Proteins in Vacuo. Denaturation of Highly Charged Disulfide-Reduced Lysozyme Studied by Molecular Dynamics Simulations

Journal of Physical Chemistry B

Volumn 104, Issue 11, 2000, Pages 2546-2558

  Velazquez I ^a   Reimann, C T ^b   Tapia, O ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0346856266     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9842648     Document Type: Article

References (77)

1. Hoaglund-Hyzer, C. S.; Counterman, A. E.; Clemmer, D. E. Chem. Rev. 1999, 99 3037-3079.
2. Karas, M.; Hillenkamp, F. Anal. Chem. 1988, 60, 2299-2301.
3. Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Science 1989, 246, 64-71.
4. Green, M. K.; Lebrilla, C. B. Mass Spectrom. Rev. 1997, 16, 53-71.
5. McLafferty, F. W.; Guan, Z. Q.; Haupts, U.; Wood, T. D.; Kelleher, N. L. J. Am. Chem. Soc. 1998, 120, 4732-4740.
6. von Helden, G.; Wyttenbach, T.; Bowers, M. T. Science 1995, 267, 1483-1485.
7. Clemmer, D. E.; Hudgins, R. R.; Jarrold, M. F. J. Am. Chem. Soc. 1995, 117, 10141-10142.
8. Shelimov, K. B.; Clemmer, D. E.; Hudgins, R. R.; Jarrold, M. F. J. Am. Chem. Soc. 1997, 119, 2240-2248.
9. Valentine, S. J.; Anderson, J. G.; Ellington, A. D.; Clemmer, D. E. J. Phys. Chem. B 1997, 101, 3891-3900.
10. Nesatiy, V.; Chen, Y.-L.; Collings, B. A.; Douglas, D. J. Rap. Commun. Mass Spectrom. 1998, 12, 40-44.
11. Sullivan, P. A.; Reimann, C. T.; Axelsson, J.; Altmann, S.; Quist, A. P.; Sundqvist, B. U. R. J. Am. Soc. Mass Spectrom. 1996, 7, 329-341.
12. Reimann, C. T.; Sullivan, P. A.; Axelsson, J.; Quist, A. P.; Altmann, S.; Roepstorff, P.; Veláquez, I.; Tapia, O. J. Am. Chem. Soc. 1998, 120, 7608-7616.
13. Adams, J.; Strobel, F. H.; Reiter, A.; Sullards, M. C. J. Am. Soc. Mass Spectrom. 1996, 7, 30-41.
14. Kaltashov, I. A.; Fenselau, C. Proteins - Struct. Funct. Gen. 1997, 27, 165-170.
15. Sziláyi, Z.; Drahos, L.; Vékey, K. J. Mass Spectrom. 1997, 32, 689-696.
16. Li, A.; Fenselau, C.; Kaltashov, I. A. Proteins - Struct. Funct. Gen. 1998, Suppl. 2, 22-27.
17. Reimann, C. T.; Veláquez, I.; Tapia, O. J. Phys. Chem. B 1998, 102, 9344-9352.
18. Mao, Y.; Woenckhaus, J.; Kolafa, J.; Ratner, M. A.; Jarrold, M. F. J. Am. Chem. Soc. 1999, 121, 2712-2721.
19. Reimann, C. T.; Veláquez, I.; Bittner, M.; Tapia, O. Phys. Rev. E 1999, 60, 7277-7284.
20. Arteca, G. A.; Veláquez, I.; Reimann, C. T.; Tapia, O. Phys. Rev. E 1999, 59, 5981-5986.
21. Arteca, G. A.; Veláquez, I.; Reimann, C. T.; Tapia, O. J. Chem. Phys. 1999, 111, 4774-4779.
22. Veláquez, I.; Reimann, C. T.; Tapia, O. J. Am. Chem. Soc. 1999, 121, 11468-11477.
23. Gross, D. S.; Schnier, P. D.; Rodriguez-Cruz, S. E.; Fagerquist, C. K.; Williams, E. R. Proc. Natl. Acad. Sci. 1996, 93, 3143-3148.
24. van Gunsteren, W. F.; Berendsen, H. J. C. Groningen Molecular Simulation (GROMOS) Library Manual; Biomos, Nijenborgh 16, 9747 AG Groningen, The Netherlands, 1987.
25. Wilson, K. P.; Malcolm, B. A.; Matthews, B. W. J. Biol. Chem. 1992, 267, 10842.
26. Schnier, P. D.; Gross, D. S.; Williams, E. R. J. Am. Soc. Mass Spectrom. 1995, 6, 1086-1097.
27. Miteva, M.; Demirev, P. A.; Karshikoff, A. D. J. Phys. Chem. B 1997, 101, 9645-9650.
28. Dongré, A.; Jones, J. L.; Somogyi, A.; Wysocki, V. H. J. Am. Chem. Soc. 1996, 118, 8365-8374.
29. Dobrynin, A. V.; Rubinstein, M.; Obukhov, S. P. Macromolecules 1996, 29, 2974-2979.
30. Aqvist, J.; van Gunsteren, W. F.; Leijonmarck, M.; Tapia, O. J. Mol. Biol. 1985, 183, 461-477.
31. Kaltashov, I. A.; Fenselau, C. C. J. Am. Chem. Soc. 1995, 117, 9906-9910.
32. Schnier, P. D.; Gross, D. S.; Williams, E. R. J. Am. Chem. Soc. 1995, 117, 6747-6757.
33. Veláuez, I. Doctoral Thesis, Uppsala University, 1999.
34. α.
35. Conformer length was taken to be the distance between the two atoms furthest apart in the structure.
