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Schellman loop

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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 and a characteristic main chain dihedral angle conformation. The CO group of residue i is hydrogen-bonded to the NH of residue i+5, and the CO group of residue i+1 is hydrogen-bonded to the NH of residue i+4. Residues i+1, i+2, and i+3 have negative 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] in which three mainchain NH groups (from Schellman loop residues i+3 to i+5) form a concavity for hydrogen bonding to carbonyl oxygens. The nest can be seen at the right-hand side of the Figure. About 2.5% of amino acids in proteins belong to Schellman loops. Two websites are available for finding and examining Schellman loops in proteins, Motivated Proteins: [1];[13] or PDBeMotif: [2].[14]

Schellman loop. Nitrogen atoms, blue; oxygens, red; carbons, grey. The purple and yellow lines are hydrogen bonds.

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.[15]

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 phi values while the phi value of residue i+4 is negative; the nest is of the LR, rather than the RL, kind.

Amino acid propensities for the six Schellman-loop residues have been described.[16] Residue i+4 is the one most-highly conserved, with 70% of amino acids being glycine and none proline.

The original Schellman criteria [17] result in the inclusion of features not now regarded as Schellman loops. A newer set of criteria is given above.

References

  1. ^ Schellman, C (1980). Protein Folding. Amsterdam: Elsevier. pp. 53–61.
  2. ^ Milner-White, EJ (1988). "Recurring loop motif in proteins that occurs in right-handed and left-handed forms". Journal of Molecular Biology. 199: 503–511.
  3. ^ Aurora, R; Srinivasan (1994). Science. 264: 1126–1130. {{cite journal}}: Missing or empty |title= (help)
  4. ^ Viguera, AR; Serrano, L (1995). "Experimental analysis of the Schellman motif". Journal of Molecular Biology. 251: 150–160.
  5. ^ Aurora, R; Rose G (1998). "Helic capping". Protein Science. 7: 21–38.
  6. ^ Kallenbach, N; Gong, Y (1999). "C-terminal capping motifs in model helical peptides". Bioorg Med Chem. 7: 143–151.
  7. ^ Sukumar, M. and Gierasch, L.M. 1997. Local interactions in a Schellman motif dictate interhelical arrangement in a protein fragment. Fold. Des. 2, 211–222.
  8. ^ Datta, S; Uma (1999). "Stereochemistry of Schellman motifs in peptides". Biopolymers. 50: 13–22.
  9. ^ Sagermann, M; Martensson (2002). "A test of proposed rules for helix capping: Implications for protein design". Protein Science. 11: 516–521.
  10. ^ Leader, DP; Milner-White, EJ (2011). "The structure of the ends of alpha-helices in globular proteins". Proteins. 79: 1010–1019.
  11. ^ Milner-White, EJ; Nissink, J (2004). "Recurring main-chain anion-binding motifs in short polypeptides: nests". Acta Crystallographica. D60: 1935–1942.
  12. ^ Watson, JD; Milner-White, EJ (2002). "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: 171–182.
  13. ^ Leader, DP; Milner-White, EJ (2009). "Motivated Proteins: A web application for studying small three-dimensional protein motifs". BMC Bioinformatics. 10: 60.
  14. ^ Golovin, A; Hendrick (2008). "MSDmotif: exploring protein sites and motifs". BMC Bioinformatics. 9: 312.
  15. ^ Leader, DP; Milner-White, EJ (2011). "The structure of the ends of alpha-helices in globular proteins". Proteins. 79: 1011–1022.
  16. ^ Newell, N (2011). "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: 3415–3422.
  17. ^ Schellman, C (1980). Protein Folding. Amsterdam: Elsevier. pp. 53–61.
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