Testing the diffusing boundary model for the helix-coil transition in peptides

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

Volumn 110, Issue 32, 2013, Pages 12905-12910

  Neumaier, Sabine ^a   Reiner, Andreas ^a,b   Büttner, Maren ^a   Fierz, Beat ^a,c   Kiefhaber, Thomas ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c EPFL   (Switzerland)

Author keywords

helix capping; value; Protein folding

Indexed keywords

AMINO ACID; PEPTIDE;

ALPHA HELIX; AMINO ACID SUBSTITUTION; ARTICLE; CAPPING PHENOMENON; CONTROLLED STUDY; DIFFUSION COEFFICIENT; ENERGY TRANSFER; KINETICS; LINEAR SYSTEM; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PHASE TRANSITION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STABILITY; PROTEIN SYNTHESIS; PROTEIN UNFOLDING;

Α-HELIX CAPPING; -VALUE; PROTEIN FOLDING;

ALGORITHMS; COMPUTER SIMULATION; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; PEPTIDES; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS; UREA;

EID: 84881424833     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1303515110     Document Type: Article

References (43)

1. Marqusee S, Robbins VH, Baldwin RL (1989) Unusually stable helix formation in short alanine-based peptides. Proc Natl Acad Sci USA 86(14):5286-5290.
2. Zimm BH, Bragg JK (1959) Theory of phase transition between helix and random coil in polypeptide chains. J Chem Phys 31(2):526-535.
3. Lifson S, Roig A (1961) On the theory of helix-coil transition in polypeptides. J Chem Phys 34(6):1963-1974.
4. Schwarz G, Seelig J (1968) Kinetic properties and the electric field effect of the helixcoil transition of poly(gamma-benzyl L-glutamate) determined from dielectric relaxation measurements. Biopolymers 6(9):1263-1277.
5. Gruenewald B, Nicola CU, Lustig A, Schwarz G, Klump H (1979) Kinetics of the helixcoil transition of a polypeptide with non-ionic side groups, derived from ultrasonic relaxation measurements. Biophys Chem 9(2):137-147.
6. Chakrabartty A, Schellman JA, Baldwin RL (1991) Large differences in the helix propensities of alanine and glycine. Nature 351(6327):586-588.
7. Qian H, Schellman JA (1992) Helix-coil theories: A comparative study for finite length polypeptides. J Phys Chem 96(10):3978-3994.
8. Huang CY, Klemke JW, Getahun Z, DeGrado WF, Gai F (2001) Temperature-dependent helix-coil transition of an alanine based peptide. J Am ChemSoc 123(38):9235-9238.
9. Thompson PA, Eaton WA, Hofrichter J (1997) Laser temperature jump study of the helixcoil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model. Biochemistry 36(30):9200-9210.
10. 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.
11. Schwarz G (1965) On the kinetics of the helix-coil transition of polypeptides in solution. J Mol Biol 11(1):64-77.
12. Krieger F, Fierz B, Bieri O, Drewello M, Kiefhaber T (2003) Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. J Mol Biol 332(1): 265-274.
13. Satzger H, et al. (2004) Ultrafast quenching of the xanthone triplet by energy transfer: new insight into the intersystem crossing kinetics. J Phys Chem A 108(46): 10072-10079.
14. Heinz B, et al. (2006) On the unusual fluorescence properties of xanthone in water. Phys Chem Chem Phys 8(29):3432-3439.
15. Rohl CA, Scholtz JM, York EJ, Stewart JM, Baldwin RL (1992) Kinetics of amide proton exchange in helical peptides of varying chain lengths. Interpretation by the Lifson- Roig equation. Biochemistry 31(5):1263-1269.
16. Fierz B, et al. (2007) Loop formation in unfolded polypeptide chains on the picoseconds to microseconds time scale. Proc Natl Acad Sci USA 104(7):2163-2168.
17. Fierz B, Kiefhaber T (2007) End-to-end vs interior loop formation kinetics in unfolded polypeptide chains. J Am Chem Soc 129(3):672-679.
