Advertisement

Proteins and Protein Structure

  • Natalya Kurochkina
Chapter

Abstract

Proteins such as enzymes, channels, signaling molecules and adaptors carry out important functions in living organisms. Fibrous and globular proteins comprise two large groups. Long stretches of coiled coil α-helices in fibers and fibrils, triple helices of collagen, and globular heme binding subunits of hemoglobin give us main representatives and show how diverse these molecules are. Protein polypeptide chain exhibits left-handed and right handed, parallel and antiparallel arrangements of secondary structure elements such as alpha, 310 , polyproline, gamma and pi helices, strands and turns. This chapter describes structural principles of protein molecule, its conformation and relationships between primary, secondary, tertiary, and quaternary structure.

Keywords

Fibrous protein Globular protein Protein conformation Amino acid Protein structure 

References

  1. Adam A, Haberhauer G, Wölper C (2017) Bio-inspired herringbone foldamers: strategy for changing the structure of helices. J Org Chem 82(8):4203–4215.  https://doi.org/10.1021/acs.joc.7b00185. Epub 2017 Apr 12CrossRefPubMedGoogle Scholar
  2. Adam C, Peters AD, Lizio MG, Whitehead GFS, Diemer V, Cooper JA, Cockroft SL, Clayden J, Webb SJ (2018) The Role of terminal functionality in the membrane and antibacterial activity of peptaibol-mimetic aib foldamers. Chemistry 24(9):2249–2256.  https://doi.org/10.1002/chem.201705299. Epub 2018 Jan 17. PubMed PMID: 29210477CrossRefPubMedGoogle Scholar
  3. Aggeli A, Nyrkova IA, Bell M, Harding R, Carrick L, McLeish TCB, Semenov AN, Boden N (2001) Hierarchical self-assembly of chiral rod-like molecules as a model for peptide beta -sheet tapes, ribbons, fibrils, and fibers. Proc Natl Acad Sci USA 98:11857–11862PubMedCrossRefGoogle Scholar
  4. Ago H, Kanaoka AH, Irikura D et al (2007) Crystal structure of a human membrane protein involved in cysteinyl leukotriene biosynthesis. Nature 448:609–612PubMedCrossRefGoogle Scholar
  5. De Alba E (2009) Structure and interdomain dynamics of apoptosis-associated speck-like protein containing a CARD (ASC). J Biol Chem 284:32932–32941PubMedPubMedCentralCrossRefGoogle Scholar
  6. Al Khamici H, Hossain KR, Cornell BA, Valenzuela SM (2016) Investigating sterol and redox regulation of the ion channel activity of CLIC1 using tethered bilayer membranes. Membranes (Basel). 6(4). pii: E51. PubMed PMID: 27941637; PubMed Central PMCID: PMC5192407PubMedCentralCrossRefPubMedGoogle Scholar
  7. Alushin GM, Ramey VH, Pasqualato S, Ball DA, Grigorieff N, Musacchio A, Nogales E (2010) The Ndc80 kinetochore complex forms oligomeric arrays along microtubules. Nature 467:805–810PubMedPubMedCentralCrossRefGoogle Scholar
  8. Alvarez BH, Gruber M, Ursinus A, Dunin-Horkawicz S, Lupas AN, Zeth K (2010) A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins. J Struct Biol 170(2):236–245.  https://doi.org/10.1016/j.jsb.2010.02.009. Epub 2010 Feb 21. PubMed PMID: 20178846CrossRefPubMedGoogle Scholar
  9. Andrade MA, Perez-Iratxeta C, Ponting CP (2001) Protein repeats: structures, functions, and evolutions. J Struct Biol 134:117–131CrossRefGoogle Scholar
  10. Andrews SC, Smith JM, Guest JR, Harrison PM (1989) Amino acid sequence of the bacterioferritin (cytochrome b1) of Escherichia coli-K12. Biochem Biophys Res Commun 158(2):489–496. PubMed PMID: 2644932PubMedCrossRefGoogle Scholar
  11. Aravinda S, Shamala N, Balaram P (2008) Aib residues in peptaibiotics and synthetic sequences: analysis of nonhelical conformations. Chem Biodivers 5(7):1238–1262.  https://doi.org/10.1002/cbdv.200890112 CrossRefPubMedGoogle Scholar
  12. Arcy SD, Davies OR, Blundell TL, Bolanos-Garcia VM (2010) Defining the molecular basis of BubR1 kinetochore interactions and APC/C-CDC20 inhibition. J Biol Chem 285:14764–14776PubMedPubMedCentralCrossRefGoogle Scholar
  13. Balasco N, Smaldone G, Ruggiero A, De Simone A, Vitagliano L (2018) Local structural motifs in proteins: Detection and characterization of fragments inserted in helices. Int J Biol Macromol. pii: S0141-8130(18)32822–32828.  https://doi.org/10.1016/j.ijbiomac.2018.07.047. [Epub ahead of print] PubMed PMID: 30017977PubMedCrossRefGoogle Scholar
  14. Balashova TA, Shenkarev ZO, Tagaev AA, Ovchinnikova TV, Raap J, Arseniev AS (2000) NMR structure of the channel-former zervamicin IIB in isotropic solvents. FEBS Lett 466(2-3):333–336. PubMed PMID: 10682854PubMedCrossRefGoogle Scholar
  15. Banci L, Bertini I, Cefaro C, Ciofi-Baffoni S, Gallo A (2011) Functional role of two interhelical disulfide bonds in human Cox17 protein from a structural perspective. J Biol Chem 286(39):34382–34390.  https://doi.org/10.1074/jbc.M111.246223. Epub 2011 Aug 4. PubMed PMID: 21816817; PubMed Central PMCID: PMC3190761CrossRefPubMedPubMedCentralGoogle Scholar
  16. Banner DW, Kokkinidis M, Tsernoglou D (1987) Structure of the ColE1 rop protein at 1.7 A resolution. J Mol Biol 196(3):657–675. PubMed PMID: 3681971PubMedCrossRefGoogle Scholar
  17. Barua B (2013) Periodicities designed in the tropomyosin sequence and structure define its functions. Bioarchitecture 3(3):51–56.  https://doi.org/10.4161/bioa.2561 CrossRefPubMedPubMedCentralGoogle Scholar
  18. Berisio R, Vitagliano L (2012) Polyproline and triple helix motifs in host-pathogen recognition. Curr Protein Pept Sci 13(8):855–865.  https://doi.org/10.2174/138920312804871157 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Bhyravbhatla B, Watowich SJ, Caspar DL (1998) Refined atomic model of the four-layer aggregate of the tobacco mosaic virus coat protein at 2.4-Å resolution. Biophys J 74:604–615PubMedPubMedCentralCrossRefGoogle Scholar
  20. Blatch GL, Lassle M (1999) The tetratricopeptide repeat: a structural motif mediating protein-protein interactions. Bioassays 21:932–939CrossRefGoogle Scholar
  21. Boscutti G, Nardon C, Marchiò L, Crisma M, Biondi B, Dalzoppo D, Dalla Via L, Formaggio F, Casini A, Fregona D (2018) Anticancer gold(III) peptidomimetics: from synthesis to in vitro and ex vivo biological evaluation. ChemMedChem.  https://doi.org/10.1002/cmdc.201800098. [Epub ahead of print] PubMed PMID: 29570944PubMedCrossRefGoogle Scholar
  22. Boudko SP, Bächinger HP (2016) Structural insight for chain selection and stagger control in collagen. Sci Rep 6:37831.  https://doi.org/10.1038/srep37831 CrossRefPubMedPubMedCentralGoogle Scholar
