The effect of the polyproline II (PPII) conformation on the denatured state entropy

Protein Science

Volumn 12, Issue 3, 2003, Pages 447-457

  Ferreon, Josephine C ^a   Hilser, Vincent J ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

Ala and Gly mutants; Conformational entropy; ITC; Polyproline II helix; Protein folding; Sem 5; SH3; Thermodynamics

Indexed keywords

PROLINE;

ALPHA HELIX; AMINO ACID SUBSTITUTION; ARTICLE; CALORIMETRY; CONFORMATIONAL TRANSITION; ENTROPY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STABILITY; THERMODYNAMICS;

ALANINE; ANIMALS; BINDING SITES; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; ENTROPY; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MICE; MODELS, MOLECULAR; MUTATION; PEPTIDE FRAGMENTS; PEPTIDES; PROLINE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; SON OF SEVENLESS PROTEINS; SRC HOMOLOGY DOMAINS;

EID: 0037372297     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0237803     Document Type: Article

References (29)

1. Blaber, M., Zhang, X.J., Lindstrom, J.L., Pepiot, S.D., Baase, W.A., and Matthews, B.W. 1994. Determination of α-helix propensity within the context of a folded protein, sites 44 and 131 in bacteriophage T4 lysozyme. J. Mol. Biol. 235: 600-624.
2. Creamer, T.P. 1998. Left-handed polyproline II helix formation is (very) locally driven. Proteins 33: 218-226.
3. D'Aquino, J.A., Gomez, J., Hilser, V.J., Lee, K.H., Amzel, L.M., and Freire, E. 1996. The magnitude of the backbone conformational entropy change in protein folding. Proteins 25: 143-156.
4. Drake, A.F., Siligardi, G., and Gibbons, W.A. 1988. Reassessment of the electronic circular dichroism criteria for random coil conformations of poly(L-lysine) and the implications for protein folding and denaturation studies. Biophys. Chem. 31: 143-146.
5. Dukor, R.K. and Keiderling, T.A. 1991. Reassessment of the random coil conformation: Vibrational CD study of proline oligopeptides and related polypeptides. Biopolymers 31: 1747-1761.
6. Edelhoch, H. 1967. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6: 1948-1954.
7. Gill, S.C. and von Hippel, P.H. 1989. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182: 319-326.
8. Gómez, J. and Freire, E. 1995. Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin. J. Mol. Biol. 252: 337-350.
9. Huyghues-Despointes, B.M.P., Scholtz, J.M., and Pace, C.N. 1999. Protein conformational stabilities can be determined from hydrogen exchange rates. Nat. Struct. Biol. 6: 910-912.
10. Jameson, C.J. 1996. Understanding NMR chemical shifts. Annu. Rev. Phys. Chem. 47: 135-169.
11. Kelly, M., Chellgren, B.W., Rucker, A.L., Troutman, J.M., Fried, M.G., Miller, A.-F., and Creamer, T.P. 2001. Host-guest study of left-handed polyproline II helix formation. Biochemistry 40: 14376-14383.
12. Krimm, S. and Tiffany, M.L. 1974. The circular dichroism spectrum and structure of unordered polypeptides and proteins. Israel J. Chem. 12: 189-200.
13. Lee, K.H., Xie, D., Freire, E., and Amzel, L.M. 1994. Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation. Proteins Struct. Funct. Genet. 20: 68-84.
14. Lim, W.A., Richards, F.M., and Fox, R.O. 1994. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature 372: 375-379.
15. MacArthur, M.W. and Thornton, J.M. 1991. Influence of proline residues on protein conformation. J. Mol. Biol. 218: 397-412.
16. Pappu, R.V. and Rose, G.D. 2002. A simple model for polyproline II structure in unfolded states of alanine-based peptides. Protein Sci. 11: 2437-2455.
17. Park, S.H., Shalongo, W., and Stellwagen, E. 1997. The role of PII conformations in the calculation of peptide fractional helix content. Protein Sci. 6: 1694-1700.
18. Ramachandran, G.N. and Sasisekharan, V. 1968. Conformation in polypeptides and proteins. Adv. Protein Chem. 23: 283-437.
19. Reimer, U., Scherer, G., Drewello, M., Kruber, S., Schutkowski, M., and Fischer, G. 1998. Side-chain effects on peptidyl-prolyl cis/trans isomerisation. J. Mol. Biol. 279: 449-460.
20. Rucker, A.L. and Creamer, T.P. 2002. Polyproline II helical structure in protein unfolded states: Lysine peptides revisited. Protein Sci. 11: 980-985.
21. Shi, Z., Olson, C.A., Rose, G.D., Baldwin, R.L., and Kallenbach, N.R. 2002. Polyproline II structure in a sequence of seven alanine residues. Proc. Natl. Acad. Sci. 99: 9190-9195.
22. Sreerama, N. and Woody, R.W. 1999. Molecular dynamics simulations of polypeptide conformations in water: A comparison of a, b, and poly(Pro)II conformations. Proteins 36: 400-406.
23. Tiffany, M.L. and Krimm, S. 1968. New chain conformations of poly(glutamic acid) and polylysine. Biopolymers 6: 1379-1382.
24. -. 1972. Effect of temperature on the circular dichroism spectra of polypeptides in the extended states. Biopolymers 11: 2309-2316.
25. Wilson, G., Hecht, L., and Barron, L.D. 1996. Residual structure in unfolded proteins revealed by Raman optical activity. Biochemistry 35: 12518-12525.
26. Wiseman, T., Williston, S., Brandts, J.F., and Lin, L. 1989. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal. Biochem. 179: 131-137.
27. Wittekind, M., Mapelli, C., Farmer II, B.T., Suen, K., Goldfarb, V., Tsao, J., Lavoie, T., Barbacid, M., Meyers, C.A., and Mueller, L. 1994. Orientation of peptide fragments from Sos proteins bound to the N-terminal SH3 domain of Grb2 determined by NMR spectroscopy. Biochemistry 33: 13531-13539.
28. 13C chemical shifts. J. Mol. Biol. 267: 933-952.
29. Woody, R.W. 1992. Circular dichroism and conformation of unordered polypeptides. Adv. Biophys. Chem. 2: 37-79.