Unfolded state of peptides

Advances in Protein Chemistry

Volumn 62, Issue , 2002, Pages 341-360

  Daura, Xavier ^a   Glättli, Alice ^a   Gee, Peter ^a   Peter, Christine ^a   Van Gunsteren, Wilfred F ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE DERIVATIVE;

CLUSTER ANALYSIS; CORRELATION ANALYSIS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; REVIEW; SIMULATION; STRUCTURE ANALYSIS; THERMOSTABILITY;

EID: 0036399212     PISSN: 00653233     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0065-3233(02)62013-3     Document Type: Review

References (57)

1. Bai, Y. W., Chung, J., Dyson, H. J., and Wright, P. E. (2001). Structural and dynamic characterization of an unfolded state of poplar apo-plastocyanin formed under non-denaturing conditions. Protein Sci. 10, 1056-1066
2. Bellanda, M., Peggion, E., Bürgi, R., van Gunsteren, W. F., and Mammi, S. (2001). Conformational study of an Aib-rich peptide in DMSO by NMR. J. Pept. Res. 57, 97-106
3. Bryngelson, J. D., Onuchic, J. N., Socci, N. D., and Wolynes, P. G. (1995). Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins: Struct. Funct. Genet. 21, 167-195
4. Bürgi, R., Daura, X., Mark, A., Bellanda, M., Mammi, S., Peggion, E., and van Gunsteren, W. F. (2001). Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations. J. Pept. Res. 57, 107-118
5. Bursulaya, B. D., and Brooks, C. L. (1999). Folding free energy surface of a three-stranded β-sheet protein. J. Am. Chem. Soc. 121, 9947-9951
6. Bursulaya, B. D., and Brooks, C. L. (2000). Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models. J. Phys. Chem. B 104, 12378-12383
7. Callender, R. H., Dyer, R. B., Gilmanshin, R., and Woodruff, W. H. (1998). Fast events in protein folding: The time evolution of primary processes. Annu. Rev. Phys. Chem. 49, 173-202
8. Chakraborty, S., Ittah, V., Bai, P., Luo, L., Haas, E., and Peng, Z. Y. (2001). Structure and dynamics of the alpha-lactalbumin molten globule: Fluorescence studies using proteins containing a single tryptophan residue. Biochemistry 40, 7228-7238
9. Chan, H. S., and Dill, K. A. (1998). Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics. Proteins: Struct. Funct. Genet. 30, 2-33
10. Choy, W. Y., Mulder, F. A. A., Crowhurst, K. A., Muhandiram, D. R., Millett, I. S., Doniach, S., Forman-Kay, J. D., and Kay, L. E. (2002). Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques. J. Mol. Biol. 316, 101-112
11. Colombo, G., Roccatano, D., and Mark, A. E. (2002). Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulations. Proteins: Struct. Funct. Genet. 46, 380-392
12. Daggett, V. (2002). Molecular dynamics simulations of the protein unfolding/folding reaction. Acc. Chem. Res. 35, 422-429. Available at http://pubs.acs.org
13. Daura, X., Gademann, K., Jaun, B., Seebach, D., van Gunsteren, W. F., and Mark, A. E. (1999a). Peptide folding: When simulation meets experiment. Angew. Chem. Int. Ed. 38, 236-240
14. Daura, X., Gademann, K., Schäfer, H., Jaun, B., Seebach, D., and van Gunsteren, W. F. (2001). The β-peptide hairpin in solution: Conformational study of a β-hexapeptide in methanol by NMR spectroscopy and MD simulation. J. Am. Chem. Soc. 123, 2393-2404
15. Daura, X., Jaun, B., Seebach, D., van Gunsteren, W. F., and Mark, A. E. (1998). Reversible peptide folding in solution by molecular dynamics simulation. J. Mol. Biol. 280, 925-932
16. Daura, X., van Gunsteren, W. F., and Mark, A. E. (1999b). Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations. Proteins: Struct. Funct. Genet. 34, 269-280