  23. Branden, C., Tooze, J (1991) Introduction to protein structure.Google Scholar
  24. Brennan SO (2015) Variation of fibrinogen oligosaccharide structure in the acute phase response: possible haemorrhagic implications. BBA Clinical 3:221–226.  https://doi.org/10.1016/j.bbacli.2015.02.007 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Brinkmann U, Di Carlo A, Vasmatzis G, Kurochkina N, Beers R, Lee B, Pastan I (1997) Stabilization of a recombinant Fv fragment by base loop interconnection and VH-VL permutation. J Mol Biol 268:107–117PubMedCrossRefGoogle Scholar
  26. Brunner JD, Lim NK, Schenck S, Duerst A, Dutzler R (2014) X-ray structure of a calcium-activated TMEM16 lipid scramblase. Nature 516(7530):207–212.  https://doi.org/10.1038/nature13984. Epub 2014 Nov 12. PubMed PMID: 25383531CrossRefPubMedGoogle Scholar
  27. Bunick CG, Milstone LM (2017) The X-ray crystal structure of the keratin 1-keratin 10 helix 2B heterodimer reveals molecular surface properties and biochemical insights into human skin disease. J Invest Dermatol;137(1):142–150.:  https://doi.org/10.1016/j.jid.2016.08.018. Epub 2016 Sep 3.PubMedCrossRefGoogle Scholar
  28. Burgess AW, Leach SJ (1973) An obligatory alpha-helical amino acid residue. Biopolymers 12(11):2599–2605. PubMed PMID: 4780721PubMedCrossRefGoogle Scholar
  29. Cabrele C, Langer M, Bader R, Wieland HA, Doods HN, Zerbe O, Beck-Sickinger AG (2000) The first selective agonist for the neuropeptide YY5 receptor increases food intake in rats. J Biol Chem 275(46):36043–36048PubMedCrossRefGoogle Scholar
  30. Caffrey M, Cai M, Kaufman J, Stahl SJ, Wingfield PT, Covell DG, Gronenborn AM, Clore GM (1998) Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41. Embo J 17:4572–4584PubMedPubMedCentralCrossRefGoogle Scholar
  31. Cervantes-Madrid D, Dominguez-Gomez G, Gonzalez-Fierro A, Perez-Cardenas E, Taja-Chayeb L, Trejo-Becerril C, Duenas-Gonzalez A (2017) Feasibility and antitumor efficacy in vivo, of simultaneously targeting glycolysis, glutaminolysis and fatty acid synthesis using lonidamine, 6-diazo-5-oxo-L-norleucine and orlistat in colon cancer. Oncology Letters 13(3):1905–1910.  https://doi.org/10.3892/ol.2017.5615 CrossRefPubMedPubMedCentralGoogle Scholar
  32. Chen Q, Wells MM, Arjunan P, Tillman TS, Cohen AE, Xu Y, Tang P (2018) Structural basis of neurosteroid anesthetic action on GABA(A) receptors. Nat Commun 9(1):3972.  https://doi.org/10.1038/s41467-018-06361-4. PubMed PMID: 30266951; PubMed Central PMCID: PMC6162318CrossRefPubMedPubMedCentralGoogle Scholar
  33. Chingle R, Proulx C, Lubell WD (2017) Azapeptide synthesis methods for expanding side-chain diversity for biomedical applications. Acc Chem Res 50(7):1541–1556.  https://doi.org/10.1021/acs.accounts.7b00114. Epub 2017 Jun 9CrossRefPubMedGoogle Scholar
  34. Chothia C (1973) Conformation of twisted beta-pleated sheets in proteins. J Mol Biol 75:295–302PubMedCrossRefGoogle Scholar
  35. Chothia C (1975) Structural invariants in protein folding. Nature 254:304–308PubMedPubMedCentralCrossRefGoogle Scholar
  36. Chothia C, Levitt M, Richardson D (1981) Helix to helix packing in proteins. J Mol Biol 145:215–250CrossRefGoogle Scholar
  37. Chothia C, Janin J (1982) Orthogonal packing of beta-pleated sheets in proteins. Biochemistry 21(17):3955–3965. PubMed PMID: 6751382PubMedCrossRefGoogle Scholar
  38. Chou KC (1988) Review: Low-frequency collective motion in biomacromolecules and its biological functions. Biophysical Chemistry 30:3–48PubMedCrossRefGoogle Scholar
  39. Chou KC (1992) Energy-optimized structure of antifreeze protein and its binding mechanism. J Mol Biol 223:509–517PubMedCrossRefGoogle Scholar
  40. Chou KC, Nemethy G, Scheraga HA (1990) Review: Energetics of interactions of regular structural elements in proteins. Acc Chem Res 23:134–141CrossRefGoogle Scholar
  41. Chou KC, Maggiora GM, Nemethy G, Scheraga HA (1988) Energetics of the structure of the four-alpha-helix bundle in proteins. Proc Natl Acad Sci USA 85:4295–4299PubMedCrossRefPubMedCentralGoogle Scholar
  42. Chou KC, Maggiora GM, Scheraga HA (1992) The role of loop-helix interactions in stabilizing four-helix bundle proteins. Proc Natl Acad Sci USA 89:7315–7319PubMedCrossRefGoogle Scholar
  43. Cook JD, Soto-Montoya H, Korpela MK, Lee JE (2015) Electrostatic architecture of the Infectious Salmon Anemia Virus (ISAV) Core fusion protein illustrates a Carboxyl-Carboxylate pH Sensor. J Biol Chem 290(30):18495–18504.  https://doi.org/10.1074/jbc.M115.644781. Epub 2015 Jun 16. PubMed PMID: 26082488; PubMed Central PMCID: PMC4513110CrossRefPubMedPubMedCentralGoogle Scholar
  44. Cordopatis P, Manessi-Zoupa E, Theodoropoulos D, Bossé R, Bouley R, Gagnon S, Escher E (1994) Methylation in positions 1 and 7 of angiotensin II. A structure-activity relationship study. Int J Pept Protein Res 44(4):320–324. PubMed PMID: 7875933PubMedCrossRefPubMedCentralGoogle Scholar
  45. Costil R, Fernández-Nieto F, Atkinson RC, Clayden J (2018) α-Methyl phenylglycines by asymmetric α-arylation of alanine and their effect on the conformational preference of helical Aib foldamers. Org Biomol Chem doi: 10.1039/c8ob00551f. [Epub ahead of print] PubMed PMID: 29595846CrossRefGoogle Scholar
  46. Crick F (1953) Acta Crystallogr 6:689CrossRefGoogle Scholar
  47. Dadheech T, Shah R, Pandit R, Hinsu A, Chauhan PS, Jakhesara S, Kunjadiya A, Rank D, Joshi C (2018) Cloning, molecular modeling and characterization of acidic cellulase from buffalo rumen and its applicability in saccharification of lignocellulosic biomass. Int J Biol Macromol 113:73–81.  https://doi.org/10.1016/j.ijbiomac.2018.02.100. Epub 2018 Feb 15. PubMed PMID: 29454942CrossRefPubMedPubMedCentralGoogle Scholar
  48. Das T, Häring M, Haldar D, Díaz DD (2017) Phenylalanine and derivatives as versatile low-molecular-weight gelators: design, structure and tailored function. Biomater Sci 6(1):38–59.  https://doi.org/10.1039/c7bm00882a. Review. PubMed PMID: 29164186CrossRefPubMedPubMedCentralGoogle Scholar
  49. Davies TG, Hubbard RE, Tame JR (1999) Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Protein Sci 8(7):1432–1444PubMedPubMedCentralCrossRefGoogle Scholar
