β-hairpin polypeptides by design and selection

Spectroscopy

Volumn 17, Issue 2-3, 2003, Pages 213-230

  Skelton, Nicholas J ^a   Blandl, Tamas ^a   Russell, Stephen J ^a   Starovasnik, Melissa A ^a   Cochran, Andrea G ^a  

^a GENENTECH INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGES; CONFORMATIONS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE; PROTEINS; SPECTROSCOPIC ANALYSIS; THERMODYNAMIC STABILITY;

INTERSTRAND INTERACTIONS;

POLYPEPTIDES;

ERYTHROPOIETIN; ERYTHROPOIETIN AGONIST PEPTIDE; PEPTIDE LIBRARY; POLYPEPTIDE; TRYPTOPHAN; UNCLASSIFIED DRUG;

ALPHA HELIX; CIRCULAR DICHROISM; CONFERENCE PAPER; DISULFIDE BOND; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PEPTIDE SYNTHESIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SPECTROSCOPY; STEREOCHEMISTRY; THERMODYNAMICS;

EID: 0038219827     PISSN: 07124813     EISSN: None     Source Type: Journal    
DOI: 10.1155/2003/148024     Document Type: Conference Paper

References (63)

1. P. Alexander, S. Fahnestock, T. Lee, J. Orban and P. Bryan, Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2: why small proteins tend to have high denaturation temperatures, Biochemistry 31 (1992), 3597-3603.
2. W.J. Becktel and J.A. Schellman, Protein stability curves, Biopolymers 26 (1987), 1859-1877.
3. F.J. Blanco, G. Rivas and L. Serrano, A short linear peptide that folds into a native stable β-hairpin in aqueous solution, Nature Struct. Biol. 1 (1994), 584-590.
4. T. Blandl, A. Cochran and N.J. Skelton, Turn stability in β-hairpins: 3:5 Type I G1 bulge turns, in press.
5. D.A. Case, Calibration of ring-current effects in proteins and nucleic acids, J. Biomolec. NMR 6 (1995), 341-346.
6. J. Cavanagh, W.J. Fairbrother, A.G. Palmer and N.J. Skelton, Protein NMR Spectroscopy, Principles and Practice, Academic Press, New York, 1995.
7. A. Chakrabartty and R.L. Baldwin, Stability of α-helices, Adv. Prot. Chem. 46 (1995), 141-176.
8. A.G. Cochran, N.J. Skelton and M.A. Starovasnik, Correction: Tryptophan zippers: stable, monomeric β-hairpins, Proc. Natl. Acad. Sci. USA 99 (2002), 9081.
9. A.G. Cochran, N.J. Skelton and M.A. Starovasnik, Tryptophan zippers: stable, monomeric β-hairpins, Proc. Natl. Acad. Sci. USA 98 (2001), 5578-5583.
10. A.G. Cochran, R.T. Tong, M.A. Starovasnik, E.J. Park, R.S. McDowell, J.E. Theaker and N.J. Skelton, A minimal peptide scaffold for β-turn display: optimizing a strand position in disulfide-cyclized β-hairpins, J. Am. Chem. Soc. 123 (2001), 625-632.
11. C. Das, G.A. Naganagowda, I.L. Karle and P. Balaram, Designed beta-hairpin peptides with defined tight turn stereochemistry, Biopolymers 58 (2001), 335-346.
12. E. de Alba, M.A. Jiménez and M. Rico, Turn residue sequence determines β-hairpin conformation in designed peptides, J. Am. Chem. Soc. 119 (1997), 175-183.
13. W.F. DeGrado, C.M. Summa, V. Pavone, F. Nastri and A. Lombardi, De novo design and structural characterization of proteins and metalloproteins, Ann. Rev. Biochem. 68 (1999), 779-819.
14. J. Espinosa and S. Gellman, A designed β-hairpin containing a natural hydrophobic cluster, Angew. Chem. Int. Ed. 39 (2000), 2330-2333.
15. C. Falcomer, Y. Meinwald, I. Choudhary, S. Talluri, P. Milburn, J. Clardy and H. Scheraga, Chain reversals in model peptides: Studies of cystine-containing peptides. 3. Conformational free energies of cyclization of tetrapeptides of sequence Ac-Cys-Pro-X-Cys-NHMe, J. Am. Chem. Soc. 114 (1992), 4036.
16. S.H. Gellman, Minimal model systems for beta sheet secondary structure in proteins, Curr. Op. Chem. Biol. 2 (1998), 717-725.
17. S. Gillmor, A. Villasenor, R. Fletterick, E. Sigal and M. Browner, The structure of mammalian 15-lipoxygenase reveals similarity to the lipases and the determinants of substrate specificity, Nature Struct. Biol. 4 (1997), 1003-1009.
18. I.B. Grishina and R.W. Woody, Contributions of tryptophan side chains to the circular dichroism of globular proteins: exciton couplets and coupled oscillators, Faraday Discussions (1994), 245-262.
