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Schellman loop

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

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 φ (phi) angle values and the phi value of residue i+4 is positive. Schellman loops incorporate a threeamino 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. About 2.5% of amino acids in proteins belong to Schellman loops.

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 six Schellman-loop residues have been described.[13] Residue i+4 is the one most-highly conserved, with 70% of amino acids being glycine and none proline.

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

References

  1. ^ a b 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. ISSN 0022-2836. PMID 3351939.
  3. ^ Aurora, R; Srinivasan, R; Rose, G D (1994-05-20). "Rules for alpha-helix termination by glycine" (PDF). Science. 264 (5162). New York: 1126–1130. 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.
  5. ^ Aurora, R; Rose, G D (1998-01). "Helix capping". Protein science: a publication of the Protein Society. 7 (1): 21–38. doi:10.1002/pro.5560070103. ISSN 0961-8368. PMC 2143812. PMID 9514257. {{cite journal}}: Check date values in: |date= (help)
  6. ^ Kallenbach, Neville R.; Gong, Youxiang (1999-01). "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. {{cite journal}}: Check date values in: |date= (help)
  7. ^ Sukumar, Muppalla; Gierasch, Lila M (1997-08). "Local interactions in a Schellman motif dictate interhelical arrangement in a protein fragment". Folding and Design. 2 (4): 211–222. doi:10.1016/S1359-0278(97)00030-8. ISSN 1359-0278. {{cite journal}}: Check date values in: |date= (help)
  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. 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.
  10. ^ a b Leader, DP; Milner-White, EJ (2011). "The structure of the ends of alpha-helices in globular proteins". Proteins. 79: 1010–1019.
  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 Biological Crystallography. 60 (11): 1935–1942. doi:10.1107/S0907444904021390. ISSN 0907-4449.
  12. ^ 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.
  13. ^ 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 (Oxford, England). 27 (24): 3415–3422. doi:10.1093/bioinformatics/btr594. ISSN 1367-4811. PMID 22039211.
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