Beyond the nearest-neighbor Zimm-Bragg model for helix-coil transition in peptides

Biopolymers

Volumn 91, Issue 2, 2009, Pages 120-131

  Murza, Adrian ^a,b   Kubelka, Jan ^a  

^a UNIVERSITY OF WYOMING   (United States)

^b INSTITUTO DE FÍSICA INTERDISCIPLINAR Y SISTEMAS COMPLEJOS IFISC CSIC UIB   (Spain)

Author keywords

Alanine peptide; Helix coil transition; Zimm Bragg model

Indexed keywords

ABSOLUTE VALUES; ALANINE PEPTIDE; AS DISTRIBUTIONS; CIRCULAR DICHROISMS; COOPERATIVITY; EXPERIMENTAL DATUM; EXPERIMENTAL SPECTRUM; FOURIER TRANSFORM INFRARED; FREE ENERGY BARRIERS; FREE ENERGY SURFACES; HELICITY; HELIX NUCLEATIONS; HELIX-COIL TRANSITION; LONG-RANGE INTERACTIONS; MATRIX APPROACHES; MICROSCOPIC PARAMETERS; MODEL FITS; MODEL PARAMETERS; NEAREST NEIGHBORS; NUCLEATION PARAMETERS; PROPAGATION PARAMETERS; STATISTICAL WEIGHTS; TEMPERATURE DEPENDENTS; ZIMM-BRAGG MODEL;

BIOPOLYMERS; DICHROISM; FOURIER TRANSFORMS; FREE ENERGY; INFRARED SPECTROSCOPY; NUCLEATION; POLYMERS; PROBABILITY DISTRIBUTIONS;

AMINES;

AMINO ACID SEQUENCE; CIRCULAR DICHROISM; MODELS, MOLECULAR; OLIGOPEPTIDES; PEPTIDES; PROBABILITY; PROTEIN CONFORMATION; PROTEIN DENATURATION; SPECTROPHOTOMETRY, ULTRAVIOLET; THERMODYNAMICS;

EID: 59949101046     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.21093     Document Type: Article

References (55)

