An improved capping unit for stabilizing the ends of associated β-strands

FEBS Letters

Volumn 588, Issue 24, 2014, Pages 4749-4753

  Anderson, Jordan M ^a   Kier, Brandon L ^a   Shcherbakov, Alexander A ^a   Andersen, Niels H ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Beta Hairpin; Beta sheet; Capping stabilization; Peptide; Trp Trp interaction

Indexed keywords

PEPTIDE DERIVATIVE; DISULFIDE; PEPTIDE; PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; CAPPING STABILIZATION; CARBOXY TERMINAL SEQUENCE; CIRCULAR DICHROISM; PROTEIN FOLDING; PROTEIN MODIFICATION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; DIMERIZATION; MOLECULAR GENETICS; PROTEIN MOTIF;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; DIMERIZATION; DISULFIDES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN STABILITY; PROTEINS;

EID: 84915746435     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2014.11.006     Document Type: Article

References (32)

1. L. Serrano, and A.R. Fersht Capping and α-helix stability Nature 342 1989 296 299
2. M. Pertukhov, Y. Tatsu, K. Tamaki, S. Murase, H. Uekawa, S. Yoshikawa, L. Serrano, and N. Yumoto Design of stable α-helices using global sequence optimization J. Pept. Sci. 15 2009 359 365
3. N.H. Andersen, and H. Tong Empirical parameterization of a model for predicting peptide helix/coil equilibrium populations Protein Sci. 6 1997 1920 1936
4. I. Ruczinski, C. Kooperberg, R. Bonneau, and D. Baker Distributions of beta sheets in proteins with application to structure prediction Proteins: Struct. Funct. Genet. 48 2002 85 97
5. A. Subramani, and C.A. Floudas β-sheet topology prediction with high precision and recall for β and mixed α/β proteins PLoS One 7 2014 e32461
6. J.A. Cuff, M.E. Clamp, A.S. Siddiqui, M. Finlay, and G.J. Barton JPred: a consensus secondary structure prediction server Bioinformatics 14 1998 892 893
7. K.N. Huggins, M. Bisaglia, L. Bubacco, M. Tatarek-Nossol, A. Kapurniotu, and N.H. Andersen Designed hairpin peptides interfere with amyloidogenesis pathways: fibril formation and cytotoxicity inhibition, interception of preamyloid state Biochemistry 50 2011 8202 8212
8. K. Kar, C.L. Hoop, K.W. Drombosky, W.A. Baker, R. Kodali, I. Arduini, P.C. van der Wel, W.S. Horne, and R. Wetzel β-Hairpin-mediated nucleation of polyglutamine amyloid formation J. Mol. Biol. 425 2013 1183 1197
9. F. Chiti, and C.M. Dobson Protein misfolding, functional amyloid, and human disease Annu. Rev. Biochem. 75 2006 333 366
10. F.J. Blanco, G. Rivas, and L. Serrano A short linear peptide that folds into a native stable β-hairpin in aqueous solution Nat. Struct. Biol. 1 1994 584 590
11. M.S. Searle, D.H. Williams, and L.C. Packman A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable non-native β-hairpin Nat. Struct. Biol. 2 1995 999 1006
12. A.G. Cochran, N.J. Skelton, and M.A. Starovasnik Tryptophan zippers: stable, monomeric β-hairpins Proc. Natl. Acad. Sci. 98 2001 5578 5583
13. R.M. Fesinmeyer, F.M. Hudson, and N.H. Andersen Enhanced hairpin stability through loop design: the case of the protein G B1 domain hairpin J. Am. Chem. Soc. 126 2004 7238
14. K.A. Olsen, R.M. Fesinmeyer, J.M. Stewart, and N.H. Andersen Hairpin folding rates reflect mutations within and remote from the turn region Proc. Natl. Acad. Sci. 102 2005 15483 15487
15. B.L. Kier, and N.H. Andersen Probing the lower size limit for protein-like fold stability: ten-residue microproteins with specific, rigid structures in water J. Am. Chem. Soc. 130 2008 14675 14683
16. J.H. Park, and M.L. Waters Positional effects of click cyclization on β-hairpin structure, stability, and function Org. Biomol. Chem. 11 2013 69 77
17. A.J. Riemen, and M.L. Waters Positional effects of phosphoserine on β-hairpin stability Org. Biomol. Chem. 8 2010 5411 5417
18. A.J. Riemen, and M.L. Waters Design of highly stabilized β-hairpin peptides through cation-π interactions of lysine and N-methyllysine with an aromatic pocket Biochemistry 48 2009 1525 1531
19. T.S. Haque, and S.H. Gellman Insights into 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
20. M. Favre, K. Moehle, L. Jiang, B. Pfeiffer, and J. Robinson Structure mimicry of canonical conformation in antibody hypervariable loops using cyclic peptides containing a heterochiral diproline template J. Am. Chem. Soc. 121 1999 2679 2685
21. I.L. Karle, S.K. Awasthi, and P.A. Balaram A designed β-hairpin peptide in crystals Proc. Natl. Acad. Sci. 93 1996 8189 8193
22. F.A. Syud, J.F. Espinosa, and S.H. Gellman 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 1999 11577 11578
23. C.M. Santiveri, and M.A. Jiménez Tryptophan residues: scarce in proteins but strong stabilizers of β-hairpin peptides Biopolymers 94 2010 779 790
24. L. Wu, D. McElheny, T. Takekiyo, and T.A. Keiderling Geometry and efficacy of cross-strand Trp/Trp, Trp/Tyr, and Tyr/Tyr aromatic interaction in a β-hairpin peptide Biochemistry 49 2010 4705 4714
25. N.H. Andersen, K.A. Olsen, R.M. Fesinmeyer, X. Tan, F.M. Hudson, L.A. Eidenschink, and S.R. Farazi Minimization and optimization of designed β-hairpin folds J. Am. Chem. Soc. 128 2006 6101 6110
26. B.L. Kier, J.M. Anderson, and N.H. Andersen Circular permutation of a WW domain: folding still occurs after excising the turn of the folding-nucleating hairpin J. Am. Chem. Soc. 136 2014 741 749
27. B.L. Kier, I. Shu, L.A. Eidenschink, and N.H. Andersen Stabilizing capping motif for β-hairpins and sheets Proc. Natl. Acad. Sci. 23 2010 10466 10471
28. R.M. Fesinmeyer, F.M. Hudson, K.A. Olsen, G.W.N. White, A. Euser, and N.H. Andersen Chemical shifts provide fold populations and register of β hairpins and β sheets J. Biomol. NMR 33 2005 213 231
29. L. Wu, D. McElheny, R. Huang, and T.A. Keiderling Role of tryptophan-tryptophan interactions in Trpzip β-hairpin formation, structure, and stability Biochemistry 48 2009 10362 10371
30. L. Eidenschink, B.L. Kier, K.N.L. Huggins, and N.H. Andersen Very short peptides with stable folds: building on the interrelationship of Trp/Trp. Trp/cation, and Trp/backbone-amide interaction geometries Proteins 75 2008 308 322
31. M. Scian, I. Shu, H.A. Olsen, K. Hassam, and N.H. Andersen Mutational effects on the folding dynamics of a minimized hairpin Biochemistry 52 2013 2556 2560
32. M. Jäger, H. Nguyen, J.C. Crane, J.W. Kelly, and M. Gruebele The folding mechanism of a β-sheet: the WW domain J. Mol. Biol. 311 2001 373 393