Site specificity of theαC - H bond dissociation energy for a naturally occurring β-hairpin peptide - An ab initio study

Journal of Computational Chemistry

Volumn 30, Issue 3, 2009, Pages 407-414

  Cheng, Wan Chun ^a   Jang, Soonmin ^b   Wu, Chen Chang ^a   Lin, Ren Jie ^a   Lu, Hsiu Feng ^c   Li, Feng Yin ^a  

^a NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

^b Sejong University   (South Korea)

^c INSTITUTE OF CHEMISTRY   (Taiwan)

Author keywords

Alpha C center radical; Beta hairpin; Bond dissociation energy; Naturally occurring

Indexed keywords

ABSTRACTING; AMINES; ELECTRONIC STRUCTURE; OXIDATION;

AB INITIO STUDIES; AB-INITIO CALCULATIONS; ALPHA-C-CENTER RADICAL; BETA-HAIRPIN; BOND DISSOCIATION ENERGY; C-H BOND DISSOCIATION ENERGIES; C-H BONDS; NATURALLY OCCURRING;

DISSOCIATION;

PEPTIDE; PROTEIN;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; HYDROGEN BOND; OXIDATION REDUCTION REACTION; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; QUANTUM THEORY; VIBRATION;

COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, CHEMICAL; OXIDATION-REDUCTION; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; QUANTUM THEORY; VIBRATION;

EID: 59849126349     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21066     Document Type: Article

References (56)