  50. Dowling DP, Croft AK, Drennan CL (2012) Radical use of Rossmann and TIM barrel architectures for controlling coenzyme B12 chemistry. Annu Rev Biophys 41:403–427.  https://doi.org/10.1146/annurev-biophys-050511-102225. Review. PubMed PMID: 22577824CrossRefPubMedPubMedCentralGoogle Scholar
  51. Dulhunty A, Gage P, Curtis S et al (2001) The glutathione transferase structural family includes a nuclear chloride channel and a ryanodine receptor calcium release channel modulator. J Biol Chem 276:3319–3323PubMedCrossRefPubMedCentralGoogle Scholar
  52. Efimov AV (1979) Packing of alpha-helices in globular proteins. Layer-structure of globin hydrophobic cores. J Mol Biol 134(1):23–40PubMedPubMedCentralCrossRefGoogle Scholar
  53. Elkin I, Maris T, Melkoumov A, Hildgen P, Banquy X, Leclair G, Barrett C (2018) Crystal structure of 2-oxopyrrolidin-3-yl 4-(2-phenyl-diazen-1-yl)benzoate. Acta Crystallogr E Crystallogr Commun 6;74(Pt 4):458–460. doi: 10.1107/S205698901800333X. eCollection 2018 Apr 1. PubMed PMID: 29765745; PubMed Central PMCID: PMC5946967PubMedCentralCrossRefGoogle Scholar
  54. Eriksson M, Hassan S, Larsson R, Linder S, Ramqvist T, Lövborg H, Vikinge T, Figgemeier E, Müller J, Stetefeld J, Dalianis T, Ozbek S (2009) Utilization of a right-handed coiled-coil protein from archaebacterium Staphylothermus marinus as a carrier for cisplatin. Anticancer Res 29(1):11–18. PubMed PMID: 19331128PubMedPubMedCentralGoogle Scholar
  55. Ferguson AD, Mckeever BM, Wisniewski D et al (2007) Crystal structure of inhibitor-bound human 5-lipoxygenase-activating protein. Science 317:510–512PubMedCrossRefPubMedCentralGoogle Scholar
  56. Ferner J, Suhartono M, Breitung S, Jonker HR, Hennig M, Wöhnert J, Göbel M, Schwalbe H (2009) Structures of HIV TAR RNA-ligand complexes reveal higher binding stoichiometries. Chembiochem 10(9):1490–1494.  https://doi.org/10.1002/cbic.200900220 CrossRefPubMedPubMedCentralGoogle Scholar
  57. Ferrone FA (2016) Sickle cell disease: Its molecular mechanism and the one drug that treats it. Int J Biol Macromol 93(Pt A):1168–1173.  https://doi.org/10.1016/j.ijbiomac.2016.09.073. Epub 2016 Sep 22CrossRefPubMedPubMedCentralGoogle Scholar
  58. Ferofontov A, Strulovich R, Marom M, Giladi M, Haitin Y (2018) Inherent flexibility of CLIC6 revealed by crystallographic and solution studies. Sci Rep 8(1):6882.  https://doi.org/10.1038/s41598-018-25231-z. PubMed PMID: 29720717; PubMed Central PMCID: PMC5931990CrossRefPubMedPubMedCentralGoogle Scholar
  59. Fisher E (1901) Z Physiol Chem 33:151CrossRefGoogle Scholar
  60. Fisher E (1902) Chem Ber 35:2660CrossRefGoogle Scholar
  61. Formaggio F, Crisma M, Bonora GM, Pantano M, Valle G, Toniolo C, Aubry A, Bayeul D, Kamphuis J (1995) (R)-isovaline homo-peptides adopt the left-handed 3(10)-helical structure. Pept Res 8(1):6–15. PubMed PMID: 7756755PubMedGoogle Scholar
  62. Fung T, Asiri YI, Wall R, Schwarz SKW, Puil E, MacLeod BA (2017) Variations of isovaline structure related to activity in the formalin foot assay in mice. Amino Acids 49(7):1203–1213.  https://doi.org/10.1007/s00726-017-2421-6. Epub 2017 Apr 21. PubMed PMID: 28432424CrossRefPubMedGoogle Scholar
  63. Gamlin CR, Yu WQ, Wong ROL, Hoon M (2018) Assembly and maintenance of GABAergic and Glycinergic circuits in the mammalian nervous system. Neural Dev 13(1):12.  https://doi.org/10.1186/s13064-018-0109-6. Review. PubMed PMID: 29875009; PubMed Central PMCID: PMC5991458CrossRefPubMedPubMedCentralGoogle Scholar
  64. Gernert KM, Surles MC, Labean TH, Richardson JS, Richardson DC (1995) Alacoil: a very tight, antiparallel coiled-coil of helices. Protein Science 4:2252–2260PubMedPubMedCentralCrossRefGoogle Scholar
  65. Goh KL, Holmes DF (2017) Collagenous extracellular matrix biomaterials for tissue engineering: lessons from the common sea urchin tissue. Int J Mol Sci 18(5):901.  https://doi.org/10.3390/ijms18050901 CrossRefPubMedCentralPubMedGoogle Scholar
  66. Görbitz CH, Karen P, Dušek M, Petrícek V (2016) An exceptional series of phase transitions in hydrophobic amino acids with linear side chains. IUCrJ 3(Pt 5):341–353.  https://doi.org/10.1107/S2052252516010472 CrossRefPubMedPubMedCentralGoogle Scholar
  67. Gord JR, Hewett DM, Hernandez-Castillo AO, Blodgett KN, Rotondaro MC, Varuolo A, Kubasik MA, Zwier TS (2016) Conformation-specific spectroscopy of capped, gas-phase Aib oligomers: tests of the Aib residue as a 310-helix former. Phys Chem Chem Phys 18(36):25512–25527PubMedCrossRefGoogle Scholar
  68. Grauer AA, Cabrele C, Zabel M, König B (2009) Stable right- and left-handed peptide helices containing C(alpha)-tetrasubstituted alpha-amino acids. J Org Chem 74(10):3718–3726. doi:  https://doi.org/10.1021/jo900222g. PubMed PMID: 19354242PubMedCrossRefGoogle Scholar
  69. Guerra ME, Fadel V, Maltarollo VG, Baldissera G, Honorio KM, Ruggiero JR, Dos Santos Cabrera MP (2017) MD simulations and multivariate studies for modeling the antileishmanial activity of peptides. Chem Biol Drug Des 2017 Mar 7.  https://doi.org/10.1111/cbdd.12970. [Epub ahead of print]CrossRefGoogle Scholar
  70. Gunning PW, Hardeman EC, Lappalainen P, Mulvihill DP (2015) Tropomyosin - master regulator of actin filament function in the cytoskeleton. J Cell Sci 128(16):2965–2974.  https://doi.org/10.1242/jcs.172502. Epub 2015 Aug 3CrossRefPubMedGoogle Scholar
  71. Harbury PB, Zhang T, Kim PS, Alber T (1993) A switch between two-, three-. and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262(5138):1401–1407PubMedCrossRefGoogle Scholar
  72. Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS (1998) High-resolution protein design with backbone freedom. Science 282(5393):1462–1467. PubMed PMID: 9822371PubMedCrossRefGoogle Scholar
  73. Harris NL, Presnell SR, Cohen FE (1994) Four helix bundle diversity in proteins. J Mol Biol 236:1356–1368PubMedCrossRefGoogle Scholar
  74. Harrop SJ, DeMaere MZ, Fairlie WD et al (2001) Crystal structure of a soluble form of the intracellular chloride ion channel CLIC1 (NCC27) at 1.4-A resolution. J Biol Chem 276:44993–45000PubMedCrossRefGoogle Scholar
  75. Harsini FM, Chebrolu S, Fuson KL, White MA, Rice AM, Sutton RB (2018) FerA is a membrane-associating four-helix bundle domain in the Ferlin family of membrane-fusion proteins. Sci Rep;8(1):10949.  https://doi.org/10.1038/s41598-018-29184-1. PubMed PMID: 30026467; PubMed Central PMCID: PMC6053371.