17. de Alba, E., Rico, M., and Jiménez, M. A. (1997). Cross-strand side-chain interactions versus turn conformation in β-hairpins. Protein Sci. 6, 2548-2560
18. Dill, K. A., and Chan, H. S. (1997). From Levinthal to pathways to funnels. Nat. Struct. Biol. 4, 10-19
19. Dinner, A. R., and Karplus, M. (2001). Comment on the communication "The key to solving the protein-folding problem lies in an accurate description of the denatured state" by van Gunsteren et al. Angew. Chem. Int. Ed. 40, 4615-4616
20. Dinner, A. R., Lazaridis, T., and Karplus, M. (1999). Understanding β-hairpin formation. Proc. Natl. Acad. Sci. USA 96, 9068-9073
21. Dinner, A. R., Sali, A., Smith, L.J., Dobson, C. M., and Karplus, M. (2000). Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem. Sci. 25, 331-339
22. Dobson, C. M., and Hore, P.J. (1998). Kinetic studies of protein folding using NMR spectroscopy. Nat. Struct. Biol. 5, 504-507
23. Duan, Y, and Kollman, P. A. (1998). Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282, 740-744
24. Dyson, H.J., and Wright, P. E. (1998). Equilibrium NMR studies of unfolded and partially folded proteins. Nat. Struct. Biol. 5, 499-503
25. Evans, P. A., and Radford, S. E. (1994). Probing the structure of folding intermediates. Curr Opin. Struct. Biol. 4, 100-106
26. Ferrara, P., Apostolakis, J., and Caflisch, A. (2000). Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. J. Phys. Chem. B 104, 5000-5010
27. Ferrara, P., and Caflisch, A. (2001). Native topology or specific interactions: What is more important for protein folding? J. Mol. Biol. 306, 837-850
28. Fersht, A. R., Matouschek, A., and Serrano, L. (1992). The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224, 771-782
29. García, A. E., and Sanbonmatsu, K. Y. (2002). α-helical stabilization by side chain shielding of backbone hydrogen bonds. Proc. Natl. Acad. Sci. USA 99, 2782-2787
30. Glättli, A., Daura, X., Seebach, D., and van Gunsteren, W. F. (2002). Can One Derive the Conformational Preference of a Peptide from its CD Spectrum. Submitted
31. Hansmann, U. H. E., and Onuchic, J. N. (2001). Thermodynamics and kinetics of folding of a small peptide. J. Chem. Phys. 115, 1601-1606
32. Higo, J., Galzitskaya, O. V., Ono, S., and Nakamura, H. (2001). Energy landscape of a β-hairpin peptide in explicit water studied by multicanonical molecular dynamics. Chem. Phys. Lett. 337, 169-175
33. Hummer, G., Garcia, A. E., and Garde, S. (2001). Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins: Struct. Funct. Genet. 42, 77-84
34. Kobayashi, T., Ikeguchi, M., and Sugai, S. (2000). Molten globule structure of equine beta-lactoglobulin probed by hydrogen exchange. J. Mol. Biol. 299, 757-770
35. Matouschek, A., Kellis, J. T., Serrano, L., and Fersht, A. R. (1989). Mapping the transitionstate and pathway of protein folding by protein engineering. Nature 340, 122-126
36. Mirny, L., and Shakhnovich, E. (2001). Protein folding theory: From lattice to all-atom models. Annu. Rev. Biophys. Biomolec. Struct. 30, 361-396
37. Onuchic, J. N., LutheySchulten, Z., and Wolynes, P. G. (1997). Theory of protein folding: The energy landscape perspective. Annu. Rev. Phys. Chem. 48, 545-600
38. Pappu, R. V., Srinivasan, R., and Rose, G. D. (2000). The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding. Proc. Natl. Acad. Sci. USA 97, 12565-12570
39. Peter, C., Daura, X., and van Gunsteren, W. F. (2000). Peptides of aminoxy acids: A molecular dynamics simulation study of conformational equilibria under various conditions. J. Am. Chem. Soc. 122, 7461-7466
