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

proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, re ...

and

polypeptides 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 ami ...

. Each has six

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 ...

residues (labelled residues ''i'' to ''i''+5) with two specific inter-mainchain

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, Covalent bond, covalently b ...

s (as in lower figure, i) and a characteristic main chain dihedral angle conformation. The CO group of residue ''i'' 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 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 Structural motif, 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 ...

, 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 with the formula , composed of a carbon atom double bond, double-bonded to an oxygen atom, and it is divalent at the C atom. It is common to several classes of organic compounds (such a ...

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 The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, carboxy tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein Proteins are large biomolecules and macromolecules that comp ...

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 secondary structure of proteins. It is also the most extreme type of ...

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. Glycine is one of the proteinogenic amino acids. It is encoded by all the codons starting with GG (G ...

and none are

proline Proline (symbol Pro or P) is an organic acid classed as a proteinogenic amino acid (used in the biosynthesis of proteins), although it does not contain the amino group but is rather a secondary amine. The secondary amine nitrogen is in the p ...

. 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