The Trp-cage: Optimizing the stability of a globular miniprotein

Protein Engineering, Design and Selection

Volumn 21, Issue 3, 2008, Pages 171-185

  Barua, Bipasha ^a   Lin, Jasper C ^a   Williams, Victoria D ^a   Kummler, Phillip ^a   Neidigh, Jonathan W ^a   Andersen, Niels H ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Buried polar sidechain; Fast folding miniprotein; Hydrophobic core formation; Motif minimization; Proline tryptophan interactions

Indexed keywords

HYDROPHOBICITY; MELTING POINT; SOLVENTS;

HYDROPHOBIC CORE FORMATION; PROLINE-TRYPTOPHAN INTERACTIONS;

PROTEIN FOLDING;

ALANINE; ARGININE; ASPARAGINE; INDOLE; PEPTIDE; PROLINE; SERINE; SOLVENT; TRYPTOPHAN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; ENTROPY; HYDROGEN BOND; HYDROPHOBICITY; MELTING POINT; MOLECULAR INTERACTION; MUTATION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STABILITY; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; CIRCULAR DICHROISM; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; KINETICS; MOLECULAR SEQUENCE DATA; PROLINE; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS; TRYPTOPHAN; TYROSINE;

EID: 40049110562     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzm082     Document Type: Article

References (67)

