Exploring the impact of polyproline II (PII) conformational bias on the binding of peptides to the SEM-5 SH3 domain

Protein Science

Volumn 17, Issue 7, 2008, Pages 1200-1211

  Whitten, Steven T ^a,b   Yang, Huan Wang ^a   Fox, Robert O ^a   Hilser, Vincent J ^a  

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

^b RedStorm Scientific Inc   (United States)

Author keywords

Calorimetry; Ensembles; Forces and stability; Polyproline II; Protein structure folding

Indexed keywords

ADAPTOR PROTEIN; POLYPEPTIDE; PROLINE; PROTEIN SEM 5; PROTEIN SH3; SOS PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; CALORIMETRY; CARBOXY TERMINAL SEQUENCE; COMPUTER SIMULATION; ENERGY TRANSFER; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STABILITY; STEREOCHEMISTRY;

ALGORITHMS; PEPTIDES; PROTEIN CONFORMATION; SRC HOMOLOGY DOMAINS;

EID: 46449135086     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.033647.107     Document Type: Article

References (55)

1. Baldwin, R.L. 1986. Temperature dependence of the hydrophobic interaction in protein folding. Proc. Natl. Acad. Sci. 83: 8069-8072.
2. Bruccoleri, R.E. and Karplus, M. 1987. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 26: 137-168.
3. Chellgren, B.W. and Creamer, T.P. 2004. Short sequences of non-proline residues can adopt the polyproline II helical conformation. Biochemistry 43: 5864-5869.
4. Cowan, P.M. and McGavin, S. 1955. Structure of poly-L-proline. Nature 176: 501-503.
5. D'Aquino, J.A., Gómez, 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.
6. Deber, C.M., Bovey, F.A., Carver, J.P., and Blout, E.R. 1970. Nuclear magnetic resonance evidence for cis-peptide bonds in proline oligomers. J. Am. Chem. Soc. 92: 6191-6198.
7. II conformation. J. Am. Chem. Soc. 125: 8092-8093.
8. 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.
9. 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.
10. Dukor, R.K., Keiderling, T.A., and Gut, V. 1991. Vibrational circular dichroism spectra of unblocked proline oligomers. Int. J. Pept. Protein Res. 38: 198-203.
11. Eker, F., Cao, X., Nafie, L., and Schweitzer-Stenner, R. 2002. Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study. J. Am. Chem. Soc. 124: 14330-14341.
12. Eker, F., Griebenow, K., and Schweitzer-Stennar, R. 2003. Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy. J. Am. Chem. Soc. 125: 8178-8185.
13. Ferreon, J.C. and Hilser, V.J. 2003. The effect of the polyproline II (PPII) conformation on the denatured state entropy. Protein Sci. 12: 447-457.
14. II) helix formation. Biochemistry 43: 7787-7797.
15. Gavezzotti, A. 1983. The calculation of molecular volumes and the use of volume analysis in the investigation of structured media and of solid-state organic reactivity. J. Am. Chem. Soc. 105: 5220-5225.
16. Go, N. and Scheraga, H.A. 1970. Ring closure and local conformational deformations of chain molecules. Macromolecules 3: 178-187.
17. Gómez, J., Hilser, V.J., Xie, D., and Freire, E. 1995. The heat capacity of proteins. Proteins 22: 404-412.
18. II) structural bias in the denatured states of proteins. Biochemistry 43: 9790-9799.
19. Han, W.-G., Jalkanen, K.J., Elstner, M., and Suhai, S. 1998. Theoretical study of aqueous N-acetyl-L-alanine N′-methyl-amide: Structures and Raman, VCD, and ROA spectra. J. Phys. Chem. B 102: 2587-2602.
20. Hebermann, S.M. and Murphy, K.P. 1996. Energetics of hydrogen bonding in proteins: A model compound study. Protein Sci. 5: 1229-1239.
21. Helbecque, N. and Loucheux-Lefebvre, M.H. 1982. Critical chain length for polyproline-II structure formation in H-Gly-(Pro)n-OH. Int. J. Pept. Protein Res. 19: 94-101.
22. Hinderaker, M.P. and Raines, R.T. 2003. An electronic effect on protein structure. Protein Sci. 12: 1188-1194.
23. Iijima, H., Dunbar Jr., J.B., and Marshall, G.R. 1987. Calibration of effective van der Waals atomic contact radii for proteins and peptides. Proteins 2: 330-339.
24. Jeffreys, H. and Jeffreys, B.S. 1950. Methods of mathematical physics, p. 122. Cambridge University Press, New York.
25. Knuth, D.E. 1981. The art of computer programming, Volume 2: Seminumerical Algorithms, 2nd ed. Addison-Wesley, Reading, MA.
26. Krimm, S. and Tiffany, M.L. 1974. The circular dichroism spectrum and structure of unordered polypeptides and proteins. Isr. J. Chem. 12: 189-200.
