Abstract
In the previous chapter, we investigated the structure of the polypeptide backbone in the two main types of secondary structure elements, the α-helix and the β-sheet. In this chapter, the secondary structure elements themselves will be presented in more detail. First, we will learn how residues are assigned to such elements by different algorithms. This will reveal that the assignments of secondary structures are subject to some uncertainty and may vary depending on whether an algorithm uses torsional angles or hydrogen-bonding possibilities or both to make assignments. We will compare and contrast the hydrogen-bonding properties of α-helices and β-sheets and examine some variations of these structures that occur in protein structures. The chapter will also introduce the various types of turns that link the secondary structure elements together and show how the turns can be characterized by their torsion angles and hydrogen-bonding properties. A discussion of preferences of the amino acids to be found in α-helices, β-sheets, or turns will round off the chapter.
Wool gave me a glimpse of the loom on which the web of life was woven. William Astbury
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References
Astbury WT, Woods HJ (1930) The X-ray interpretation of the structure and elastic properties of hair keratin. Nature 126:913–914. https://doi.org/10.1038/126913b0
Astbury WT, Woods HJ (1934) X-ray studies of the structure of hair, wool, and related fabrics II – the molecular structure and elastic properties of hair keratin. Philos Trans R Soc Lond 232:333–U367. https://doi.org/10.1098/rsta.1934.0010
Chou PY, Fasman GD (1977) Beta-turns in proteins. J Mol Biol 115(2):135–175
Creighton TE (2013) Proteins: structure and molecular properties, 2nd edn. W H Freeman & Co, San Francisco
Drin G, Casella JF, Gautier R, Boehmer T, Schwartz TU, Antonny B (2007) A general amphipathic alpha-helical motif for sensing membrane curvature. Nat Struct Mol Biol 14(2):138–146. https://doi.org/10.1038/nsmb1194
Enkhbayar P, Hikichi K, Osaki M, Kretsinger RH, Matsushima N (2006) 3(10)-helices in proteins are parahelices. Proteins 64(3):691–699. https://doi.org/10.1002/prot.21026
Fersht AR, Shi JP, Knill-Jones J, Lowe DM, Wilkinson AJ, Blow DM, Brick P, Carter P, Waye MM, Winter G (1985) Hydrogen bonding and biological specificity analysed by protein engineering. Nature 314(6008):235–238
Gonzalez A, Cordomi A, Caltabiano G, Pardo L (2012) Impact of helix irregularities on sequence alignment and homology modeling of G protein-coupled receptors. Chembiochem 13(10):1393–1399. https://doi.org/10.1002/cbic.201200189
Hager T (1998) Linus Pauling and the chemistry of life. Oxford portraits in science. Oxford University Press, New York
Hol WG (1985) Effects of the alpha-helix dipole upon the functioning and structure of proteins and peptides. Adv Biophys 19:133–165
Hol WG, van Duijnen PT, Berendsen HJ (1978) The alpha-helix dipole and the properties of proteins. Nature 273(5662):443–446
Huggins ML (1943) The structure of fibrous proteins. Chem Rev 32:195–218. https://doi.org/10.1021/cr60102a002
Hutchinson EG, Thornton JM (1994) A revised set of potentials for beta-turn formation in proteins. Protein Sci 3(12):2207–2216. https://doi.org/10.1002/pro.5560031206
Hutchinson EG, Thornton JM (1996) PROMOTIF--a program to identify and analyze structural motifs in proteins. Protein Sci 5(2):212–220. https://doi.org/10.1002/pro.5560050204
Kabsch W, Sander C (1983a) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22(12):2577–2637. https://doi.org/10.1002/bip.360221211
Kabsch W, Sander C (1983b) How good are predictions of protein secondary structure? FEBS Lett 155(2):179–182
Kamphuis IG, Kalk KH, Swarte MB, Drenth J (1984) Structure of papain refined at 1.65 A resolution. J Mol Biol 179(2):233–256