  76. Hodges RS, Sodek J, Smillie LB et al (1972) Amino-acid sequence of rabbit skeletal tropomyosin and its coiled-coil structure. Proc Natl Acad Sci 69:3800–3804PubMedPubMedCentralCrossRefGoogle Scholar
  77. Hollman AL, Tchounwou PB, Huang HC (2016) The Association between gene-environment interactions and diseases involving the human GST superfamily with SNP variants. Int J Environ Res Public Health 13(4):379.  https://doi.org/10.3390/ijerph13040379. Review. PubMed PMID: 27043589; PubMed Central PMCID: PMC4847041CrossRefPubMedPubMedCentralGoogle Scholar
  78. Holm PJ, Bhakat P, Jegerschold C, Gyobu N, Mitsuoka K, Fujiyoshi Y, Morgenstern R, Hebert H (2006) Structural basis for detoxification and oxidative stress protection in membranes. J Mol Biol 360:934–945PubMedCrossRefGoogle Scholar
  79. Holmes TC (2002) Novel peptide-based biomaterial scaffolds for tissue engineering. Trends Biotechnol 20(1):16–21. Review. PubMed PMID: 11742673PubMedCrossRefGoogle Scholar
  80. Holton A, Alber J (2004) Automated protein crystal structure determination using elves. Proc Natl Acad Sci 101:1537–1542PubMedCrossRefGoogle Scholar
  81. Hou Q, Bourgeas R, Pucci F, Rooman M (2018) Computational analysis of the amino acid interactions that promote or decrease protein solubility. Sci Rep 8(1):14661.  https://doi.org/10.1038/s41598-018-32988-w. PubMed PMID: 30279585; PubMed Central PMCID: PMC6168528CrossRefPubMedPubMedCentralGoogle Scholar
  82. Huber R, Romish J, Paques EP (1990) The crystal and molecular structure of human annexin V, an anticoagulant protein that binds to calcium and membranes. Embo J 9:3867–3874PubMedPubMedCentralCrossRefGoogle Scholar
  83. Ida M, Sato A, Matsumoto I et al (2004) Human annexin V binds to sulfatide: contribution to regulation of blood coagulation. J Mol Biol 135:583–588Google Scholar
  84. Ishitsuka R, Kojima K, Utsumi H et al (1998) Glycosaminoglycan Binding Properties of Annexin IV, V, and VI. J Biol Chem 273:9935–9941PubMedCrossRefGoogle Scholar
  85. Jaffe EK (2017) New protein structures provide an updated understanding of phenylketonuria. Mol Genet Metab 121(4):289–296.  https://doi.org/10.1016/j.ymgme.2017.06.005. Epub 2017 Jun 15. Review. PubMed PMID: 28645531; PubMed Central PMCID: PMC5549558CrossRefPubMedPubMedCentralGoogle Scholar
  86. Jeppesen MG, Ortiz P, Shepard W et al (2003) The Crystal Structure of the Glutathione S-Transferase-like Domain of Elongation Factor 1B from Saccharomyces cerevisiae. J Biol Chem 278:47190–47198CrossRefGoogle Scholar
  87. Jiang Q, Li K, Lu WJ, Li S, Chen X, Liu XJ, Yuan J, Ding Q, Lan F, Cai SQ (2018) Identification of small-molecule ion channel modulators in C. elegans channelopathy models. Nat Commun 9(1):3941.  https://doi.org/10.1038/s41467-018-06514-5. PubMed PMID: 30258187; PubMed Central PMCID: PMC6158242CrossRefPubMedPubMedCentralGoogle Scholar
  88. Juncosa JI, Takaya K, Le HV, Moschitto MJ, Weerawarna PM, Mascarenhas R, Liu D, Dewey SL, Silverman RB (2018) Design and Mechanism of (S)-3-Amino-4-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic Acid, a Highly Potent ?-Aminobutyric Acid Aminotransferase Inactivator for the Treatment of Addiction. J Am Chem Soc 140(6):2151–2164.  https://doi.org/10.1021/jacs.7b10965. Epub 2018 Jan 30. PubMed PMID: 29381352; PubMed Central PMCID: PMC5812813CrossRefPubMedPubMedCentralGoogle Scholar
  89. Kadir M, Wang X, Zhu B, Liu J, Harland D, Popescu C (2017) The structure of the “amorphous” matrix of keratins. J Struct Biol 198(2):116–123. doi: 10.1016/j.jsb.2017.04.001. Epub 2017 Apr 5PubMedCrossRefGoogle Scholar
  90. Kantharaju RS, Aravinda S, Shamala N, Balaram P (2010) Helical conformations of hexapeptides containing N-terminus diproline segments. Biopolymers 94(3):360–370.  https://doi.org/10.1002/bip.21395 CrossRefGoogle Scholar
  91. Kapinos LE, Burkhard P, Herrmann H, Aebi U, Strelkov SV (2011) Simultaneous formation of right- and left-handed anti-parallel coiled-coil interfaces by a coil2 fragment of human lamin A. J Mol Biol 408(1):135–146.  https://doi.org/10.1016/j.jmb.2011.02.037. Epub 2011 Feb 24. PubMed PMID: 21354179CrossRefPubMedGoogle Scholar
  92. Kasznel AJ, Zhang Y, Hai Y, Chenoweth DM (2017) Structural basis for aza-glycine stabilization of collagen. J Am Chem Soc 2017 Jul 19;139(28):9427–9430.  https://doi.org/10.1021/jacs.7b03398. Epub 2017 Jul 6.PubMedCrossRefGoogle Scholar
  93. Kendrew JC (1959) Structure and function in myoglobin and other proteins. Fed Proc 18(2, Part 1):740–751. PubMed PMID: 136722PubMedGoogle Scholar
  94. Khanapur M, Alvala M, Prabhakar M, Shiva Kumar K, Edwin RK, Sri Saranya PS, Patel RK, Bulusu G, Misra P, Pal M (2017) Mycobacterium tuberculosis chorismate mutase: A potential target for TB. Bioorg Med Chem 25(6):1725–1736.  https://doi.org/10.1016/j.bmc.2017.02.001. Epub 2017 Feb 4. Review. PubMed PMID: 28202315CrossRefPubMedGoogle Scholar
  95. Kikuchi N, Fujiwara K, Ikeguchi M (2018) ß-strand twisting/bending in soluble and transmembrane ß-barrel structures. Proteins.  https://doi.org/10.1002/prot.25576. [Epub ahead of print] PubMed PMID: 30019770CrossRefGoogle Scholar
  96. Kitaigorodsky AI (1973) Molecular crystals and molecules. Academic Press, New YorkGoogle Scholar
  97. Kohn WD, Mant CT, Hodges RS (1977) Helical protein assembly motifs. J Biol Chem 272:2583–2586CrossRefGoogle Scholar
  98. Kollman JM, Pandi L, Sawaya MR, Riley M, Doolittle RF (2009) Crystal structure of human fibrinogen. Biochemistry 48(18):3877–3886.  https://doi.org/10.1021/bi802205g CrossRefPubMedGoogle Scholar
  99. Konno K, Rangel M, Oliveira JS, Dos Santos Cabrera MP, Fontana R, Hirata IY, Hide I, Nakata Y, Mori K, Kawano M, Fuchino H, Sekita S, Neto JR (2017) Decoralin, a novel linear cationic alpha-helical peptide from the venom of the solitary eumenine wasp Oreumenes decoratus. Peptides 28(12):2320–2327. Epub 2007 Sep 29CrossRefGoogle Scholar
