Applications of model β-hairpin peptides

Journal of Pharmaceutical Sciences

Volumn 93, Issue 12, 2004, Pages 2881-2894

  Stotz, Carol E ^a   Topp, Elizabeth M ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

Beta hairpin; Peptides; Protein folding refolding; Secondary structure; Stability

Indexed keywords

BETA HAIRPIN PEPTIDE; PEPTIDE; UNCLASSIFIED DRUG;

BETA SHEET; CIRCULAR DICHROISM; CYCLIZATION; HYDROGEN BOND; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; POINT MUTATION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SHORT SURVEY; STRUCTURE ANALYSIS; THERMODYNAMICS;

EID: 10644297361     PISSN: 00223549     EISSN: None     Source Type: Journal    
DOI: 10.1002/jps.20188     Document Type: Short Survey

References (62)

1. Griffiths-Jones SR, Maynard AJ, Sharman GJ, Searle MS. 1998. NMR evidence for the nucleation of a β-hairpin peptide conformation in water by an Asn-Gly type I′ β-turn sequence. Chem Commun (Cambridge, UK) 789-790.
2. Jourdan M, Searle MS. 2000. Cooperative assembly of a native-like ubiquitin structure through peptide fragment complexation: Energetics of peptide association and folding. Biochemistry 39:12355-12364.
3. Hutchinson EG, Sessions RB, Thornton JM, Woolfson DN. 1998. Determinants of strand register in antiparallel β-sheets of proteins. Protein Sci 7:2287-2300.
4. Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
5. Hutchinson EG, Thornton JM. 1994. A revised set of potentials for β-turn formation in proteins. Protein Sci 3:2207-2216.
6. Kuntz ID. 1972. Protein folding. J Am Chem Soc 94:4009-4012.
7. Chan AW, Hutchinson EG, Harris D, Thornton JM. 1993. Identification, classification, and analysis of beta-bulges in proteins. Protein Sci 2:1574-1590.
8. Sibanda BL, Thornton JM. 1985. β-Hairpin families in globular proteins. Nature (London, UK) 316:170-176.
9. Lewis PN, Momany FA, Scheraga HA. 1973. Chain reversals in proteins. Biochim Biophys Acta 303:211-229.
10. Chothia C. 1973. Conformation of twisted beta-pleated sheets in proteins. J Mol Biol 75:295-302.
11. Sibanda BL, Blundell TL, Thornton JM. 1989. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol 206:759-777.
12. Espinosa JF, Munoz V, Gellman SH. 2001. Interplay between hydrophobic cluster and loop propensity in β-hairpin formation. J Mol Biol 306:397-402.
13. Ramirez-Alvarado M, Blanco FJ, Serrano L. 2001. Elongation of the BH8 β-hairpin peptide: Electrostatic interactions in β-hairpin formation and stability. Protein Sci 10:1381-1392.
14. Haque TS, Gellman SH. 1997. Insights on β-hairpin stability in aqueous solution from peptides with enforced type I′ and type II′ β-turns. J Am Chem Soc 119:2303-2304.
15. Cochran AG, Skelton NJ, Starovasnik MA. 2002. Tryptophan zippers: Stable, monomeric β-hairpins. Proc Natl Acad Sci USA 99:5578-5583.
16. Syud FA, Stanger HE, Gellman SH. 2001. Interstrand side chain-side chain interactions in a designed β-hairpin: Significance of both lateral and diagonal pairings. J Am Chem Soc 123:8667-8677.
17. Gellman SH. 1998. Minimal model systems for β-sheet secondary structure in proteins. Curr Opin Chem Biol 2:717-725.
18. Ramirez-Alvarado M, Kortemme T, Blanco FJ, Serrano L. 1999. β-Hairpin and β-sheet formation in designed linear peptides. Bioorg Med Chem 7:93-103.
19. Wuthrich K. 1986. NMR of proteins and nucleic acids. New York: Wiley, p 304.
20. Wishart DS, Sykes BD, Richards FM. 1991. Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 222:311-333.
21. α chemical shifts in peptide and protein β-sheet. J Am Chem Soc 123:12318-12324.
