Schellman loop

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Schellman loop. Nitrogen atoms, blue; oxygens, red; carbons, grey. The purple and yellow lines are hydrogen bonds. Side chain and hydrogen atoms omitted. Hydrogen bond arrangement as in ii of the lower figure. Schellman loop.pdf
Schellman loop. Nitrogen atoms, blue; oxygens, red; carbons, grey. The purple and yellow lines are hydrogen bonds. Side chain and hydrogen atoms omitted. Hydrogen bond arrangement as in ii of the lower figure.

Schellman loops (also called Schellman motifs or paperclips) [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] are commonly occurring structural features of proteins and polypeptides. [11] Each has six amino acid 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 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, 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), [12] [13] in which three mainchain NH groups (from Schellman loop residues i+3 to i+5) form a concavity for hydrogen bonding to carbonyl 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: ; [14] or PDBeMotif: . [15]

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. [10]

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. [16] Residue i+4 is the one most-highly conserved; it has positive φ values; 70% of amino acids are glycine and none are proline.

Hydrogen bond arrangements of Schellman loops. Residues are represented by black filled circles. Mainchain-mainchain hydrogen bonds are shown as dashed lines. The grey shading indicates the three nest residues. Hydrogen bond arrangements in Schellman loops.pdf
Hydrogen bond arrangements of Schellman loops. Residues are represented by black filled circles. Mainchain-mainchain hydrogen bonds are shown as dashed lines. The grey shading indicates the three nest residues.

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. [17] It seems that Schellman loops are less homogeneous than might have been expected.

The original Schellman criteria [1] result in the inclusion of features not now regarded as Schellman loops. A newer set of criteria is given in the first paragraph.

Related Research Articles

<span class="mw-page-title-main">Alpha helix</span> Type of secondary structure of proteins

An alpha helix is a sequence of amino acids in a protein that are twisted into a coil.

<span class="mw-page-title-main">Beta sheet</span> Protein structural motif

The beta sheet, (β-sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, Alzheimer's disease and other proteinopathies.

<span class="mw-page-title-main">Protein secondary structure</span> General three-dimensional form of local segments of proteins

Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure.

In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules. A structural motif does not have to be associated with a sequence motif; it can be represented by different and completely unrelated sequences in different proteins or RNA.

A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.

3<sub>10</sub> helix Type of secondary structure

A 310 helix is a type of secondary structure found in proteins and polypeptides. Of the numerous protein secondary structures present, the 310-helix is the fourth most common type observed; following α-helices, β-sheets and reverse turns. 310-helices constitute nearly 10–15% of all helices in protein secondary structures, and are typically observed as extensions of α-helices found at either their N- or C- termini. Because of the α-helices tendency to consistently fold and unfold, it has been proposed that the 310-helix serves as an intermediary conformation of sorts, and provides insight into the initiation of α-helix folding.

β 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 motifs in proteins and polypeptides. Each consists of four amino acid residues. They can be defined in two ways:

  1. By the possession of an intra-main-chain hydrogen bond between the CO of residue i and the NH of residue i+3;
  2. By having a distance of less than 7Å between the Cα atoms of residues i and i+3.

The Walker A and Walker B motifs are protein sequence motifs, known to have highly conserved three-dimensional structures. These were first reported in ATP-binding proteins by Walker and co-workers in 1982.

<span class="mw-page-title-main">Nest (protein structural motif)</span>

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 while the side chain atoms are often not involved. Proline residues lack NH groups so are rare in nests. About one in 12 of amino acid residues in proteins, on average, belongs to a nest.

The Asx turn is a structural feature in proteins and polypeptides. It consists of three amino acid residues in which residue i is an aspartate (Asp) or asparagine (Asn) that forms a hydrogen bond from its sidechain CO group to the mainchain NH group of residue i+2. About 14% of Asx residues present in proteins belong to Asx turns.

<span class="mw-page-title-main">Catgrip</span> Molecular binding feature

Catgrips are small cation-binding molecular features of proteins and peptides. Each consists of the main chain atoms only of three consecutive amino acid residues. The first and third main chain CO groups bind the cations, often calcium, magnesium, potassium or sodium, with no side chain involvement. Many catgrips bind a water molecule instead of a cation; it is hydrogen-bonded to the first and third main chain CO groups. Catgrips are found as calcium-binding features in annexins, matrix metalloproteinases (e.g.serralysins), subtilisins and phospholipase A2. They are also observed in synthetic peptides and in cyclic hexapeptides made from alternating D,L amino acids.

<span class="mw-page-title-main">ST turn</span>

The ST turn is a structural feature in proteins and polypeptides. Each consists of three amino acid residues in which residue i is a serine (S) or threonine (T) that forms a hydrogen bond from its sidechain oxygen group to the mainchain NH group of residue i + 2.