1. Doty, P.; Holtzer, A. M.; Bradbury, J. H.; Blout, E. R. J Am Chem Soc 1954, 76, 4493-4494.
2. Blout, E. R.; Karlson, R. H. J Am Chem Soc 1958, 80, 1259-1260.
3. Poland, D.; Scheraga, H. A. Theory of Helix-Coil Transition in Biopolymers; Academic Press: New York, 1970.
4. Marqusee, S.; Robbins, V. H.; Baldwin, R. L. Proc Natl Acad Sci USA 1989, 86, 5286-5290.
5. Scholtz, J. M.; Baldwin, R. L. Annu Rev Biophys Biomol Struct 1992, 21, 95-118.
6. Qian, H.; Schellman, J. A. J Phys Chem 1992, 96, 3987-3994.
7. Munõz, V.; Serrano, L. Struct Biol 1994, 1, 399-409.
8. Scheraga, H. A.; Vila, J. A.; Ripoll, D. R. Biophys Chem 2002, 101, 255-265.
9. Doig, A. J. Biophys Chem 2002, 101, 281-293.
10. Zimm, B. H.; Bragg, J. K. J Chem Phys 1959, 31, 526-535.
11. Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry. III. The Behavior of Biological Macromolecules; W. H. Freeman: New York, 1980.
12. Saroff, H. A.; Kiefer, J. E. Biopolymers 1999, 49, 425-440.
13. Vasquez, M.; Scheraga, H. A. Biopolymers 1988, 27, 41-58.
14. Gans, P. J.; Lyu, P. C.; Manning, M. C.; Woody, R. W.; Kallenbach, N. R. Biopolymers 1991, 31, 1605-1614.
15. Robert, C. H. Biopolymers 1990, 30, 335-347.
16. Finkelstein, A. V.; Badretdinov, A. Y.; Ptitsyn, O. B. Protein Struct Funct Genet 1991, 10, 287-299.
17. Andersen, N. H.; Tong, H. Protein Sci 1997, 6, 1920-1936.
18. Wako, H.; Saito, N.; Scheraga, H. A. J Protein Chem 1983, 2, 221-249.
19. Wako, H.; Saito, N. J Phys Soc Jpn 1978, 44, 1931-1938.
20. Wako, H.; Saito, N. J Phys Soc Jpn 1978, 44, 1939-1945.
21. Bruscolini, P.; Pelizzola, A. Phys Rev Lett 2002, 88, 1-4.
22. Henry, E. R.; Hofricheter, J. Methods Enzymol 1992, 210, 129-192.
23. Williams, S.; Causgrove, T. P.; Gilmanshin, R.; Fang, K. S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Biochemistry 1996, 35, 691-697.
24. Yoder, G.; Pancoska, P.; Keiderling, T. A. Biochemistry 1997, 36, 15123-15133.
25. Huang, C.-Y.; Klemke, J. W.; Getahun, Z.; DeGrado, W F.; Gai, F. J Am Chem Soc 2001, 123, 9235-9238.
26. Rialdi, G.; Hermans, J. J Am Chem Soc 1966, 88, 5719-5720.
27. Chou, P. Y.; Scheraga, H. A. Biopolymers 1971, 10, 657-680.
28. Scholtz, J. M.; Qian, H.; York, E. J.; Stewart, J. M.; Baldwin, R. L. Biopolymers 1991, 31, 1463-1470.
29. Scholtz, J. M.; Marqusee, S.; Baldwin, R. L.; York, E. J.; Stewart, J. M.; Santoro, M.; Bolen, D. W. Proc Natl Acad Sci USA 1991, 88, 2854-2858.
30. Chakrabartty, A.; Kortemme, T.; Baldwin, R. L. Protein Sci 1994, 3, 843-852.
31. Yang, A. S.; Honig, B. J Mol Biol 1995, 252, 351-365.
32. Lopez, M. M.; Chin, D. H.; Baldwin, R. L.; Makhatadze, G. I. Proc Natl Acad Sci USA 2002, 99, 1298-1302.
33. Goch, G.; Maciejczyk, M.; Oleszczuk, M.; Stachowiak, D.; Malicka, J.; Bierzynski, A. Biochemistry 2003, 42, 6840-6847.
34. Ingwall, R. T.; Scheraga, H. A.; Lotan, N.; Berger, A.; Katchals, E. Biopolymers 1968, 6, 331-368.
35. Platzer, K. E. B.; Scheraga, H. A.; Andreatt, R. H.; Ananthan V S. Macromolecules 1972, 5, 177-187.
36. Williams, L.; Kather, K.; Kemp, D. S. J Am Chem Soc 1998, 120, 11033-11043.
37. Vila, J. A.; Ripoll, D. R.; Scheraga, H. A. Proc Natl Acad Sci USA 2000, 97, 13075-13079.
38. Vila, J. A.; Ripoll, D. R.; Scheraga, H. A. Biopolymers 2001, 58, 235-246.
39. Decatur, S. M. Biopolymers 2000, 54, 180-185.
40. Silva, R.; Kubelka, J.; Bour, P.; Decatur, S. M.; Keiderling, T. A. Proc Natl Acad Sci USA 2000, 97, 8318-8323.
41. Ianoul, A.; Mikhonin, A.; Lednev, I. K.; Asher, S. A. J Phys Chem A 2002, 106, 3621-3624.
42. Schwarz, G. J Mol Biol 1965, 11, 64-77.
43. Poland, D.; Scheraga, H. A. J Chem Phys 1966, 45, 2071-2090.
44. Doshi, U.; Mun ñoz, V. Chem Phys 2004, 307, 129-136.
45. Decatur, S. M.; Antonic, J. J Am Chem Soc 1999, 121, 11914-11915.
46. Huang, C. Y.; Getahun, Z.; Wang, T.; DeGrado, W. F.; Gai, F. J Am Chem Soc 2001, 123, 12111-12112.
47. Huang, C. Y.; Getahun, Z.; Zhu, Y. J.; Klemke, J. W.; DeGrado, W. F.; Gai, F. Proc Natl Acad Sci USA 2002, 99, 2788-2793.
48. Venyaminov, S. Y.; Hedstrom, J. F.; Prendergast, F. G. Protein Struct Funct Genet 2001, 45, 81-89.
49. Decatur, S. M. Acc Chem Res 2006, 39, 169-175.
50. Mikhonin, A. V.; Asher, S. A.; Bykov, S. V.; Murza, A. J Phys Chem B 2007, 111, 3280-3292.
51. Liff, M. I.; Lyu, P. C.; Kallenbach, N. R. J Am Chem Soc 1991, 113, 1014-1019.
52. Millhauser, G. L.; Stenland, C. J.; Bolin, K. A.; van deVen, F. J. M. J Biomol NMR 1996, 7, 331-334.
53. Thompson, P. A.; Eaton, W. A.; Hofrichter, J. Biochemistry 1997, 36, 9200-9210.
54. Jas, G. S.; Eaton, W. A.; Hofrichter, J. J Phys Chem B 2001, 105, 261-272.
55. Kemp, D. S.; Oslick, S. L.; Allen, T. J. J Am Chem Soc 1996, 118, 4249-4255.