19. K. Gunasekaran, C. Ramakrishnan and P. Balaram, Beta-hairpins in proteins revisited: lessons for de novo design, Protein Eng. 10 (1997), 1131-1141.
20. T.S. Haque and S.H. Gellman, Insights on β-hairpin stability in aqueous solution from peptides with enforced type I′ and type II′ β-turns, J. Am. Chem. Soc. 119 (1997), 2303-2304.
21. T. Havel, The precision of protein structures determined from NMR data: reality or illusion?, in: Proteins: Structure, Dynamics, Design, V. Renugopalakrishnan, P.R. Carey, I.C.P. Smith, S.-G. Huansand and A.L. Storer, eds, ESCOM Science Publishers, Leiden, Holland, 1991, pp. 110-115.
22. T.F. Havel, An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance, Prog. Biophys. Mol. Biol. 56 (1991), 43-78.
23. E.G. Hutchinson, R.B. Sessions, J.M. Thornton and D.N. Woolfson, Determinants of strand register in antiparallel beta-sheets of proteins, Protein Sci. 7 (1998), 2287-2300.
24. E.G. Hutchinson and J.M. Thornton, A revised set of potentials for β-turn formation in proteins, Protein Sci. 3 (1994), 2207-2216.
25. D.L. Johnson, F.X. Farrell, F.P. Barbone, F.J. McMahon, J. Tullai, K. Hoey, O. Livnah, N.C. Wrighton, S.A. Middleton, D.A. Loughney, E.A. Stura, W.J. Dower, L.S. Mulcahy, I.A. Wilson and L.K. Jolliffe, Identification of a 13 amino acid peptide mimetic of erythropoietin and description of amino acids critical for the mimetic activity of EMP1, Biochemistry 37 (1998), 3699-3710.
26. P.D. Kwong, R. Wyatt, J. Robinson, R.W. Sweet, J. Sodroski and W.A. Hendrickson, Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing antibody, Nature 393 (1998), 648-659.
27. E. Lacroix, T. Kortemme, M. Lopez de la Paz and L. Serrano, The design of linear peptides that fold as monomeric beta-sheet structures, Curr. Op. Struct. Biol. 9 (1999), 487-493.
28. O. Livnah, E.A. Stura, D.L. Johnson, S.A. Middleton, L.S. Mulcahy, N.C. Wrighton, W.J. Dower, L.K. Jolliffe and I.A. Wilson, Functional mimicry of a protein hormone by a peptide agonist: the EPO receptor complex at 2.8 Å, Science 273 (1996), 464-471.
29. H.B. Lowman, Y.M. Chen, N.J. Skelton, D.L. Mortensen, E.E. Tomlinson, M.D. Sadick, I.C.A. Robinson and R.G. Clark, Molecular mimetics of insulin-like growth factor 1 (IGF-1) for inhibiting IGF-1:IGF-binding protein interactions, Biochemistry 37 (1998), 8870-8878.
30. C. Mattos, G.A. Petsko and M. Karplus, Analysis of two-residue turns in proteins, J. Mol. Biol. 238 (1994), 733-747.
31. A.J. Maynard, G.J. Sharman and M.S. Searle, Origin of β-hairpin stability in solution: structural and thermodynamic analysis of the folding of a model peptide supports hydrophobic stabilization in water, J. Am. Chem. Soc. 120 (1998), 1996-2007.
32. P. Milburn, Y. Konishi, Y. Meinwald and H. Scheraga, Chain reversals in model peptides: Studies of cystine-containing peptides. 1. Conformational free energies of cyclization of hexapeptides of sequence Ac-Cys-X-Pro-Gly-Y-NHMe, J. Am. Chem. Soc. 109 (1987), 4486-4496.
33. P. Milburn, Y. Meinwald, S. Takahashi, T. Ooi and H. Scheraga, Chain reversal in model peptides: studies of cystine-containing cyclic peptides, Int. J. Peptide Protein Res. 31 (1988), 311-321.
34. D.L. Minor and P.S. Kim, Context is a major determinant of β-sheet propensity, Nature 371 (1994), 264-267.
35. D.L. Minor and P.S. Kim, Measurement of the β-sheet-forming propensities of the amino acids, Nature 367 (1994), 660-663.
36. V. Munoz, P.A. Thompson, J. Hofrichter and W.A. Eaton, Folding dynamics and mechanism of beta-hairpin formation, Nature 390 (1997), 196-199.
37. G.R. Nakamura, M.A. Starovasnik, M.E. Reynolds and H.B. Lowman, A novel family of β-hairpin peptides that inhibit IgE activity by binding to the high-affinity IgE receptor, Biochemistry 40 (2001), 9828-9835.
38. K.T. O'Neil and W.F. DeGrado, A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids, Science 250 (1990), 646-651.
39. M. Ramírez-Alvarado, F.J. Blanco and L. Serrano, De novo design and structural analysis of a model β-hairpin peptide system, Nature Struct. Biol. 3 (1996), 604-611.