40. Plaxco, K. W., and Dobson, C. M. (1996). Time-resolved biophysical methods in the study of protein folding. Curr Opin. Struct. Biol. 6, 630-636
41. Plaxco, K. W., and Gross, M. (2001). Unfolded, yes, but random? Never! Nat. Struct. Biol. 8, 659-660
42. Santiveri, C. M., Jiménez, M. A., Rico, M., van Gunsteren, W. F., and Daura, X. (2002). β-Hairpin Folding and Stability: Molecular Dynamics Simulations of Designed Peptides in Aqueous Solution. Submitted
43. Schaefer, M., Bartels, C., and Karplus, M. (1998). Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model. J. Mol. Biol. 284, 835-848
44. Schäfer, H., Daura, X., Mark, A. E., and van Gunsteren, W. F. (2001). Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior. Proteins: Struct. Funct. Genet. 43, 45-56
45. 3-peptides with proteinaceous side chains: Synthesis and solution structures of constitutional isomers, a novel helical secondary structure and the influence of solvation and hydrophobic interactions on folding. Helv. Chim. Acta 81, 932-982
46. Seebach, D., Ciceri, P. E., Overhand, M., Jaun, B., Rigo, D., Oberer, L., Hommel, U., Amstutz, R., and Widmer, H. (1996). Probing the helical secondary structure of short-chain β-peptides. Helv. Chim. Acta 79, 2043-2066
47. Seebach, D., Gademann, K., Schreiber, J. V., Matthews, J. L., Hintermann, T., Jaun, B., Oberer, L., Hommel, U., and Widmer, H. (1997). 'Mixed' β-peptides: A unique helical secondary structure in solution. Helv. Chim. Acta 80, 2033-2038
48. Seebach, D., Sifferlen, T., Mathieu, P. A., Hane, A. M., Krell, C. M., Bierbaum, D. J., and Abele, S. (2000). CD spectra in methanol of β-oligopeptides consisting of β-amino acids with functionalized side chains, with alternating configuration, and with geminal backbone substituents. Fingerprints of new secondary structures? Helv. Chim. Acta 83, 2849-2864
49. Shea, J. E., and Brooks, C. L. (2001). From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52, 499-535
50. Shortle, D., and Ackerman, M. S. (2001). Persistence of native-like topology in a denatured protein in 8 M urea. Science 293, 487-489
51. Takano, M., Yamato, T., Higo, J., Suyama, A., and Nagayama, K. (1999). Molecular dynamics of a 15-residue poly (L-alanine) in water: Helix formation and energetics. J. Am. Chem. Soc. 121, 605-612
52. Thirumalai, D., and Klimov, D. K. (1999). Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. Curr. Opin. Struct. Biol. 9, 197-207
53. Troullier, A., Reinstädler, D., Dupont, Y., Naumann, D., and Forge, V. (2000). Transient non-native secondary structures during the refolding of alpha-lactalbumin detected by infrared spectroscopy. Nat. Struct. Biol. 7, 78-86
54. van Gunsteren, W. F., Bürgi, P., Peter, C., and Daura, X. (2001a). The key to solving the protein-folding problem lies in an accurate description of the denatured state. Angew. Chem. Int. Ed. 40, 351-355
55. van Gunsteren, W. E, Bürgi, R., Peter, C., and Daura, X. (2001b). Comment on the communication "The key to solving the protein-folding problem lies in an accurate description of the denatured state" by van Gunsteren et al. - Reply. Angew. Chem. Int. Ed. 40, 4616-4618
56. Wang, H. W., and Sung, S.-S. (2000). Molecular dynamics simulations of three-strand β-sheet folding. J. Am. Chem. Soc. 122, 1999-2009
57. Yang, D., Qu, J., Li, B., Ng, F. F., Wang, X. C., Cheung, K. K., Wang, D. P., and Wu, Y. D. (1999). Novel turns and helices in peptides of chiral α-aminoxy acids. J. Am. Chem. Soc. 121, 589-590