22. Tatko CD, Waters ML. 2002. Selective aromatic interactions in β-hairpin peptides. J Am Chem Soc 124:9372-9373.
23. Butterfield SM, Waters ML. 2003. A designed β-hairpin peptide for molecular recognition of ATP in water. J Am Chem Soc 125:9580-9581.
24. Sharman GJ, Searle MS. 1998. Cooperative interaction between the three strands of a designed antiparallel β-sheet. J Am Chem Soc 120:5291-5300.
25. Stanger HE, Syud FA, Espinosa JF, Giriat I, Muir T, Gellman SH. 2001. Length-dependent stability and strand length limits in antiparallel β-sheet secondary structure. Proc Natl Acad Sci USA 98:12015-12020.
26. de Alba E, Santoro J, Rico M, Jimenez MA. 1999. De novo design of a monomeric three-stranded anti-parallel beta-sheet. Protein Sci 8:854-865.
27. Santiveri CM, Rico M, Jimenez MA. 2001. 13C(α) and 13C(β) chemical shifts as a tool to delineate β-hairpin structures in peptides. J Biomol NMR 19:331-345.
28. Arrondo JLR, Blanco FJ, Serrano L, Goni FM. 1996. Infrared evidence of a β-hairpin peptide structure in solution. FEES Lett 384:35-37.
29. Hilario J, Kubelka J, Keiderling TA. 2003. Optical spectroscopic investigations of model β-sheet hairpins in aqueous solution. J Am Chem Soc 125:7562-7574.
30. Colombo G, De Mori GMS, Roccatano D. 2003. Interplay between hydrophobic cluster and loop propensity in β-hairpin formation: A mechanistic study. Protein Sci 12:538-550.
31. Griffiths-Jones SR, Maynard AJ, Searle MS. 1999. Dissecting the stability of a β-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the β-turn and β-strand contributions to folding. J Mol Biol 292:1051-1069.
32. Roccatano D, Colombo G, Fioroni M, Mark AE. 2002. Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study. Proc Natl Acad Sci USA 99:12179-12184.
33. Maynard AJ, Sharman GJ, Searle MS. 1998. 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 120:1996-2007.
34. Espinosa JF, Syud FA, Gellman SH. 2002. Analysis of the factors that stabilize a designed two-stranded antiparallel β-sheet. Protein Sci 11:1492-1505.
35. Cochran AG, Tong RT, Starovasnik MA, Park EJ, McDowell RS, Theaker JE, Skelton NJ. 2001. A minimal peptide scaffold for β-turn display: Optimizing a strand position in disulfide-cyclized β-hairpins. J Am Chem Soc 123:625-632.
36. Lin TY, Kim PS. 1989. Urea dependence of thioldisulfide equilibria in thioredoxin: Confirmation of the linkage relationship and a sensitive assay for structure. Biochemistry 28:5282-5287.
37. Russell SJ, Blandl T, Skelton NJ, Cochran AG. 2003. Stability of cyclic β-hairpins: Asymmetric contributions from side chains of a hydrogenbonded cross-strand residue pair. J Am Chem Soc 125:388-395.
38. de Alba E, Jimenez MA, Rico M, Nieto JL. 1996. Conformational investigation of designed short linear peptides able to fold into beta-hairpin structures in aqueous solution. Fold Des 1:133-144.
39. de Alba E, Jimenez MA, Rico M. 1997. Turn residue sequence determines β-hairpin conformation in designed peptides. J Am Chem Soc 119:175-183.
40. de Alba E, Rico M, Jimenez MA. 1997. Cross-strand side-chain interactions versus turn conformation in β-hairpins. Protein Sci 6:2548-2560.
41. de Alba E, Rico M, Jimenez MA. 1999. The turn sequence directs β-strand alignment in designed β-hairpins. Protein Sci 8:2234-2244.
42. Syud FA, Espinosa JF, Gellman SH. 1999. NMR-based quantification of β-sheet populations in aqueous solution through use of reference peptides for the folded and unfolded states. J Am Chem Soc 121:11577-11578.