  100. Krzywda S, Brzozowski AM, Higashitsuji H, Fujita J, Welchman R, Dawson S, Mayer RJ, Wilkinson AJ (2004) The Crystal Structure of Gankyrin, an Oncoprotein Found in Complexes with Cyclin-dependent Kinase 4, a 19 S Proteasomal ATPase Regulator, and the Tumor Suppressors Rb and p53. J Biol Chem 279:1541–1545CrossRefGoogle Scholar
  101. Kuang Q, Purhonen P, Ålander J, Svensson R, Hoogland V, Winerdal J, Spahiu L, Ottosson-Wadlund A, Jegerschöld C, Morgenstern R, Hebert H (2017) Dead-end complex, lipid interactions and catalytic mechanism of microsomal glutathione transferase 1, an electron crystallography and mutagenesis investigation. Sci Rep 7(1):7897.  https://doi.org/10.1038/s41598-017-07912-3. PubMed PMID: 28801553; PubMed Central PMCID: PMC5554250CrossRefPubMedPubMedCentralGoogle Scholar
  102. Kurochkina N (2007) J Theor Biol 247:110–121PubMedPubMedCentralCrossRefGoogle Scholar
  103. Kurochkina N (2008) J Theor Biol 255:188–198PubMedPubMedCentralCrossRefGoogle Scholar
  104. Kurochkina N (2011) Common structural characteristics of fibrous and globular proteins. In: Haggerty LM (ed) Protein Structure. Nova Science Publishers, Inc, Hauppauge. https://www.springer.com/us/book/9783319200972
  105. Kurochkina N, Choekyi T (2011) Helix-helix interfaces and ligand binding. J Theor Biol 283:92–102PubMedPubMedCentralCrossRefGoogle Scholar
  106. Ladner JE, Parsons JF, Rife CL, Gilliland GL, Armstrong RN (2004) Parallel evolutionary pathways for glutathione transferases: structure and mechanism of the mitochondrial class kappa enzyme rGSTK1-1. Biochemistry 43(2):352–361. PubMed PMID: 14717589PubMedCrossRefGoogle Scholar
  107. Lance E, Arnich N, Maignien T, Biré R (2018) Occurrence of β-N-methylamino-l-alanine (BMAA) and Isomers in Aquatic Environments and Aquatic Food Sources for Humans. Toxins (Basel) 10(2):pii: E83.  https://doi.org/10.3390/toxins10020083. Review.PubMed PMID: 29443939; PubMed Central PMCID: PMC5848184CrossRefGoogle Scholar
  108. Lasker MV, Gajjar MM, Nair SK (2005) Molecular Structure of the IL-1R-Associated Kinase-4 Death Domain and Its Implications for TLR signaling. J Immun 175:4175–4179CrossRefGoogle Scholar
  109. Lee C-H, Kim M-S, Chung BM, Leahy DJ, Coulombe PA (2012) Structural basis for heteromeric assembly and perinuclear organization of keratin filaments. Nat Struct Mol Biol 19(7).  https://doi.org/10.1038/nsmb.2330 CrossRefGoogle Scholar
  110. Lee B, Richards FM (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55:379–400PubMedCrossRefGoogle Scholar
  111. Lee H, Song C, Hong YS, Kim MS, Cho HR, Kang T, Shin K, Choi SH, Hyeon T, Kim DH (2017) Wearable/disposable sweat-based glucose monitoring device with multistage transdermal drug delivery module. Sci Adv 3(3):e1601314. doi:10.1126/sciadv.1601314. eCollection 2017 Mar. PubMed PMID: 28345030; PubMed Central PMCID: PMC5342654PubMedPubMedCentralCrossRefGoogle Scholar
  112. Lee LK, Stewart AG, Donohoe M, Bernal RA, Stock D (2010) The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase. Nat Struct Mol Biol. 17(3):373–378.  https://doi.org/10.1038/nsmb.1761. Epub 2010 Feb 21. PubMed PMID: 20173764; PubMed Central PMCID: PMC2912985CrossRefPubMedPubMedCentralGoogle Scholar
  113. Leung K. (2010) (R)-3-[(18)F]Fluoro-2-methyl-2-N-(methylamino)propanoic acid. [updated 2010 Jul 29]. Molecular Imaging and Contrast Agent Database (MICAD) [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2004-2013. Available from http://www.ncbi.nlm.nih.gov/books/NBK45198/ PubMed PMID: 20662134.
  114. Li Y, Zhou M, Hu Q, Bai XC, Huang W, Scheres SH, Shi Y (2017) Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme. Proc Natl Acad Sci U S A 114(7):1542–1547.  https://doi.org/10.1073/pnas.1620626114. Epub 2017 Jan 31. PubMed PMID: 28143931; PubMed Central PMCID: PMC5320974CrossRefPubMedPubMedCentralGoogle Scholar
  115. Lin S-C, Lo Y-C, Wu H (2010) Helical assembly in the MyD88–IRAK4–IRAK2 complex in TLR/IL-1R signaling. Nature 465:885–890PubMedPubMedCentralCrossRefGoogle Scholar
  116. Littler DR, Harrop SJ, Brown LJ et al (2008) Comparison of vertebrate and invertebrate CLIC proteins: the crystal structures of Caenorhabditis elegans EXC-4 and Drosophila melanogaster DmCLIC. Proteins 71:364–378PubMedCrossRefGoogle Scholar
  117. Liu J, Deng Y, Dey AK, Moore JP, Lu M (2009) Structure of the HIV-1 gp41membrane-proximal ectodomain region in a putative prefusion conformation. Biochemistry 48(13):2915–2923.  https://doi.org/10.1021/bi802303b. PubMed PMID: 19226163; PubMed Central PMCID: PMC2765501CrossRefPubMedPubMedCentralGoogle Scholar
  118. Liu J, Taylor DW, Krementsova EB, Trybus KM, Taylor KA (2006a) Three-dimensional structure of the myosin V inhibited state by cryoelectron tomography. Nature 442(7099):208–211. Epub 2006 Apr 16.PubMedCrossRefGoogle Scholar
  119. Liu J, Deng Y, Zheng Q, Cheng CS, Kallenbach NR, Lu M (2006b) A parallel coiled-coil tetramer with offset helices. Biochemistry 45(51):15224–15231. Epub 2006b Nov 29. PubMed PMID: 17176044PubMedCrossRefGoogle Scholar
  120. Lovejoy B, Choe S, Cascio D, McRorie DK, DeGrado WF, Eisenberg D (1993) Crystal structure of a synthetic triple-stranded alpha-helical bundle. Science 259:1288–1293PubMedCrossRefGoogle Scholar
  121. Lovejoy B, Le TC, Luthy R, Cascio D, O’Neil KT, DeGrado WF, Eisenberg D (1992) X-ray grade crystals of a designed a-helical coiled coil. Protein Sci 1:956–957PubMedPubMedCentralCrossRefGoogle Scholar
  122. Malashkevich VN, Schneider BJ, McNally ML, Milhollen MA, Pang JX, Kim PS (1999) Core structure of the envelope glycoprotein GP2 from Ebola virus at 1.9-A resolution. Proc Natl Acad Sci U S A. 96(6):2662–2667. PubMed PMID: 10077567; PubMed Central PMCID: PMC15825PubMedPubMedCentralCrossRefGoogle Scholar
  123. Martins DB, Vieira MR, Fadel V, Santana VAC, Guerra MER, Lima ML, Tempone AG, Dos Santos Cabrera MP (2017) Membrane targeting peptides toward antileishmanial activity: design, structural determination and mechanism of interaction. Biochim Biophys Acta pii: S0304-4165(17):30248–30249.  https://doi.org/10.1016/j.bbagen.2017.08.003. [Epub ahead of print]CrossRefGoogle Scholar