1. Ahmed,Z., Ilir,A.B., Mikhonin,A.V. and Asher,S.A. (2005) J. Am. Chem. Soc., 127, 10943-10950.
2. Andersen,N.H. and Tong,H. (1997) Protein Sci., 6, 1920-1936.
3. Andersen,N.H., Neidigh,J.W., Harris,S.M., Lee,G.M., Liu,Z. and Tong,H. (1997) J. Am. Chem. Soc., 119, 8547-8561.
4. Andersen,N.H., Fesinmeyer,R.M., Neidigh,J.W. and Barua,B. (2001) In: Martinez,J. and Fehrentz,J-A. (eds), The Trp-Cage: A Notably Stable Mini-Protein Fold in Peptides 2000. EDK, Paris, France.
5. Andersen,N.H., Olsen,K.A., Fesinmeyer,R.M., Tan,X., Hudson,F.M., Eidenschink,L.A. and Farazi,S.R. (2006) J. Am. Chem. Soc., 128, 6101-6110.
6. Asensio,J.L., Cañada,F.J., Bruix,M., Rodriguez-Romero,A. and Jimenez-Barbero,J. (1995) Eur. J. Biochem., 230, 621-633.
7. Bai,Y., Milne,J.S., Mayne,L. and Englander,S.W. (1993) Proteins, 17, 75-86.
8. Baldwin,R.L. (2003) J. Biol. Chem., 278, 17581-17588.
9. Barua,B. and Andersen,N.H. (2002) Lett. Pept. Sci., 8, 221-226.
10. Bax,A. and Davis,D.G. (1985) J. Magn. Reson., 65, 355-360.
11. Brünger,A.T., et al. (1998) Acta Crystallogr. D Biol. Crystallogr., D54, 905-921.
12. Bunagan,M.R., Yang,X., Saven,J.G. and Gai,F. (2006) J. Phys. Chem. B, 110, 3759-3763.
13. Cao,B. (1993) NMR structural studies of bound peptides and hevein, a small protein. PhD.
14. Carnevali,P., Toth,G., Toubassi,G. and Siavash,N. (2003) J. Am. Chem. Soc., 125, 14244-14245.
15. Chen,J., Im,W. and Brooks,C.L., III (2006) J. Am. Chem. Soc., 128, 3728-3736.
16. Chowdhury,S., Lee,M.C., Xiong,G. and Duan,Y. (2003) J. Mol. Biol., 327, 711-717.
17. Ding,F., Buldyrev,S.V. and Dokholyan,N.V. (2005) Biophys. J., 88, 147-155.
18. Doig,A.J. and Baldwin,R.L. (1995) Protein Sci., 4, 1325-1336.
19. Ferguson,N., Sharpe,T.D., Schartau,P.J., Sato,S., Allen,M.D., Johnson,C.M., Rutherford,T.J. and Fersht,A.R. (2005) J. Mol. Biol., 353, 427-446.
20. Fesinmeyer,R.M. (2005) Chemical shifts define the structure and folding thermodynamics of polypeptides. PhD.
21. Fesinmeyer,R.M., Hudson,F.M. and Andersen,N.H. (2004) J. Am. Chem. Soc., 126, 7238-7243.
22. Fesinmeyer,R.M., Hudson,F.M., White,G.W.N., Olsen,K.A., Euser,A. and Andersen,N.H. (2005) J. Biomol. NMR, 33, 213-231.
23. Fezoui,Y. and Braswell,E.H. (1999) Biochemistry, 38, 2796-2804.
24. Fleming,P.J. and Rose,G.D. (2005) Protein Sci., 14, 1911-1917.
25. Ghosh,K., Ozkan,S.B. and Dill,K.A. (2007) J. Am. Chem. Soc., 129, 11920-11927.
26. Hudson,F.M. and Andersen,N.H. (2004) Biopolymers (Pept. Sci.), 76, 298-308.
27. Huyghues-Despointes,B.M., Scholtz,J.M. and Baldwin,R.L. (1993) Protein Sci., 2, 1604-1611.
28. Huyghues-Despointes,B.M., Klinger,T.M. and Baldwin,R.L. (1995) Biochemistry, 34, 13267-13271.
29. Ivankov,D.M., Garbuzynskiy,S.O., Alm,E., Plaxco,K.W., Baker,D. and Finkelstein,A.V. (2003) Protein Sci., 12, 2057-2062.
30. Jackups,R.J. and Liang,J. (2005) J. Mol. Biol., 354, 979-993.
31. Juraszek,J. and Bolhuis,P.G. (2006) Proc. Natl Acad. Sci. USA, 103, 15859-15864.
32. Karle,I.L. and Balaram,P. (1990) Biochemistry, 29, 6747-6756.
33. Kemmink,J., van Mierlo,C.P.M., Scheek,R.M. and Creighton,T.E. (1993) J. Mol. Biol., 230, 312-322.
34. Kentsis,A., Gindin,T., Mezei,M. and Osman,R. (2007), PLoS ONE, 2, e446.
35. Koga,N. and Takada,S. (2001) J. Mol. Biol., 313, 171-180.
36. Koradi,R., Billeter,M. and Wührich,K. (1996) J. Mol. Graph., 14, 51-55.
37. Kubelka,J., Hofrichter,J. and Eaton,W.A. (2004) Curr. Opin. Struct. Biol., 14, 76-88.
38. Liepinsh,E., Otting,G. and Wüthrich,K. (1992) J. Biomol. NMR, 2, 447-465.
39. Lin,J.C., Barua,B. and Andersen,N.H. (2004) J. Am. Chem. Soc., 126, 13679-13684.
40. Linhananta,A., Boer,J. and MacKay,I. (2005) J. Chem. Phys., 122, 114901/114901-114901/114915.
41. Liu,Y., Liu,Z., Androphy,E., Chen,J. and Baleja,J.D. (2004) Biochemistry, 43, 7421-7433.
42. Matthews,B.W., Nicholson,H. and Becktel,W.J. (1987) Proc. Natl Acad. Sci. USA, 84, 6663-6667.
43. Merkel,J.S. and Regan,L. (1998) Fold. Des., 3, 449-455.
44. Mok,K.H., Kuhn,L.T., Goez,M., Day,I.J., Lin,J.C., Andersen,N.H. and Hore,P.J. (2007) Nature, 447, 106-109.
45. Naduthambi,D. and Zondlo,N.J. (2006) J. Am. Chem. Soc., 128, 12430-12431.
46. Neidigh,J.W. (1999) Chemical shift tools in peptide folding and miniature protein design. PhD.
47. Neidigh,J.W. and Andersen,N.H. (2002) Biopolymers, 65, 354-361.
48. Neidigh,J.W., Fesinmeyer,R.M., Prickett,K.S. and Andersen,N.H. (2001) Biochemistry, 40, 13188-13200.
49. Neidigh,J.W., Fesinmeyer,R.M. and Andersen,N.H. (2002) Nat. Struct. Biol., 9, 425-430.
50. Neuweiler,H., Doose,S. and Sauer,M. (2005) Proc. Natl Acad. Sci. USA, 102, 16650-16655.
51. Nikiforovich,G.V., Andersen,N.H., Fesinmeyer,R.M. and Frieden,C. (2003) Proteins, 52, 292-302.
52. Olsen,K.A., Fesinmeyer,R.M., Stewart,J.M. and Andersen,N.H. (2005) Proc. Natl Acad. Sci. USA, 102, 15483-15487.
53. Ota,M., Ikeguchi,M. and Kidera,A. (2004) Proc. Natl Acad. Sci. USA, 101, 17658-17663.
54. Padmanabhan,S. and Baldwin,R.L. (1994) J. Mol. Biol., 241, 706-713.
55. Pitera,J.W. and Swope,W. (2003) Proc. Natl Acad. Sci. USA, 100, 7587-7592.
56. Plaxco,K.W., Simons,K.T., Ruczinski,I. and Baker,D. (2000) Biochemistry, 39, 11177-11183.
57. Qiu,L., Pabit,S.A., Roitberg,A.E. and Hagen,S.J. (2002) J. Am. Chem. Soc., 124, 12952-12953.
58. Schug,A., Herges,T. and Wenzel,W. (2003) Phys. Rev. Lett., 91, 158102/158101-158104.
59. Schug,A., Wenzel,W. and Hansmann,U.H.E. (2005) J. Chem. Phys., 122, 194711/194711-194717.
60. Searle,M.S. and Ciani,B. (2004) Curr. Opin. Struct. Biol., 14, 1-7.
61. Simmerling,C.L., Strockbine,B. and Roitberg,A.E. (2002) J. Am. Chem. Soc., 124, 11258-11259.
62. Snow,C.D., Zagrovic,B. and Pande,V.S. (2002) J. Am. Chem. Soc., 124, 14548-14549.
63. Stapley,B.J. and Doig,A.J. (1997) J. Mol. Biol., 272, 465-473.
64. Streicher,W.W. and Makhatadze,G.I. (2007) Biochemistry, 46, 2876-2880.
65. Ulmschneider,J.P., Ulmschneider,M.B. and Di Nola,A. (2006) J. Phys. Chem. B, 110, 16733-16742.
66. Wishart,D.S. and Sykes,B.D. (1994) Methods Enzymol., 239, 363-392.
67. Zhou,R. (2003) Proc. Natl Acad. Sci. USA, 100, 13280-13285.