1. (a) Stadtman, E. R. Science 1992, 257, 1220;
2. (b) Berlett, B. S.; Stadtman, E. R. J Biol Chem 1997, 272, 20313;
3. (c) Stadtman, E. R. Free Radic Biol Med 2002, 33, 597;
4. (d) Stadtman, E. R., Levine, R. L. Amino Acids 2003, 25, 207;
5. (e) Stadtman, E. R,; Van Remmen, H.; Richardson, A.; Wehr, N. B.; Levine, R. L. Biochim Biophys Acta 2005, 1703, 135;
6. (f) Stadtman, E. R. Free Radic Res 2006, 40, 1250.
7. Garrison, W. M. Chem Rev 1987, 87, 381 and reference therein.
8. (a) Smith, M. A.; Sayre, L. M.; Monnier, V. M.; Perry, G. TINS 1995, 18, 172;
9. (b) Zhu, X.; Raina, A. K.; Lee, H.; Casadesus, G.; Smith, M. A.; Perry, G. Brain Res 2004, 1000, 32;
10. (c) Schöneich, C. Biochim Biophys Acta 2005, 1703, 111;
11. (d) Glaser, C. B.; Yamin, G.; Uversky, V. N.; Fink, A. L. Biochim Biophys Acta 2005, 1703, 157;
12. (e) Gracy, R. W.; Talent, J. M.; Kong, Y.; Conrad, C. C. Mutat Res 1999, 428, 17;
13. (f) Dalle-Donne, I.; Giustarini, D.; Colombo, R.; Rossi, R.; Milzani, A. Trends Mol Med 2003, 9, 169;
14. (g) Akaike, T. Rev Med Virol 2001, 11, 87.
15. (a) Hawkins, C. L.; Davies, M. J. Biochim. Biophys Acta 1997, 1360, 84;
16. (b) Hawkins, C. L.; Davies, M. J. Biochim Biophys Acta 2001, 1504, 196;
17. (c) Davies, M. J. Biochim Biophys Acta 2005, 1703, 93.
18. Binda, C.; Mattevi, A.; Edmondson, D. E. J Biol Chem 2002, 277, 23973.
19. Brennan, M.-L.; Hazen, S. L. Amino Acids 2003, 25, 365.
20. (a) Lin, M. T.; Beal, M. F. Clin Neurosci Res 2003, 2, 305.
21. (b) Beal, M. F. Free Radic Biol Med 2002, 32, 797.
22. (c) Sohal, R. S. Free Radic Biol Med 2002, 33, 37;
23. (d) Cadenas, E.; Davies, K. J. A. Radic Biol Med 2000, 29, 222;
24. (e) Van Remmen, H.; Richardson, A. Exp Gerontol 2001, 36, 957.
25. Dalle-Donne, I.; Scaloni, A.; Giustarini, D.; Cavarra, E.; Tell, G.; Lungarella, G.; Colombo, B.; Rossi, R.; Milzani, A. Mass Spectrom. Rev 2005, 24, 55.
26. Murahashi, S.-I.; Mitani, A.; Kitao, K. Tetrahedron Lett 2000, 41, 10245.
27. Pius, K.; Chandrasekhar, J. Chem Commun 1900, 41.
28. (a) Armstrong, D. A.; Yu, D.; Rauk, A. Can J Chem. 1996, 74, 1192;
29. (b) Rauk, A,; Yu, D.; Armstrong, D. A. J. Am Chem Soc 1997, 119, 208;
30. (c) Block, D. A.; Yu, D.; Armstrong, D. A.; Rauk, A. Can J Chem 1998, 76, 1042;
31. (d) Jonsson, M.; Wayner, D. D. M.; Armstrong, D. A.; Yu, D.; Rauk, A. J Chem Soc Perkin Trans 2, 1998, 1967;
32. (e) Rauk, A.; Yu, D.; Armstrong, D. A. J Am Chem Soc. 1998, 120, 8848;
33. (f) Rauk, A.; Yu, D.; Taylor, J.; Shustov, G. V.; Block, D. A.; Armstrong, D. A. Biochemistry 1998, 38, 9089;
34. (g) Rauk, A.; Armstrong, D. A. J Am. Chem Soc 2000, 122, 4185.
35. (a) Galano, A.; Alvarez-Idaboy, J. R.; Montero, L. A.; Vivier-Bunge, A. J Comput Chem 2001, 22, 1138;
36. (b) Galano, A.; Alvarez-Idaboy, J. R.; Bravo-Pérez, G.; Ruiz-Santoyo Ma, E. J Mol Struct (Theochem) 2002, 617, 77;
37. (c) Galano, A.; Alvarez-Idaboy, J. R.; Cruz-Torres, A.; Ruiz-Santoyo Ma, E. J Mol Struct (Theochem) 2003, 629, 165;
38. (d) Galano, A.; Alvarez-Idaboy, J. R.; Cruz-Torres, A.; Ruiz-Santoyo Ma, E. Int J Chem Kinet 2003, 35, 212;
39. (e) Galano, A.; Alvarez-Idaboy, J. R.; Agacino-Valdés, E.; Ruiz-Santoyo Ma E. J Mol Struct (Theochem) 2004, 676, 97.
40. Štefanić, I.; Bonifačić, M.; Asmus, K.-.D.; Armstrong, D. A. J Phys Chem A 2001, 105, 8681.
41. Lu, H. F, Li, F. Y., Lin, S. H. J Comput Chem 2007, 28, 783.
42. Shinya, H.; kazuhiko, Y.; Yoshito, S.; Hisayuki, M. Structure 2004, 12, 1507.
43. Fedorov, D. G.; Ishida, T.; Uebayasi, M.; Kitaura, K. J Phys Chem A 2007, 111, 2722.
44. Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M. Chem Phys Lett 1999, 313, 701.
45. (a) Barone, V.; Cossi, M. J Phys Chem A. 1998, 102, 1995;
46. (b) Cossi, M.; Rega N.; Scalmani, G.; Barone, V. J Comput Chem 2003, 24, 669.
47. Frisch, M. J.; G. Trucks, W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A.; Vreven, Jr., T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian; Gaussian, Inc.: Pittsburgh PA, 2003
48. Takano, Y.; Houk, K. N. J Chem. Theory Comput 2005, 1, 70.
49. Ding, Y.; Krogh-Jespersen. J. Comput Chem 1996, 3, 338.
50. Tortonda, F. R.; Pascual-Ahuir, J. L.; Silla, E.; Tunon, I. Chem Phys Lett 1996, 260, 21.
51. Fernadez-Romos, A.; Smedarchina, Z.; Siebrand W.; Zgierski, M. Z. J Chem Phys 2000, 113, 9714.
52. Leung, L.; Rempe, S. B. J Chem Phys 2005, 122, 184506.
53. Balta, B.; Avivente, V. J. Comput Chem 2003, 24, 1789.
54. Garrison, W. M. Chem. Rev 1987, 87, 381.
55. Guex, N.; Peitsch, M. C. Electrophoresis 1997, 18, 2714.
56. Owen, M. C.; Koma'romi, I.; Murphy, R. F.; Lovas, S. J Mol Struct (Theochem) 2006, 759, 117.