Karanasios E, Han GS, Xu Z, Carman GM, Siniossoglou S (2010) A phosphorylation-regulated amphipathic helix controls the membrane translocation and function of the yeast phosphatidate phosphatase. Proc Natl Acad Sci U S A 107(41):17539–17544. https://doi.org/10.1073/pnas.1007974107
Martin J, Letellier G, Marin A, Taly JF, de Brevern AG, Gibrat JF (2005) Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct Biol 5:17. https://doi.org/10.1186/1472-6807-5-17
Menard R, Khouri HE, Plouffe C, Dupras R, Ripoll D, Vernet T, Tessier DC, Lalberte F, Thomas DY, Storer AC (1990) A protein engineering study of the role of aspartate 158 in the catalytic mechanism of papain. Biochemistry 29(28):6706–6713
Milner-White EJ, Ross BM, Ismail R, Belhadj-Mostefa K, Poet R, (1988) One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins. Journal of Molecular Biology 204 (3):777–782
Pace CN, Shirley BA, McNutt M, Gajiwala K (1996) Forces contributing to the conformational stability of proteins. FASEB J 10(1):75–83
Padlan EA, Segal DM, Spande TF, Davies DR, Rudikoff S, Potter M (1973) Structure at 4.5 A resolution of a phosphorylcholine-binding fab. Nat New Biol 245(145):165–167
Panasik N Jr, Fleming PJ, Rose GD (2005) Hydrogen-bonded turns in proteins: the case for a recount. Protein Sci 14(11):2910–2914. https://doi.org/10.1110/ps.051625305
Pathak D, Ollis D (1990) Refined structure of dienelactone hydrolase at 1.8 A. J Mol Biol 214(2):497–525
Pauling L (1940) A theory of the structure and process of formation of antibodies. J Am Chem Soc 62:2643–2657. https://doi.org/10.1021/ja01867a018
Pauling L, Corey RB (1951) The pleated sheet, a new layer configuration of polypeptide chains. Proc Natl Acad Sci U S A 37(5):251–256
Pauling L, Corey RB, Branson HR (1951) The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 37(4):205–211
Pavone V, Gaeta G, Lombardi A, Nastri F, Maglio O, Isernia C, Saviano M (1996) Discovering protein secondary structures: classification and description of isolated alpha-turns. Biopolymers 38(6):705–721. https://doi.org/10.1002/(SICI)1097-0282(199606)38:6<705::AID-BIP3>3.0.CO;2-V
Perutz MF (1951) New X-ray evidence on the configuration of polypeptide chains. Nature 167(4261):1053–1054
Poljak RJ (1975) Three-dimensional structure, function and genetic control of immunoglobulins. Nature 256(5516):373–376
Richardson JS, Richardson DC (1988) Amino acid preferences for specific locations at the ends of alpha helices. Science 240(4859):1648–1652
Rose GD, Gierasch LM, Smith JA (1985) Turns in peptides and proteins. Adv Protein Chem 37:1–109
Satow Y, Cohen GH, Padlan EA, Davies DR (1986) Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A. J Mol Biol 190(4):593–604
Tong LA, de Vos AM, Milburn MV, Kim SH (1991) Crystal structures at 2.2 Å resolution of the catalytic domains of normal ras protein and an oncogenic mutant complexed with GDP. J Mol Biol 217(3):503–516
Vieira-Pires RS, Morais-Cabral JH (2010) 3(10) helices in channels and other membrane proteins. J Gen Physiol 136(6):585–592. https://doi.org/10.1085/jgp.201010508
Weatherford DW, Salemme FR (1979) Conformations of twisted parallel beta-sheets and the origin of chirality in protein structures. Proc Natl Acad Sci USA 76(1):19–23
Wilmot CM, Thornton JM (1988) Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol 203(1):221–232
Wilmot CM, Thornton JM (1990) Beta-turns and their distortions: a proposed new nomenclature. Protein Eng 3(6):479–493
Wlodawer A, Svensson LA, Sjolin L, Gilliland GL (1988) Structure of phosphate-free ribonuclease A refined at 1.26 A. Biochemistry 27(8):2705–2717
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Skern, T. (2018). Exploring Secondary Structure Elements. In: Exploring Protein Structure: Principles and Practice. Learning Materials in Biosciences. Springer, Cham. https://doi.org/10.1007/978-3-319-76858-8_5
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