  124. Masood R, Ullah K, Ali H, Ali I, Betzel C, Ullah A (2018) Spider’s venom phospholipases D: A structural review. Int J Biol Macromol 107(Pt A):1054–1065.  https://doi.org/10.1016/j.ijbiomac.2017.09.081. Epub 2017 Sep 23. Review. PubMed PMID: 28951301CrossRefPubMedGoogle Scholar
  125. Medved L, Nieuwenhuizen W (2003) Molecular mechanisms of initiation of fibrinolysis by fibrin. Thromb Haemost. 2003 Mar;89(3):409–419.PubMedCrossRefGoogle Scholar
  126. Moitra J, Szilak L, Krylov D, Vinson C (1997) Leucine is the most stabilizing aliphatic amino acid in the d position of a dimeric leucine zipper coiled coil. Biochemistry 36:12567–12573PubMedCrossRefGoogle Scholar
  127. Moll JR, Ruvinov SB, Pastan I, Vinson C (2001) Designed heterodimerizing leucine zippers with a ranger of pI’s and stabilities up to 10–15 M. Protein Sci 10:649–655PubMedPubMedCentralCrossRefGoogle Scholar
  128. Mykhailiuk PK, Kubyshkin V, Bach T, Budisa N (2017) Peptidyl-prolyl model study: how does the electronic effect influence the amide bond Conformation? J Org Chem.  https://doi.org/10.1021/acs.joc.7b00803. [Epub ahead of print]PubMedCrossRefGoogle Scholar
  129. Namba K, Stubbs G (1986) Structure of tobacco mosaic virus at 3.6 Angstroms resolution. Implications for assembly. Science 231:1401–1406PubMedCrossRefGoogle Scholar
  130. Namba K, Pattanayek R, Stubbs G (1989) Visualization of protein-nucleic acid interactions in a virus. Structure of intact tobacco mosaic virus at 2.9 Angstrom resolution by X-ray fiber diffraction. J Mol Biol 208:307–325PubMedCrossRefGoogle Scholar
  131. Navarro E, Fenude E, Celda B (2002) Solution structure of a D, L-alternating oligonorleucine as a model of double-stranded antiparallel beta-helix. Biopolymers 64(4):198–209PubMedCrossRefGoogle Scholar
  132. Navarro E, Fenude E, Celda (2004) Conformational and structural analysis of the equilibrium between single- and double-strand beta-helix of a D,L-alternating oligonorleucine. Biopolymers 73(2):229–241PubMedCrossRefGoogle Scholar
  133. Navarro E, Tejero R, Fenude E, Celda B (2001) Solution NMR structure of a D,L-alternating oligonorleucine as a model of beta-helix. Biopolymers 59(2):110–119PubMedCrossRefPubMedCentralGoogle Scholar
  134. Newberry RW, Raines RT (2017) 4-Fluoroprolines: conformational analysis and effects on the stability and folding of peptides and proteins. Top Heterocycl Chem 48:1–25.  https://doi.org/10.1007/7081_2015_196 CrossRefPubMedGoogle Scholar
  135. Oshaben KM, Horne WS (2014) Tuning assembly size in Peptide-based supramolecular polymers by modulation of subunit association affinity. Biomacromolecules 15(4):1436–1442.  https://doi.org/10.1021/bm5000423. Epub 2014 Mar 17PubMedCrossRefGoogle Scholar
  136. O’Shea EK, Klemm JD, Kim PS, Alber T (1991) Crystal structure of GCN4 leucine zipper, a two-stranded parallel coiled coil. Science 254:539CrossRefGoogle Scholar
  137. Paliakasis CD, Kokkinidis M (1991) The stability of the four-α-helix bundle motif in proteins. Protein Eng 4:849PubMedCrossRefPubMedCentralGoogle Scholar
  138. Park HH, Logette E, Raunser S, Cuenin S, Walz T, Tschopp J, Wu H (2007) Death domain assembly mechanism revealed by crystal structure of the oligomeric PIDDosome core complex. Cell 128:533–546PubMedPubMedCentralCrossRefGoogle Scholar
  139. Parry DAD, Fraser RD, Squire JM (2008) Fifty years of coiled-coils and α-helical bundles: a close relationship between sequence and structure. J Struct Biol 163:258–269PubMedCrossRefGoogle Scholar
  140. Passon DM, Lee M, Rackham O, Stanley WA, Sadowska A, Filipovska A, Fox AH, Bond CS (2012) Structure of the heterodimer of human NONO and paraspeckle protein component 1 and analysis of its role in subnuclear body formation. Proc Natl Acad Sci USA 109(13):4846–4850.  https://doi.org/10.1073/pnas.1120792109. Epub 2012 Mar 13. PubMed PMID: 22416126; PubMed Central PMCID: PMC3324020CrossRefGoogle Scholar
  141. Pauling L, Corey RB, Branson HR (1951) The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 37:205PubMedPubMedCentralCrossRefGoogle Scholar
  142. Pechik I, Madrazo J, Mosesson MW, Hernandez I, Gilliland GL, Medved L (2004) Crystal structure of the complex between thrombin and the central “E” region of fibrin. Proc Natl Acad Sci USA 101(9):2718–2723.  https://doi.org/10.1073/pnas.0303440101 CrossRefPubMedGoogle Scholar
  143. Pielak RM, Schnell JR, Chou JJ (2009) Mechanism of drug inhibition and drug resistance of influenza A M2 channel. Proc Natl Acad Sci USA 106:7379–7384PubMedCrossRefGoogle Scholar
  144. Pitman KA, Borgland SL, MacLeod B, Puil E (2015) Isovaline does not activate GABA(B) receptor-coupled potassium currents in GABA(B) expressing AtT-20 cells and cultured rat hippocampal neurons. PLoS One 10(2):e0118497.  https://doi.org/10.1371/journal.pone.0118497. eCollection 2015. PubMed PMID: 25706125; PubMed Central PMCID: PMC4337901PubMedPubMedCentralCrossRefGoogle Scholar
  145. Plecs JJ, Harbury PB, Kim PS, Alber T (2004) Structural test of the parameterized-backbone method for protein design. J Mol Biol 342(1):289–297. PubMed PMID: 15313624.PubMedCrossRefGoogle Scholar
  146. Ponder JW, Richards FM (1987) Tertiary templates for proteins. J Mol Biol 193:775PubMedCrossRefGoogle Scholar
  147. Raghavender US, Kantharaju Aravinda S, Shamala N, Balaram P (2010) Hydrophobic peptide channels and encapsulated water wires. J Am Chem Soc 132(3):1075–1086.  https://doi.org/10.1021/ja9083978 CrossRefPubMedGoogle Scholar
  148. Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) Stereochemistry of polypeptide chain configurations. J Mol Biol 7:95–99PubMedCrossRefGoogle Scholar
  149. Reinert ZE, Lengyel GA, Horne WS (2013) Protein-like tertiary folding behavior from heterogeneous backbones.J Am Chem Soc 135(34):12528–12531.  https://doi.org/10.1021/ja405422v. Epub 2013 Aug 15PubMedPubMedCentralCrossRefGoogle Scholar
  150. Richards FM (1977) Areas, volumes, packing, and protein structure. Ann Rev Biophys Bioeng 6:151–176CrossRefGoogle Scholar
  151. Ruba A, Yang W (2016) O-GlcNAc-ylation in the nuclear pore complex. Cell Mol Bioeng 9(2):227–233.  https://doi.org/10.1007/s12195-016-0440-0. Epub 2016 Apr 26. PubMed PMID: 28638491; PubMed Central PMCID: PMC5475274PubMedPubMedCentralCrossRefGoogle Scholar