<span class="mw-page-title-main">Beta bend ribbon</span>

The beta bend ribbon, or beta-bend ribbon, is a structural feature in polypeptides and proteins. The shortest possible has six amino acid residues arranged as two overlapping hydrogen bonded beta turns in which the carbonyl group of residue i is hydrogen-bonded to the NH of residue i+3 while the carbonyl group of residue i+2 is hydrogen-bonded to the NH of residue i+5. In longer ribbons, this bonding is continued in peptides of 8, 10, etc., amino acid residues. A beta bend ribbon can be regarded as an aberrant 310 helix (3/10-helix) that has lost some of its hydrogen bonds. Two websites are available to facilitate finding and examining these features in proteins: Motivated Proteins; and PDBeMotif.

<span class="mw-page-title-main">Asx motif</span>

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. It is defined by two internal hydrogen bonds. One is between the side chain oxygen of residue i and the main chain NH of residue i+2 or i+3; the other is between the main chain oxygen of residue i and the main chain NH of residue i+3 or i+4. Asx motifs occur commonly in proteins and polypeptides.

<span class="mw-page-title-main">ST motif</span>

The ST motif is a commonly occurring feature in proteins and polypeptides. It consists of four or five amino acid residues with either serine or threonine as the first residue. It is defined by two internal hydrogen bonds. One is between the side chain oxygen of residue i and the main chain NH of residue i + 2 or i + 3; the other is between the main chain oxygen of residue i and the main chain NH of residue i + 3 or i + 4. Two websites are available for finding and examining ST motifs in proteins, Motivated Proteins: and PDBeMotif.

The term N cap describes an amino acid in a particular position within a protein or polypeptide. 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. Because of this it is sometimes also described as the residue prior to the helix.

The term C cap describes an amino acid in a particular position within a protein or polypeptide. The C cap residue of an alpha helix is the last amino acid residue at the C terminus of the helix. More precisely, it is defined as the last residue (i) whose NH group is hydrogen-bonded to the CO group of residue i-4. Because of this it is sometimes also described as the residue following the helix.

<span class="mw-page-title-main">Beta bulge loop</span>

Beta bulge loops are commonly occurring motifs in proteins and polypeptides consisting of five to six amino acids. There are two types: type 1, which is a pentapeptide; and type 2, with six amino acids. They are regarded as a type of beta bulge, and have the alternative name of type G1 beta bulge. Compared to other beta bulges, beta bulge loops give rise to chain reversal such that they often occur at the loop ends of beta hairpins; hairpins of this sort can be described as 3:5 or 4:6. Two websites are available for finding and examining β bulge loops in proteins, Motivated Proteins: and PDBeMotif:.

<span class="mw-page-title-main">ST staple</span>

The ST staple is a common four- or five-amino acid residue motif in proteins and polypeptides with serine or threonine as the C-terminal residue. It is characterized by a single hydrogen bond between the hydroxyl group of the serine or threonine and the main chain carbonyl group of residue i. Motifs are of two types, depending whether the motif has 4 or 5 residues. Most ST staples occur in conjunction with an alpha helix, and are usually associated with a slight bend in the helix. Two websites are available for finding and examining ST staples in proteins: Motivated Proteins and PDBeMotif.

<span class="mw-page-title-main">Gamma helix</span>

Gamma helix (or γ-helix) is a type of secondary structure in proteins that has been predicted by Pauling, Corey, and Branson, but has never been observed in natural proteins. The hydrogen bond in this type of helix was predicted to be between N-H group of one amino acid and the C=O group of the amino acid six residues earlier (or, as described by Pauling, Corey, Branson, "to the fifth amide group beyond it"). This can also be described as i + 6 → i bond and would be a continuation of the series (310 helix, alpha helix, pi helix and gamma helix). This theoretical helix contains 5.1 residues per turn.However, a fully developed gamma helix has characteristics of a structure that has 2.2 amino acid residues per turn, a rise of 2.75Å per residue, and a pseudo-cyclic (C7) structure closed by intramolecular H-bond. Depending on the amino acid's side chain (R) involved in this main-chain reversal motif, two stereoisomers can occur with their Cα-substituent located either in the axial or in the equatorial position relative to the H-bonded pseudo-cycle.