40. J.S. Richardson and D.C. Richardson, Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation, Proc. Natl. Acad. Sci. USA 99 (2002), 2754-2759.
41. S.J. Russell, T. Blandl, N.J. Skelton and A. Cochran, Stability of cyclic β-hairpins: asymmetric contributions from side chains of a hydrogen-bonded cross-strand resdidue pair, in press.
42. S.J. Russell and A.G. Cochran, Designing stable β-hairpins: energetic contributions from cross-strand residues, J. Am. Chem. Soc. 122 (2000), 12 600-12 601.
43. 13Cβ chemical shifts as a tool to delineate beta-hairpin structures in peptides, J. Biomolec. NMR. 19 (2001), 331-345.
44. M.S. Searle, Peptide models of protein β-sheets: design, folding and insights into stabilizing weak interactions, J. Chem. Soc., Perkin Trans. 2 (2001), 1011-1020.
45. B.L. Sibanda, T.L. Blundell and J.M. Thornton, Conformation of β-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering, J. Mol. Biol. 206 (1989), 759-777.
46. S.S. Sidhu, H.B. Lowman, B.C. Cunningham and J.A. Wells, Phage display for selection of novel binding peptides, Methods Enzymol. 328 (2000), 333-363.
47. V. Sieber and G.R. Moe, Interactions contributing to the formation of a β-hairpin-like structure in a small peptide, Biochemistry 35 (1996), 181-188.
48. N.J. Skelton, Y.M. Chen, N. Dubree, C. Quan, D.Y. Jackson, A.G. Cochran, K. Zobel, K. Deshayes, M. Baca, M.T. Pisabarro and H.B. Lowman, Structure-function analysis of a phage-derived peptide that binds to IGFBP-1, Biochemistry 40 (2001), 8487-8498.
49. N.J. Skelton, K.C. Garcia, D.V. Goeddel, C. Quan and J.P. Burnier, Determination of the solution structure of guanylin, Biochemistry 33 (1994), 13 581-13 592.
50. N.J. Skelton, S. Russell, F. de Sauvage and A.G. Cochran, Amino acid determinants of beta-hairpin conformation in erythropoeitin receptor agonist peptides derived from a phage display library, J. Mol. Biol. 316 (2002), 1111-1125.
51. C.K. Smith, J.M. Withka and L. Regan, A thermodynamic scale for the β-sheet forming tendencies of the amino acids, Biochemistry 33 (1994), 5510-5517.
52. 13C nuclear magnetic resonance chemical shifts, J. Am. Chem. Soc. 113 (1991), 5490-5492.
53. N. Srinivasan, R. Sowdhamini, C. Ramakrishnan and P. Balaram, Conformations of disulfide bidges in proteins, Int. J. Peptide Protein Res. 36 (1990), 147-155.
54. F.A. Syud, H.E. Stanger and S.H. Gellman, Interstrand side chain-side chain interactions in a designed β-hairpin: significance of both lateral and diagonal pairings, J. Am. Chem. Soc. 123 (2001), 8667-8677.
55. C. Vita, E. Drakopoulou, J. Vizzavona, S. Rochette, L. Martin, A. Menez, C. Roumestand, Y.S. Yang, L. Ylisastigui, A. Benjouad and J.C. Gluckman, Rational engineering of a miniprotein that reproduces the core of the CD4 site interacting with HIV-1 envelope glycoprotein, Proc. Natl. Acad. Sci. USA 96 (1999), 13 091-13 096.
56. L. Wang, T. O'Connell, A. Tropsha and J. Hermans, Molecular simulations of beta-sheet twisting, J. Mol. Biol. 262 (1996), 283-293.
57. S.J. Weiner, P.A. Kollman, D.A. Case, U.C. Singh, C. Ghio, G. Alagona, J.S. Profeta and P. Weiner, A new force field for molecular mechanical simulation of nucleic acids and proteins, J. Am. Chem. Soc. 106 (1984), 765-784.
58. S.J. Weiner, P.A. Kollman, D.T. Nguyen and D.A. Case, An all-atom force field for simulations of proteins and nucleic acids, J. Comput. Chem. 7 (1986), 230-252.
59. C.M. Wilmot and J.M. Thornton, Analysis and prediction of the different types of β-turns in proteins, J. Mol. Biol. 203 (1988), 221-232.
60. M.A. Wouters and P.M.G. Curmi, An analysis of side chain interactions and pair correlations within antiparallel β-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs, Proteins 22 (1995), 119-131.
61. K. Wüthrich, NMR of Proteins and Nucleic Acids, Wiley, New York, 1986.
62. 13C′ chemical shifts in proteins using a density functional database, J. Biomolec. NMR 21 (2002), 321-333.
63. A.S. Yang and B. Honig, Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets, J. Mol. Biol. 252 (1995), 366-376.