18. Wang T, et al. (2004) Length dependent helix-coil transition kinetics of nine alaninebased peptides. J Phys Chem B 108(39):15301-15310.
19. van Holde KE (1971) Biophysical Chemistry (Prentice-Hall, London).
20. Granéli A, Yeykal CC, Robertson RB, Greene EC (2006) Long-distance lateral diffusion of human Rad51 on double-stranded DNA. Proc Natl Acad Sci USA 103(5):1221-1226.
21. Wang YM, Austin RH, Cox EC (2006) Single molecule measurements of repressor protein 1D diffusion on DNA. Phys Rev Lett 97(4):048302.
22. Blainey PC, et al. (2013) Regulation of a viral proteinase by a peptide and DNA in onedimensional space: IV. viral proteinase slides along DNA to locate and process its substrates. J Biol Chem 288(3):2092-2102.
23. Presta LG, Rose GD (1988) Helix signals in proteins. Science 240(4859):1632-1641.
24. Richardson JS, Richardson DC (1988) Amino acid preferences for specific locations at the ends of alpha helices. Science 240(4859):1648-1652.
25. Aurora R, Rose GD (1998) Helix capping. Protein Sci 7(1):21-38.
26. Hol WGJ (1985) The role of the alpha-helix dipole in protein structure and function. Prog Biophys Mol Biol 45:149-195.
27. Shoemaker KR, Kim PS, York EJ, Stewart JM, Baldwin RL (1987) Tests of the helix dipole model for stabilization of α-helices. Nature 326(6113):563-567.
28. Sali D, Bycroft M, Fersht AR (1988) Stabilization of protein structure by interaction of alpha-helix dipole with a charged side chain. Nature 335(6192):740-743.
29. Doig AJ, Baldwin RL (1995) N- and C-capping preferences for all 20 amino acids in alpha-helical peptides. Protein Sci 4(7):1325-1336.
30. Doig AJ, Errington N, Iqbalsyah TM (2005) Stability and design of alpha-helices. Protein Folding Handbook, eds Buchner J, Kiefhaber T (Wiley-VCH, Weinheim, Germany), Vol 1, pp 247-313.
31. Shoemaker KR, et al. (1985) Nature of the charged-group effect on the stability of the C-peptide helix. Proc Natl Acad Sci USA 82(8):2349-2353.
32. Leffler JE (1953) Parameters for the description of transition states. Science 117(3039): 340-341.
33. Matouschek A, Kellis JT, Jr., Serrano L, Fersht AR (1989) Mapping the transition state and pathway of protein folding by protein engineering. Nature 340(6229):122-126.
34. Sánchez IE, Kiefhaber T (2003) Hammond behavior versus ground state effects in protein folding: Evidence for narrow free energy barriers and residual structure in unfolded states. J Mol Biol 327(4):867-884.
35. 3 domain folding transition state. J Mol Biol 320(2):389-402.
36. Sánchez IE, Kiefhaber T (2003) Origin of unusual phi-values in protein folding: evidence against specific nucleation sites. J Mol Biol 334(5):1077-1085.
37. Scholtz JM, Baldwin RL (1992) The mechanism of alpha-helix formation by peptides. Annu Rev Biophys Biomol Struct 21:95-118.
38. Chakrabartty A, Kortemme T, Baldwin RL (1994) Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci 3(5):843-852.
39. Lin MM, Mohammed OF, Jas GS, Zewail AH (2011) Speed limit of protein folding evidenced in secondary structure dynamics. Proc Natl Acad Sci USA 108(40):16622-16627.
40. Naganathan AN, Muñoz V (2010) Insights into protein folding mechanisms from large scale analysis of mutational effects. Proc Natl Acad Sci USA 107(19):8611-8616.
41. Gans PJ, Lyu PC, Manning MC, Woody RW, Kallenbach NR (1991) The helix-coil transition in heterogeneous peptides with specific side-chain interactions: Theory and comparison with CD spectral data. Biopolymers 31(13):1605-1614.
42. Pace CN (1986) Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol 131:266-280.
43. Möglich A, Krieger F, Kiefhaber T (2005) Molecular basis for the effect of urea and guanidinium chloride on the dynamics of unfolded polypeptide chains. J Mol Biol 345(1):153-162.