  152. Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman BF (2010) An unprecedented nucleic acid capture mechanism for excision of DNA damage. Nature 468:406–411PubMedPubMedCentralCrossRefGoogle Scholar
  153. Le Rumeur E, Hubert JF, Winder SJ (2012) A new twist to coiled coil. FEBS Lett 586(17):2717–2722.  https://doi.org/10.1016/j.febslet.2012.05.004. Epub 2012 May 11. Review. PubMed PMID: 22584055PubMedCrossRefPubMedCentralGoogle Scholar
  154. Sakai H (2017) Overview of potential clinical applications of Hemoglobin Vesicles (HbV) as artificial red cells, evidenced by preclinical studies of the academic research consortium. J Funct Biomater 8(1):10.  https://doi.org/10.3390/jfb8010010 CrossRefPubMedCentralGoogle Scholar
  155. Salnikov ES, Anantharamaiah GM, Bechinger B (2018) Supramolecular organization of apolipoprotein-A-I-derived peptides within disc-like arrangements. Biophys J 115(3):467–477.  https://doi.org/10.1016/j.bpj.2018.06.026. Epub 2018 Jul 11. PubMed PMID: 30054032; PubMed Central PMCID: PMC6085177PubMedPubMedCentralCrossRefGoogle Scholar
  156. Samatey FA, Imada K, Nagashima S, Vonderviszt F, Kumasaka T, Yamamoto M, Namba K (2001) Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling. Nature 410:331–337PubMedCrossRefPubMedCentralGoogle Scholar
  157. Schrauber H, Eisenhaber F, Argos P (1993) Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol 230(2):592–612PubMedCrossRefGoogle Scholar
  158. Scott FL, Stec B, Pop C, Dobaczewska MK, Lee JJ, Monosov E, Robinson H, Salvesen GS, Schwarzenbacher R, Riedl SJ (2009) The Fas/FADD death domain complex structure unravels signaling by receptor clustering. Nature 457:1019–1022CrossRefGoogle Scholar
  159. Shao C, Zhang F, Kemp MM, Linhardt RJ, Waisman DM, Head JF, Seaton BA (2006) Crystallographic analysis of calcium-dependent heparin binding to Annexin A2. J Biol Chem 281:31689–31695PubMedPubMedCentralCrossRefGoogle Scholar
  160. Sharma K, Dhillon A, Goyal A (2018) Insights into structure and reaction mechanism of β-mannanases. Curr Protein Pept Sci 19(1):34–47.  https://doi.org/10.2174/1389203717666161013115724. Review. PubMed PMID: 27739373
  161. Sheehan D, Meade G, Foley VM, Dowd CA (2001) Structure, function and evolution of glutathione transferases: implications for classification of non-mammalian members of an ancient enzyme superfamily. Biochem J 360:1–16PubMedPubMedCentralCrossRefGoogle Scholar
  162. Sheriff S, Hendrickson WA, Smith JL (1987) Structure of myohemerythrin in the azidomet state at 1.7/1.3 angstroms resolution. J Mol Biol 197:273–296PubMedCrossRefGoogle Scholar
  163. Shoulders MD, Raines RT (2009) Collagen structure and stability. Annu Rev Biochem 78:929–958.  https://doi.org/10.1146/annurev.biochem.77.032207.120833 CrossRefPubMedPubMedCentralGoogle Scholar
  164. Smith AI, Lew RA, Shrimpton CN, Evans RG, Abbenante G (2000) A novel stable inhibitor of endopeptidases EC 3.4.24.15 and 3.4.24.16 potentiates bradykinin-induced hypotension. Hypertension 35(2):626–630. PubMed PMID: 10679508PubMedCrossRefPubMedCentralGoogle Scholar
  165. Song X, Zhang Y, Wang Y (2011) Antimicrobial peptides peptaibols from trichoderma—a review. Wei Sheng Wu Xue Bao 51(4):438–444. Review. Chinese. PubMed PMID: 21796977Google Scholar
  166. Spyroulias GA, Papazacharias S, Pairas G, Cordopatis P (2002) Monitoring the structural consequences of Phe12—>D-Phe and Leu15—>Aib substitution in human/rat corticotropin releasing hormone. Implications for design of CRH antagonists. Eur J Biochem 269(24):6009–6019. PubMed PMID: 12473096Google Scholar
  167. Squire JM, Paul DM, Morris EP (2017) Myosin and actin filaments in muscle: structures and interactions. Subcell Biochem 82:319–371.  https://doi.org/10.1007/978-3-319-49674-0_11 CrossRefPubMedPubMedCentralGoogle Scholar
  168. Stanfield R, Cabezas E, Satterthwait A, Stura E, Profy A, Wilson I (1999) Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs. Structure 7(2):131–142. PubMed PMID: 10368281PubMedCrossRefPubMedCentralGoogle Scholar
  169. Stetefeld J, Jenny M, Schulthess T, Landwehr R, Engel J, Kammerer RA (2000) Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer. Nat Str Biol 7:772–776CrossRefGoogle Scholar
  170. Stevens J, Corper AL, Basler CF, Taubenberger JK, Palese P, Wilson IA (2004) Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus. Science 303:1866–1870PubMedCrossRefPubMedCentralGoogle Scholar
  171. Strelkov SV, Herrmann H, Geisler N, Wedig T, Zimbelmann R, Aebi U, Burkhard P (2002) Conserved segments 1A and 2B of the intermediate filament dimer: their atomic structures and role in filament assembly. EMBO J 21(6):1255–1266. PubMed PMID: 11889032; PubMed Central PMCID: PMC125921PubMedPubMedCentralCrossRefGoogle Scholar
  172. Subbalakshmi C, Basak P, Nagaraj R (2017) Self-assembly of t-Butyloxycarbonyl protected dipeptide methyl esters composed of leucine, isoleucine and valine into highly organized structures from alcohol and aqueous alcohol mixtures. Biopolymers  https://doi.org/10.1002/bip.23033. [Epub ahead of print]CrossRefGoogle Scholar
  173. Sudha G, Singh P, Swapna LS, Srinivasan N (2015) Weak conservation of structural features in the interfaces of homologous transient protein–protein complexes. Protein Sci A Publ Protein Soc 24(11):1856–1873.  https://doi.org/10.1002/pro.2792 CrossRefGoogle Scholar
  174. Sutton RB, Fasshauer F, Jahn R, Brunger AT (1998) Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution. Nature 395:347–353PubMedCrossRefPubMedCentralGoogle Scholar
  175. Taylor KC, Buvoli M, Korkmaz EN, Buvoli A, Zheng Y, Heinze NT, Cui Q, Leinwand LA, Rayment I (2015) Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly. Proc Natl Acad Sci USA 112(29):E3806–E3815.  https://doi.org/10.1073/pnas.1505813112. Epub 2015 Jul 6. PubMed PMID: 26150528; PubMed Central PMCID: PMC4517226CrossRefGoogle Scholar
