consists of three amino acid residues (labeled ''i'', ''i'' + 1 and ''i'' + 2) in which residue ''i'' is a serine (S) or threonine (T) that forms a hydrogen b ...
s, and
asx motif
The Asx motif is a commonly occurring feature in proteins and polypeptides. It consists of four or five amino acid residues with either aspartate or asparagine as the first residue (residue i). It is defined by two internal hydrogen bonds. One is ...
s are often found at such situations, with the asx or
serine
Serine
(symbol Ser or S) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α- amino group (which is in the protonated − form under biological conditions), a carboxyl group (which is in the deprotonated − ...
or
threonine
Threonine (symbol Thr or T) is an amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH form when dissolved in water), a carboxyl group (which is in the deprotonated −COO− ...
residue at the N cap.
The
C cap is the corresponding amino acid residue at the other end of the helix
References
Amino acids