α-Helix folding in the presence of structural constraints

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

Volumn 105, Issue 28, 2008, Pages 9588-9593

  Ihalainen, Janne A ^a   Paoli, Beatrice ^a   Muff, Stefanie ^a   Backus, Ellen H G ^a   Bredenbeck, Jens ^a   Woolley, G Andrew ^b   Caflisch, Amedeo ^a   Hamm, Peter ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Cooperativity; Infrared spectroscopy; Molecular dynamics simulation; Peptide folding

Indexed keywords

CARBON; GLOBULAR PROTEIN; OXYGEN;

ALPHA HELIX; ARTICLE; CROSS LINKING; HIGH TEMPERATURE; INFRARED SPECTROSCOPY; ISOTOPE LABELING; KINETICS; LOW TEMPERATURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; SIMULATION;

AMINO ACID SEQUENCE; ISOTOPES; KINETICS; PEPTIDES; PHOTOCHEMISTRY; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; THERMODYNAMICS;

EID: 47749149231     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0712099105     Document Type: Article

References (45)

1. Eaton WA, Henry ER, Hofrichter J, Mozzarelli A (1999) Is cooperative oxygen binding by hemoglobin really understood? Nat Struct Biol 6:351-358.
2. Creighton TE (1993) Proteins. (Freeman, New York).
3. Zimm BH, Bragg JK (1959) Theory of the phase transition between helix and random coil in polypeptide chains. J Chem Phys 31:526-535.
4. Lifson S, Roig A (1961) On the theory of helix-coil transition in polypeptides. J Chem Phys 34:1963-1974.
5. Scholtz JM, Qian H, York EJ, Stewart JM, Baldwin RL (1991) Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water. Biopolymers 31:1463-1470.
6. Muñoz V, Serrano L (1995) Helix design, prediction and stability. Curr Opin Biotechnol 6:382-386.
7. Doig AJ (2002) Recent advances in helix-coil theory. Biophys Chem 101:281-293.
8. Scheraga HA, Vila JA, Ripoll DR (2002) Helix-coil transitions re-visited. Biophys Chem 101-102:255-265.
9. Kaya H, Chan HS (2000) Polymer principles of protein calorimetric two-state cooperativity. Proteins 40:637-661.
10. 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 36:9200-9210.
11. Thompson PA, et al. (2000) The helix-coil kinetics of a heteropeptide. J Phys Chem B 104:378-389.
12. Huang C-Y, et al. (2002) Helix formation via conformation diffusion search. Proc Natl Acad Sci USA 99:2788-2793.
13. Sadqi M, Fushman D, Muñoz V (2006) Atom-by-atom analysis of global downhill protein folding. Nature 442:317-321.
14. Krimm S, Bandekar J (1986) Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Adv Protein Chem 38:181-364.
15. Silva RAGD, Kubelka J, Bour P, Decatur SM, Keiderling T (2002) A site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution. Proc Natl Acad Sci USA 97:8318-8323.
16. Doshi U, Muñoz V (2004) The principles of α-helix formation: Explaining complex kinetics with nucleation-elongation theory. J Phys Chem B 108:8497-8506.
17. Brewer SH, Song B, Raleigh DP, Dyer RB (2007) Residue specific resolution of protein folding dynamics using isotope-edited infrared temperature jump spectroscopy. Biochemistry 46:3279-3285.
18. Kumita JR, Smart OS, Woolley GA (2000) Photo-control of helix content in a short peptide. Proc Natl Acad Sci USA 97:3803-3808.
19. Bredenbeck J, Helbing J, Kumita JR, Woolley GA, Hamm P (2005) α-Helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time resolved IR spectroscopy. Proc Natl Acad Sci USA 102:2379-2384.
20. Ihalainen JA, et al. (2007) Folding and unfolding of a photoswitchable peptide. Proc Natl Acad Sci USA 104:5383-5388.
21. Hamm P, Helbing J, Bredenbeck J (2006) Stretched versus compressed exponential kinetics in α-helix folding. Chem Phys 323:54-65.
22. Rao F, Caflisch A (2004) The protein folding network. J Mol Biol 342:299-306.
23. Krivov SV, Karplus M (2004) Hidden complexity of free energy surfaces for peptide (protein) folding. Proc Natl Acad Sci USA 101:14766-14770.
24. Hummer G, Garcia AE, Garde S (2001) Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins 42:77-84.
25. Caflisch A (2006) Network and graph analyses of folding free energy surfaces. Curr Opin Struct Biol 16:71-78.
26. Chekmarev SF, Krivov SV, Karplus M (2006) Folding of ubiquitin: A simple model describes the strange kinetics. J Phys Chem B 110:8865-8869.
27. Chowdhury S, Zhang W, Wu C, Xiong G, Duan Y (2003) Breaking non-native hydrophobic clusters is the rate limiting step in the folding of an alanine-based peptide. Biopolymers 68:63-75.
28. Makowska J, et al. (2006) Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. Proc Natl Acad Sci USA 103:1744-1749.
29. Muff S, Caflisch A (2008) Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a β-sheet miniprotein. Proteins Struct Funct Bioinf 70:1185-1195.
30. Ferrara P, Apostolakis J, Caflisch A (2002) Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins Struct Funct Bioinf 46:24-33.
31. Brooks BR, et al. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217.
32. Nguyen PH, Stock G (2006) Nonequilibrium molecular dynamics simulation of a photoswitchable peptide. Chem Phys 323:36-44.
33. Nguyen PH, Gorbunov RD, Stock G (2006) Photoinduced conformational dynamics of a photoswitchable peptide: A nonequilibrium molecular dynamics simulation study. Biophys J 91:1224-1234.
34. Marqusee S, Robbins VH, Baldwin RL (1989) Unusually stable helix formation in short alaninen-based peptides. Proc Natl Acad Sci USA 86:5286-5290.
35. Huang C-Y, Klemke JW, Getahun Z, DeGrado WF, Gai F (2001) Temperature-dependent helix- coil transition of an alanine based peptide. J Am Chem Soc 123:9235-9238.
36. Werner JH, Dyer RB, Fesinmeyer RM, Andersen NH (2002) Dynamics of the primary processes of protein folding: Helix nucleation. J Phys Chem B 106:487-494.
37. Gooding EA, et al. (2005) The effects of individual amino acids on the fast folding dynamics of α-helical peptides. Chem Commun 5985-5987.
38. Rohl CA, Baldwin RL (1998) Deciphering rules of helix stability in peptides. Methods Enzymol 295:1-26.
39. Andersen CAF, Palmer AG, Brunak S, Rost B (2002) Continuum secondary structure captures protein flexibility. Structure (London) 10:174-184.
40. Garcia-Mira MM, Sadqi M, Fischer N, Sanchez-Ruiz JM, Muñoz V (2002) Experimental identification of downhill protein folding. Science 298:2191-2195.
41. Yang WY, Gruebele M (2003) Folding at the speed limit. Nature 423:193-197.
42. Knott M, Chan HS (2006) Criteria for downhill protein folding: Calorimetry, chevron plot, kinetic relaxation, and single-molecule radius of gyration in chain models with subdued degrees of cooperativity. Proteins 65:373-391.
43. Carstens, H (2004) Conformation dynamics of light-stable peptide: Molecular dynamics simulations and data-driven model-building. PhD thesis (Ludwig Maxmilians University, Munich).
44. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314:141-151.
45. Seeber M, Cecchini M, Rao F, Settanni G, Caflisch A (2007) WORDOM: A program for efficient analysis of molecular dynamics simulations. Bioinformatics 23:2625-2627.