27. 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 20: 68-84.
28. 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.
29. Lovell, S.C., Word, J.M., Richardson, J.S., and Richardson, D.C. 2000. The penultimate rotamer library. Proteins 40: 389-408.
30. Luque, I., Mayorga, O.L., and Freire, E. 1996. Structure-based thermodynamic scale of a-helix propensities in amino acids. Biochemistry 35: 13681-13688.
31. MacArthur, M.W. and Thornton, J.M. 1991. Influence of proline residues on protein conformation. J. Mol. Biol. 218: 397-412.
32. Mandel, N., Mandel, G., Trus, B.L., Rosenberg, J., Carlson, G., and Dickerson, R.E. 1977. Tuna cytochrome c at 2.0 Å resolution. III. Coordinate optimization and comparison of structures. J. Biol. Chem. 252: 4619-4636.
33. Momany, F.A., McGuire, R.F., Burgess, A.W., and Scheraga, H.A. 1975. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79: 2361-2381.
34. Murphy, K.P. and Freire, E. 1992. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv. Protein Chem. 43: 313-361.
35. Murphy, K.P., Bhakuni, V., Xie, D., and Freire, E. 1992. Molecular basis of cooperativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates. J. Mol. Biol. 227: 293-306.
36. Nemethy, G. and Scheraga, H.A. 1965. Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method. Biopolymers 3: 155-184.
37. Okabayashi, H., Isemura, T., and Sakakibara, S. 1968. Steric structure of L-proline oligopeptides. II. Far-ultraviolet absorption spectra and optical rotations of L-proline oligopeptides. Biopolymers 6: 323-330.
38. 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.
39. Park, S.H., Shalongo, W., and Stellwagen, E. 1997. The role of PII conformations in the calculation of peptide factional helix content. Protein Sci. 6: 1694-1700.
40. Ramachandran, G.N. and Sasisekharan, V. 1968. Conformation of polypeptides and proteins. Adv. Protein Chem. 23: 283-438.
41. Ramachandran, G.N., Ramakrishnan, C., and Sasisekharan, V. 1963. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7: 95-99.
42. Richards, F.M. 1977. Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 6: 151-176.
43. Rucker, A.L. and Creamer, T.P. 2002. Polyproline II helical structure in protein unfolded states: Lysine peptides revisited. Protein Sci. 11: 980-985.
44. 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.
45. Shi, Z., Chen, K., Liu, S., Ng, A., Bracken, W.C., and Kallenbach, N.R. 2005. Polyproline II propensities from GGXGG peptides reveal an anticorrelation with b-sheet scales. Proc. Natl. Acad. Sci. 102: 17964-17968.
46. Shi, Z., Chen, K., Liu, Z., Sosnick, T.R., and Kallenbach, N.R. 2006. PII structure in the model peptides for unfolded proteins: Studies on ubiquitin fragments and several alanine-rich peptides containing QQQ, SSS, FFF, and VVV. Proteins 63: 312-321.
47. Sowdhamini, R., Ramakrishnan, C., and Balaram, P. 1993. Modeling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and endothelin I. Protein Eng. 6: 873-882.
48. Sreerama, N. and Woody, R.W. 1999. Molecular dynamics simulations of polypeptide conformations in water: A comparison of α, β, and poly(pro) II conformations. Proteins 36: 400-406.
49. Tiffany, M.L. and Krimm, S. 1968. New chain conformations of poly(glutamic acid) and polylysine. Biopolymers 6: 1379-1382.
50. Tiffany, M.L. and Krimm, S. 1972. Effect of temperature on the circular dichroism spectra of polypeptides in the extended states. Biopolymers 11: 2309-2316.
51. Vila, J.A., Baldoni, H.A., Ripio, D.R., Ghosh, A., and Scheraga, H.A. 2004. Polyproline II helix conformation in a proline-rich environment: A theoretical study. Biophys. J. 86: 731-742.
52. Weise, C.F. and Weisshaar, J.C. 2003. Conformational analysis of alanine dipeptide from dipolar couplings in a water-based liquid crystal. J. Phys. Chem. B 107: 3265-3277.
53. Wilson, G., Hecht, L., and Barron, L.D. 1996. Residual structure in unfolded proteins revealed by Raman optical activity. Biochemistry 35: 12518-12525.
54. Woody, R.W. 1992. Circular dichroism and conformation of unordered polypeptides. Adv. Biophys. Chem. 2: 37-79.
55. Xie, D. and Freire, E. 1994. Structure based prediction of protein folding intermediates. J. Mol. Biol. 242: 62-80.