Transition state and ground state properties of the helix-coil transition in peptides deduced from high-pressure studies

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 52, 2013, Pages 20988-20993

  Neumaier, Sabine ^a   Büttner, Maren ^a   Bachmann, Annett ^a   Kiefhaber, Thomas ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Helix dynamics; Protein dynamics; Protein stability

Indexed keywords

ALANINE;

ALPHA HELIX; ARTICLE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; HYDROGEN BOND; KINETICS; MOLECULAR DYNAMICS; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE;

EID: 84891357875     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1317973110     Document Type: Article

References (50)

1. Kauzmann W (1987) Thermodynamics of unfolding. Nature 325(6107): 763-764.
2. Meersman F, Smeller L, Heremans K (2006) Protein stability and dynamics in the pressure-temperature plane. Biochim Biophys Acta 1764(3): 346-354.
3. Royer CA (2002) Revisiting volume changes in pressure-induced protein unfolding. Biochim Biophys Acta 1595(1-2): 201-209.
4. Silva JL, Foguel D, Royer CA (2001) Pressure provides new insights into protein folding, dynamics and structure. Trends Biochem Sci 26(10): 612-618.
5. Gerstein M, Chothia C (1996) Packing at the protein-water interface. Proc Natl Acad Sci USA 93(19): 10167-10172.
6. Chalikian TV, Macgregor RB, Jr. (2009) Origins of pressure-induced protein transitions. J Mol Biol 394(5): 834-842.
7. Rasper J, Kauzman W (1962) Volume changes in protein reactions: 1. Ionization reactions of proteins. J Am Chem Soc 84: 1771-1777.
8. Roche J, et al. (2012) Cavities determine the pressure unfolding of proteins. Proc Natl Acad Sci USA 109(18): 6945-6950.
9. Pappenberger G, Saudan C, Becker M, Merbach AE, Kiefhaber T (2000) Denaturantinduced movement of the transition state of protein folding revealed by high-pressure stopped-flow measurements. Proc Natl Acad Sci USA 97(1): 17-22.
10. Jacob MH, et al. (2002) Water contributes actively to the rapid crossing of a protein unfolding barrier. J Mol Biol 318(3): 837-845.
11. Rouget JB, et al. (2011) Size and sequence and the volume change of protein folding. J Am Chem Soc 133(15): 6020-6027.
12. Panick G, Winter R (2000) Pressure-induced unfolding/refolding of ribonuclease A: Static and kinetic Fourier transform infrared spectroscopy study. Biochemistry 39(7): 1862-1869.
13. Brandts JF, Halvorson HR, Brennan M (1975) Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. Biochemistry 14(22): 4953-4963.
14. Schmid FX (1983) Mechanism of folding of ribonuclease A. Slow refolding is a sequential reaction via structural intermediates. Biochemistry 22(20): 4690-4696.
15. Kiefhaber T, Schmid FX (1992) Kinetic coupling between protein folding and prolyl isomerization. II. Folding of ribonuclease A and ribonuclease T1. JMol Biol 224(1): 231-240.
16. Houry WA, Rothwarf DM, Scheraga HA (1995) The nature of the initial step in the conformational folding of disulphide-intact ribonuclease A. Nat Struct Biol 2(6): 495-503.
17. Imamura H, Kato M (2009) Effect of pressure on helix-coil transition of an alaninebased peptide: An FTIR study. Proteins 75(4): 911-918.
18. Paschek D, Gnanakaran S, Garcia AE (2005) Simulations of the pressure and temperature unfolding of an α-helical peptide. Proc Natl Acad Sci USA 102(19): 6765-6770.
19. Vajpai N, Nisius L, Wiktor M, Grzesiek S (2013) High-pressure NMR reveals close similarity between cold and alcohol protein denaturation in ubiquitin. Proc Natl Acad Sci USA 110(5):E368-E376.
20. Fierz B, Reiner A, Kiefhaber T (2009) Local conformational dynamics in α-helices measured by fast triplet transfer. Proc Natl Acad Sci USA 106(4): 1057-1062.
21. Reiner A, Henklein P, Kiefhaber T (2010) An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain. Proc Natl Acad Sci USA 107(11): 4955-4960.
22. Neumaier S, Reiner A, Büttner M, Fierz B, Kiefhaber T (2013) Testing the diffusing boundary model for the helix-coil transition in peptides. Proc Natl Acad Sci USA 110(32): 12905-12910.
23. Bieri O, et al. (1999) The speed limit for protein folding measured by triplet-triplet energy transfer. Proc Natl Acad Sci USA 96(17): 9597-9601.