References

  1. 1 2 Schellman, C (1980). Protein Folding. Amsterdam: Elsevier. pp. 53–61.
  2. ↑ Milner-White, E J (1988-02-05). "Recurring loop motif in proteins that occurs in right-handed and left-handed forms. Its relationship with alpha-helices and beta-bulge loops". Journal of Molecular Biology. 199 (3): 503–511. doi:10.1016/0022-2836(88)90621-3. ISSN   0022-2836. PMID   3351939.
  3. ↑ Aurora, R; Srinivasan, R; Rose, G D (1994). "Rules for alpha-helix termination by glycine" (PDF). Science. 264 (5162): 1126–1130. doi:10.1126/science.8178170. ISSN   0036-8075. PMID   8178170.
  4. ↑ Viguera, Ana Rosa; Serrano, Luis (1995-08-04). "Experimental Analysis of the Schellman Motif". Journal of Molecular Biology. 251 (1): 150–160. doi:10.1006/jmbi.1995.0422. ISSN   0022-2836. PMID   7643384.
  5. ↑ Aurora, R; Rose, G D (January 1998). "Helix capping". Protein Science. 7 (1): 21–38. doi:10.1002/pro.5560070103. ISSN   0961-8368. PMC   2143812 . PMID   9514257.
  6. ↑ Kallenbach, Neville R.; Gong, Youxiang (January 1999). "C-Terminal capping motifs in model helical peptides". Bioorganic & Medicinal Chemistry. 7 (1): 143–151. doi: 10.1016/S0968-0896(98)00231-4 . ISSN   0968-0896.
  7. ↑ Sukumar, Muppalla; Gierasch, Lila M (August 1997). "Local interactions in a Schellman motif dictate interhelical arrangement in a protein fragment". Folding & Design. 2 (4): 211–222. doi: 10.1016/S1359-0278(97)00030-8 . ISSN   1359-0278. PMID   9269562.
  8. ↑ Datta, Saumen; Uma, Manjappara V.; Shamala, N.; Balaram, P. (1999). "Stereochemistry of Schellman motifs in peptides: crystal structure of a hexapeptide with a C-terminus 6→1 hydrogen bond" (PDF). Biopolymers. 50 (1): 13–22. doi:10.1002/(sici)1097-0282(199907)50:1<13::aid-bip2>3.0.co;2-k. ISSN   0006-3525.
  9. ↑ Sagermann, Martin; Mårtensson, Lars-Göran; Baase, Walter A.; Matthews, Brian W. (2002-03-01). "A test of proposed rules for helix capping: Implications for protein design". Protein Science. 11 (3): 516–521. doi:10.1110/ps.39802. ISSN   1469-896X. PMC   2373482 . PMID   11847274.
  10. 1 2 Leader, DP; Milner-White, EJ (2011). "The structure of the ends of alpha-helices in globular proteins". Proteins. 79 (3): 1010–1019. doi:10.1002/prot.22942. PMID   21287629.
  11. ↑ Milner-White, E. James; Nissink, J. Willem M.; Allen, Frank H.; Duddy, William J. (2004-11-01). "Recurring main-chain anion-binding motifs in short polypeptides: nests". Acta Crystallographica Section D. 60 (11): 1935–1942. doi: 10.1107/S0907444904021390 . ISSN   0907-4449. PMID   15502299.
  12. ↑ Datta, S; Uma, MV (1999). "Stereochemistry of Schellman motifs in peptides. Crystal structure of a hexapeptide with a C-terminal 6->1 hydrogen bond" (PDF). Biopolymers. 50 (1): 13–22. doi:10.1002/(sici)1097-0282(199907)50:1<13::aid-bip2>3.0.co;2-k.
  13. ↑ Watson, James D; Milner-White, E James (2002-01-11). "A novel main-chain anion-binding site in proteins: the nest. A particular combination of phi,psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions". Journal of Molecular Biology. 315 (2): 171–182. doi:10.1006/jmbi.2001.5227. ISSN   0022-2836. PMID   11779237.
  14. ↑ Leader, DP; Milner-White (2009). "Motivated Proteins: A web application for studying small three-dimensional protein motifs". BMC Bioinformatics. 10 (1): 60. doi: 10.1186/1471-2105-10-60 . PMC   2651126 . PMID   19210785.
  15. ↑ Golovin, A; Henrick (2008). "MSDmotif: exploring protein sites and motifs". BMC Bioinformatics. 9 (1): 312. doi: 10.1186/1471-2105-9-312 . PMC   2491636 . PMID   18637174.
  16. ↑ Newell, Nicholas E (2011-12-15). "Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop". Bioinformatics. 27 (24): 3415–3422. doi: 10.1093/bioinformatics/btr594 . ISSN   1367-4811. PMID   22039211.
  17. ↑ Afzal, AM; Al-Shubailly, F (2014). "Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins". Proteins. 82 (11): 3023–3031. doi:10.1002/prot.24663. PMID   25132631.
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