Schellman loops (also called Schellman motifs or paperclips) are commonly occurring structural features of proteins and

polypeptides Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A p ...

. Each has six

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha a ...

residues (labelled residues ''i'' to ''i''+5) with two specific inter-mainchain hydrogen bonds (as in lower figure, i) and a characteristic main chain

dihedral angle A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the un ...

conformation. The CO group of residue ''i'' is hydrogen-bonded to the NH of residue ''i''+5 (colored orange in upper figure), and the CO group of residue ''i''+1 is hydrogen-bonded to the NH of residue ''i''+4 (

beta turn β turns (also β-bends, tight turns, reverse turns, Venkatachalam turns) are the most common form of turns—a type of non-regular secondary structure in proteins that cause a change in direction of the polypeptide chain. They are very common mot ...

, colored purple). Residues ''i''+1, ''i''+2, and ''i''+3 have negative φ (phi) angle values and the phi value of residue ''i''+4 is positive. Schellman loops incorporate a three amino acid residue RL

nest (protein structural motif) The Nest is a type of protein structural motif. It is a small recurring anion-binding feature of both proteins and peptides. Each consists of the main chain atoms of three consecutive amino acid residues. The main chain NH groups bind the anions w ...

, in which three mainchain NH groups (from Schellman loop residues ''i''+3 to ''i''+5) form a concavity for hydrogen bonding to

carbonyl In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups. A compound containi ...

oxygens. About 2.5% of amino acids in proteins belong to Schellman loops. Two websites are available for examining small motifs in proteins, Motivated Proteins:

or PDBeMotif

The majority of Schellman loops (82%) occur at the C-terminus of an alpha-helix such that residues ''i'', ''i''+1, ''i''+2 and ''i''+3 are part of the helix. Over a quarter of helices (28%) have a C-terminal Schellman loop. Occasional Schellman loops occur with seven instead of six residues. In these, the CO group of residue ''i'' is hydrogen-bonded to the NH of residue ''i''+6, and the CO group of residue ''i''+1 is hydrogen-bonded to the NH of residue ''i''+5. Rare “left-handed” six-residue Schellman loops occur; these have the same hydrogen bonds, but residues ''i''+1, ''i''+2, and ''i''+3 have positive φ values while the φ value of residue ''i''+4 is negative; the nest is of the LR, rather than the RL, kind. Amino acid propensities for the residues of the common type of Schellman loop have been described. Residue ''i''+4 is the one most-highly conserved; it has positive φ values; 70% of amino acids are

glycine Glycine (symbol Gly or G; ) is an amino acid that has a single hydrogen atom as its side chain. It is the simplest stable amino acid ( carbamic acid is unstable), with the chemical formula NH2‐ CH2‐ COOH. Glycine is one of the proteinog ...

and none are proline. Consideration of the hydrogen bonding in the nests of Schellman loops bound to mainchain oxygens reveals two main types of arrangement: 1,3-bridged or not. In one (lower figure, ii) the first and third nest NH groups are bridged by an oxygen atom. In the other (lower figure, iv) the first NH group is hydrogen bonded to the CO group of an amino acid four residues behind in the sequence, and none of the nest NH groups are bridged. It seems that Schellman loops are less homogeneous than might have been expected. The original Schellman criteria result in the inclusion of features not now regarded as Schellman loops. A newer set of criteria is given in the first paragraph.

References

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External links

PDBeMotif – finding and examining Schellman loops in proteins
Organic chemistry Protein structural motifs