24. Krieger F, Fierz B, Bieri O, Drewello M, Kiefhaber T (2003) Dynamics of unfolded polypeptide chains asmodel for the earliest steps in protein folding. JMol Biol 332(1): 265-274.
25. Rohl CA, Baldwin RL (1994) Exchange kinetics of individual amide protons in 15N-labeled helical peptides measured by isotope-edited NMR. Biochemistry 33(25): 7760-7767.
26. Fierz B, Kiefhaber T (2005) Dynamics of unfolded polypeptide chains. Protein Folding Handbook, eds Buchner J, Kiefhaber T (Wiley-VCH, Weinheim), pp 805-851.
27. Neumann CRJ, Kauzmann W, Zipp A (1973) Pressure-dependence of weak acid ionization in aqueous buffers. J Phys Chem 77: 2687-2691.
28. Chakrabartty A, Schellman JA, Baldwin RL (1991) Large differences in the helix propensities of alanine and glycine. Nature 351(6327): 586-588.
29. Lifson S, Roig A (1961) On the theory of helix-coil transition in polypeptides. J Chem Phys 34: 1963-1974.
30. Scholtz JM, et al. (1991) Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water. Proc Natl Acad Sci USA 88(7): 2854-2858.
31. Qian H, Schellman JA (1992) Helix-coil theories: A comparative study for finite length polypeptides. J Phys Chem 96: 3978-3994.
32. Schwarz G (1965) On the kinetics of the helix-coil transition of polypeptides in solution. J Mol Biol 11: 64-77.
33. Thompson PA, Eaton WA, Hofrichter J (1997) Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model. Biochemistry 36(30): 9200-9210.
34. Zimm BH, Bragg JK (1959) Theory of phase transition between helix and random coil in polypeptide chains. J Chem Phys 31: 526-535.
35. Scholtz JM, Baldwin RL (1992) The mechanism of alpha-helix formation by peptides. Annu Rev Biophys Biomol Struct 21: 95-118.
36. Luo P, Baldwin RL (1999) Interaction between water and polar groups of the helix backbone: An important determinant of helix propensities. Proc Natl Acad Sci USA 96(9): 4930-4935.
37. Porter LL, Rose GD (2011) Redrawing the Ramachandran plot after inclusion of hydrogen- bonding constraints. Proc Natl Acad Sci USA 108(1): 109-113.
38. Christensen RG, Cassel JM (1967) Volume changes accompanying collagen denaturation. Biopolymers 5(8): 685-689.
39. Luo P, Baldwin RL (1997) Mechanism of helix induction by trifluoroethanol: A framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/ water mixtures back to water. Biochemistry 36(27): 8413-8421.
40. Reiner A, Wildemann D, Fischer G, Kiefhaber T (2008) Effect of thioxopeptide bonds on alpha-helix structure and stability. J Am Chem Soc 130(25): 8079-8084.
41. Bachmann A, Wildemann D, Praetorius F, Fischer G, Kiefhaber T (2011) Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction. Proc Natl Acad Sci USA 108(10): 3952-3957.
42. Tiffany ML, Krimm S (1973) Extended conformations of polypeptides and proteins in urea and guanidine hydrochloride. Biopolymers 12: 575-587.
43. Woody RW (1992) Circular dichroism and conformation of unordered polypeptides. Adv. Biophys. Chem. 2: 37-79.
44. Shi Z, Olson CA, Rose GD, Baldwin RL, Kallenbach NR (2002) Polyproline II structure in a sequence of seven alanine residues. Proc Natl Acad Sci USA 99(14): 9190-9195.
45. Roche J, et al. (2012) Remodeling of the folding free energy landscape of staphylococcal nuclease by cavity-creating mutations. Biochemistry 51(47): 9535-9546.
46. Rouget JB, et al. (2010) Unique features of the folding landscape of a repeat protein revealed by pressure perturbation. Biophys J 98(11): 2712-2721.
47. Puthenpurackal Narayanan S, et al. (2012) Extensively hydrated but folded: A novel state of globular proteins stabilized at high pressure and low temperature. Biophys J 102(2):L8-L10.
48. Prigozhin MB, et al. (2013) Misplaced helix slows down ultrafast pressure-jump protein folding. Proc Natl Acad Sci USA 110(20): 8087-8092.
49. Scholtz JM, Barrick D, York EJ, Stewart JM, Baldwin RL (1995) Urea unfolding of peptide helices as amodel for interpreting protein unfolding. Proc Natl Acad Sci USA 92(1): 185-189.
50. Smith JS, Scholtz JM (1996) Guanidine hydrochloride unfolding of peptide helices: Separation of denaturant and salt effects. Biochemistry 35(22): 7292-7297.