  176. Touw DS, Nordman CE, Stuckey JA, Pecorano VL (2007) Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled-coils. Proc Natl Acad Sci 104:11969–11974PubMedCrossRefGoogle Scholar
  177. Tseng T-S, Wang S-H, Chang T-W, Wei H-M, Wang Y-J, Tsai K-C et al (2016) Sarkosyl-induced helical structure of an antimicrobial peptide GW-Q6 plays an essential role in the binding of surface receptor OprI in Pseudomonas aeruginosa. PLoS ONE 11(10):e0164597.  https://doi.org/10.1371/journal.pone.0164597 CrossRefPubMedPubMedCentralGoogle Scholar
  178. Vasudev PG, Ananda K, Chatterjee S, Aravinda S, Shamala N, Balaram P (2007) Hybrid peptide design. Hydrogen bonded conformations in peptides containing the stereochemically constrained gamma-amino acid residue, gabapentin. J Am Chem Soc 129(13):4039–4048. Epub 2007 Mar 10PubMedCrossRefGoogle Scholar
  179. Vasudev PG, Chatterjee S, Shamala N, Balaram P (2009) Gabapentin: a stereochemically constrained gamma amino acid residue in hybrid peptide design. Acc Chem Res 42(10):1628–1639.  https://doi.org/10.1021/ar9001153. Review. PubMed PMID: 19572698PubMedCrossRefGoogle Scholar
  180. Venanzi M, Gatto E, Formaggio F, Toniolo C (2017) The importance of being Aib. Aggregation and self-assembly studies on conformationally constrained oligopeptides. J Pept Sci 23(2):104-116.  https://doi.org/10.1002/psc.2956. Epub 2017 Jan 5. Review. PubMed PMID: 28054413PubMedCrossRefGoogle Scholar
  181. Very N, Vercoutter-Edouart AS, Lefebvre T, Hardivillé S, El Yazidi-Belkoura I (2018 Oct 9) Cross-Dysregulation of O-GlcNAcylation and PI3K/AKT/mTOR Axis in Human Chronic Diseases. Front Endocrinol (Lausanne). 9:602. doi: 10.3389/fendo.2018.00602. eCollection 2018. Review. PubMed PMID: 30356686; PubMed Central PMCID: PMC6189293Google Scholar
  182. Vitagliano L, Berisio R, Mazzarella L, Zagari A (2001) Structural bases of collagen stabilization induced by proline hydroxylation. Biopolymers 58(5):459–464PubMedCrossRefGoogle Scholar
  183. Vollmar M, Schlieper D, Winn M, Büchner C, Groth G (2009) Structure of the c14 rotor ring of the proton translocating chloroplast ATP synthase. J Biol Chem 284(27):18228–18235.  https://doi.org/10.1074/jbc.M109.006916. Epub 2009 May 7. PubMed PMID: 19423706; PubMed Central PMCID: PMC2709358CrossRefGoogle Scholar
  184. Yadav MK, Redman JE, Leman LJ, Alvarez-Gutiérrez JM, Zhang Y, Stout CD, Ghadiri MR (2005) Structure-based engineering of internal cavities in coiled-coil peptides. Biochemistry 44(28):9723–9732. PubMed PMID: 16008357; PubMed Central PMCID: PMC1779508PubMedPubMedCentralCrossRefGoogle Scholar
  185. Yang J, Ma YQ, Page RC, Misra S, Plow EF, Qin J (2009) Structure of an integrin alphaIIb beta3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation. Proc Natl Acad Sci USA 106(42):17729–17734.  https://doi.org/10.1073/pnas.0909589106. Epub 2009 Oct 1. PubMed PMID: 19805198; PubMed Central PMCID: PMC2764936CrossRefGoogle Scholar
  186. Young SC (2018) A systematic review of antiamyloidogenic and metal-chelating peptoids: two structural motifs for the treatment of Alzheimer’s disease. Molecules 23(2). pii: E296.  https://doi.org/10.3390/molecules23020296. Review. PubMed PMID: 29385058PubMedCentralCrossRefPubMedGoogle Scholar
  187. Wada SI, Takesada A, Nagamura Y, Sogabe E, Ohki R, Hayashi J, Urata H (2017) Structure-activity relationship study of Aib-containing amphipathic helical peptide-cyclic RGD conjugates as carriers for siRNA delivery. Bioorg Med Chem Lett;27(24):5378–5381.  https://doi.org/10.1016/j.bmcl.2017.11.018. Epub 2017 Nov 10. PubMed PMID: 29157863CrossRefGoogle Scholar
  188. Wagschal K, Lavigna P, Mant C, Hodges RS (1999) The role of position a in determining the stability and oligomerization state of a-helical coiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins. Protein Sci 8:2312–2329PubMedPubMedCentralCrossRefGoogle Scholar
  189. Weber CH, Vincenz C (2001) The death domain superfamily: a tale of two interfaces? TIBS 26:475–481PubMedGoogle Scholar
  190. Wells WW, Yang Y, Deits TL, Gan ZR (1993) Thioltransferases. Adv Enzymol Relat Areas Mol Biol;66:149–201. Review. PubMed PMID: 8430514
  191. Woolfson DN (2010) Building fibrous biomaterials from -helical and collagen-like coiled-coil peptides. Biopolymers 94:118–127PubMedCrossRefGoogle Scholar
  192. Xie L, Yang S (2016) Brain globins in physiology and pathology. Med Gas Res 6(3):154–163.  https://doi.org/10.4103/2045-9912.191361 CrossRefPubMedPubMedCentralGoogle Scholar
  193. Yeo HJ, Yokoyama T, Walkiewicz K, Kim Y, Grass S, Geme JW (2007) The structure of the Haemophilus influenzae HMW1 pro-piece reveals a structural domain essential for bacterial two-partner secretion. J Biol Chem 282(42):31076–31084. Epub 2007 Aug 14. PubMed PMID: 17699157PubMedCrossRefGoogle Scholar
  194. Yin Z, Shi K, Banerjee S, Pandey KK, Bera S, Grandgenett DP, Aihara H (2016) Crystal structure of the Rous sarcoma virus intasome. Nature 530(7590):362–366.  https://doi.org/10.1038/nature16950. PubMed PMID: 26887497; PubMed Central PMCID: PMC4881392PubMedPubMedCentralCrossRefGoogle Scholar
  195. Zhang Y (2017) Energetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers. Protein Sci;26(7):1252–1265.  https://doi.org/10.1002/pro.3116. Epub 2017 Mar 8. Review. PubMed PMID: 28097727; PubMed Central PMCID: PMC5477538.PubMedPubMedCentralCrossRefGoogle Scholar
  196. Zhao H, Qin X, Yang D, Jiang Y, Zheng W, Wang D, Tian Y, Liu Q, Xu N, Li Z (2017) The development of activatable lytic peptides for targeting triple negative breast cancer. Cell Death Discov 3:17037.  https://doi.org/10.1038/cddiscovery.2017.37. eCollection 2017. PubMed PMID: 29263848; PubMed Central PMCID: PMC5629628
  197. Zhou GP (2011) The structural determinations of the leucine zipper coiled-coil domains of the cGMP-dependent protein kinase I alpha and its interaction with the myosin binding subunit of the myosin light chains phosphase. Proteins Pept Lett 18:966–978CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Natalya Kurochkina
    • 1
  1. 1.Department of BiophysicsSchool of Theoretical ModelingWashington, DCUSA

Personalised recommendations