43. Jourdan M, Griffiths-Jones SR, Searle MS. 2000. Folding of a β-hairpin peptide derived from the N-terminus of ubiquitin. Conformational preferences of β-turn residues dictate non-native β-strand interactions. Eur J Biochem 267:3539-3548.
44. Nowick JS, Brower JO. 2003. A new turn structure for the formation of β-hairpins in peptides. J Am Chem Soc 125:876-877.
45. Stotz CE, Borchardt RT, Middaugh CR, Siahaan TJ, Vander Velde DG, Topp EM. 2004. Secondary structure of a dynamic type I′ β-hairpin peptide. J Pept Res 63:371-382.
46. Constantine KL, Mueller L, Andersen NH, Tong H, Wandler CF, Friedrichs MS, Bruccoleri RE. 1995. Structural and dynamic properties of a β-hairpin-forming linear peptide. 1. Modeling using ensemble-averaged constraints. J Am Chem Soc 117:10841-10854.
47. Colley CS, Griffiths-Jones SR, George MW, Searle MS. 2000. Do interstrand hydrogen bonds contribute to β-hairpin peptide stability in solution? IR analysis of peptide folding in water. Chem Commun (Cambridge, UK) 593-594.
48. Ramirez-Alvarado M, Blanco FJ, Serrano L. 1996. De novo design and structural analysis of a model β-hairpin peptide system. Nat Struct Biol 3:604-612.
49. Searle MS, Griffiths-Jones SR, Skinner-Smith H. 1999. Energetics of weak interactions in a β-hairpin peptide: Electrostatic and hydrophobic contributions to stability from lysine salt bridges. J Am Chem Soc 121:11615-11620.
50. Chou PY, Fasman GD. 1974. Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins. Biochemistry 13:211-222.
51. Tatko CD, Waters ML. 2003. The geometry and efficacy of cation-π interactions in a diagonal position of a designed β-hairpin. Protein Sci 12:2443-2452.
52. Santiveri CM, Rico M, Jimenez MA. 2000. Position effect of cross-strand side-chain interactions on β-hairpin formation. Protein Sci 9:2151-2160.
53. Russell SJ, Cochran AG. 2000. Designing stable β-hairpin: Energetic contributions from cross-strand residues. J Am Chem Soc 122:12600-12601.
54. Kortemme T, Ramirez-Alvarado M, Serrano L. 1998. Design of a 20-amino acid, three-stranded β-sheet protein. Science 281:253-256.
55. Schenck HL, Gellman SH. 1998. Use of a designed triple-stranded antiparallel β-sheet to probe β-sheet cooperativity in aqueous solution. J Am Chem Soc 120:4869-4870.
56. Griffiths-Jones SR, Searle MS. 2000. Structure, folding, and energetics of cooperative interactions between the β-strands of a de novo designed three-stranded antiparallel β-sheet peptide. J Am Chem Soc 122:8350-8356.
57. 13C NMR conformational investigation of three-stranded antiparallel β-sheet-forming peptides. J Pept Res 61:177-188.
58. Stanfield RL, Gorny MK, Williams C, Zolla-Pazner S, Wilson IA. 2004. Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D. Structure 12:193-204.
59. Drakopoulou E, Zinn-Justin S, Guenneugues M, Gilquin B, Menez A, Vita C. 1996. Changing the structural context of a functional β-hairpin. Synthesis and characterization of a chimera containing the curaremimetic loop of a snake toxin in the scorpion α/β scaffold. J Biol Chem 271:11979-11987.
60. Lai JR, Huck BR, Weisblum B, Gellman SH. 2002. Design of non-cysteine-containing antimicrobial β-hairpins: Structure-activity relationship studies with linear protegrin-1 analogues. Biochemistry 41:12835-12842.
61. Bulet P, Stocklin R, Menin L. 2004. Anti-microbial peptides: From invertebrates to vertebrates. Immunol Rev 198:169-184.
62. Hosia W, Bark N, Liepinsh E, Tjernberg A, Persson B, Hallen D, Thyberg J, Johansson J, Tjernberg L. 2004. Folding into a β-hairpin can prevent amyloid fibril formation. Biochemistry 43:4655-4661.