36. Hünenberger, P. H.; Mark, A. E.; van Gunsteren, W. F. Proteins-Struct., Funct. Gen. 1995, 21, 196-213.
37. McCammon, J. A.; Gelin, B. R.; Karplus, M.; Wolynes, P. G. Nature 1976, 262, 325-326.
38. Brooks, B.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 4995-4999.
39. Yang, J. J.; van den Berg, B.; Pitkeathly, M.; Smith, L. J.; Bolin, K. A.; Keiderling, T. A.; Redfield, C.; Dobson, C. M.; Radford, S. E. Fold. Des. 1996, 1, 473-484.
40. Reimann, C. T.; Velazquez, I.; Tapia, O. J. Phys. Chem. B 1998, 102, 2277-2283.
41. 39
42. von Helden, G.; Hsu, M.-T.; Gotts, N.; Bowers. M. T. J. Phys. Chem. 1993, 97, 8182-8192.
43. Shvartsburg, A. A.; Jarrold, M. F. Chem. Phys. Lett. 1996, 261, 86-91.
44. 17 This exceeds by 5% the estimate provided in ref 9. The method employed in ref 9 employs an addilional "porosity factor" that is not included in our implementation.
45. Dividing a portion of an MD trajectory into 5000 "snapshots" instead of 1000 led to 〈σ〉 changing by much less than 1.0%.
46. A hydrogen bond was assumed to exist if the hydrogen donor-acceptor angle was less than 35°and if the distance between the hydrogen and the acceptor was less than 0.24 nm.
47. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577-2637.
48. Koradi, R.; Billeter, M.; Wührich, K. J. Mol. Graph. 1996, 14, 51-55.
49. Post, C. B.; Brooks, B. R.; Karplus, M.; Dobson, C. M.; Artymiuk, P. J.; Cheetham, J. C.; Phillips, D. C. J. Mol. Biol. 1986, 190, 455-479.
50. 2 contains H4-H7.
51. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
52. A donor - acceptor distance of less than 0.365 nm was used to spot instances of favorable self-solvation interactions.
53. Goldberg, M. E.; Guillou, Y. Prot. Sci. 1994, 3, 883-887.
54. Matthews, B. W. Adv. Protein Chem. 1995, 46, 249-278.
55. Buck, M.; Radford, S. E.; Dobson, C. M. Biochemistry 1993, 32, 669-678.
56. Myers, J. K.; Pace, C. N. Biophys. J. 1996, 71, 2033-2039.
57. Gross, D. S.; Williams, E. R. J. Am. Chem. Soc. 1995, 117, 883-890.
58. Wyttenbach, T.; von Helden, G.; Bowers, M. T. J. Am. Chem. Soc. 1996, 118, 8355-8364.
59. Hudgins, R. R.; Ratner, M. A.; Jarrold, M. F. J. Am. Chem. Soc. 1998, 120, 12974-12975.
60. Hudgins, R. R.; Ratner, M. A.; Jarrold, M. F. J. Am. Chem. Soc. 1999, 121, 3494-3501.
61. Hudgins, R. R.; Mao, Y.; Ratner, M. A.; Jarrold, M. F. Biophys. J. 1999, 76, 1591-1597.
62. Valentine, S. J.; Counterman, A. E.; Clemmer, D. E. J. Am. Soc. Mass Spectrom. 1999, 10, 1188-1211.
63. Valentine, S. J.; Counterman, A. E.; Hoaglund-Hyzer, C. S.; Clemmer, D. E. J. Phys. Chem. B 1999, 1203-1207.
64. Arteca, G.; Velźquez, I.; Reimann, C. T.; Tapia, O. To be submitted.
65. Arteca, G. A. Biopolymers 1996, 39, 671-680.
66. Kazmirski, S. L.; Daggett, V. J. Mol. Biol. 1998, 277, 487-506.
67. Lazaridis, T.; Karplus, M. Science 1997, 278, 1928-1931.
68. Daggett, V.; Levitt, M. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 5142-5146.
69. Vijayakumar, S.; Vishveshwara, S.; Ravishanker, G.; Beveridge, D. L. Biophys. J. 1993, 65, 2304-2312.
70. Li, A.; Daggett, V. J. Mol. Biol. 1996, 257, 412-429.
71. Caflisch, A.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 1746-1750.
72. Alonso, D. O. V.; Daggett, V. J. Mol. Biol. 1995, 247, 501-520.
73. Kantor, Y.; Kardar, M. Europhys. Lett. 1994, 27, 643-648.
74. Wolfling, S.; Kantor, Y. Phys. Rev. E 1998, 57, 5719-5725.
75. 0.5)129 or ≈19, about a factor of 2 too high but at least of the right order of magnitude. In Ref 29, no charge-related attractive terms are included in the model.
76. Ponder, J. W.; Richards, F. M. J. Mol. Biol. 1987, 193, 775-791.
77. Levitt, M.; Gerstein, M.; Huang, E.; Subbiah, S.; Tsai, J. Annu. Rev. Biochem. 1997, 66, 549-579.