Structural basis for the varying propensities of different amino acids to adopt the collagen conformation

Journal of Physical Chemistry B

Volumn 115, Issue 11, 2011, Pages 2593-2607

  S Sundar, Raman ^a,b   Gopalakrishnan, R ^a   Wade, R C ^b   Subramanian, V ^a  

^a CENTRAL LEATHER RESEARCH INSTITUTE   (India)

^b HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CARBOXYLIC ACIDS; COLLAGEN; CONFORMATIONS; HYDROGEN; MOLECULAR DYNAMICS; STABILITY;

CLASSICAL MOLECULAR DYNAMICS; COLLAGEN-LIKE PEPTIDES; EXPERIMENTAL STUDIES; HOST-GUESTS; INTERCHAIN HYDROGEN BONDS; MD SIMULATION; NATURALLY OCCURRING; SOLVENT INTERACTIONS; STRUCTURAL BASIS; STRUCTURAL STABILITIES; TRIPLE-HELICAL COLLAGEN;

HYDROGEN BONDS;

EID: 79952740484     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp109133v     Document Type: Article

References (77)

1. Brodskyk, B.; Persikov, A. V. Molecular structure of the collagen triple helix Fibrous Proteins: Coiled-Coils, Collagen and Elastomers 2005, 70, 301
2. Hulmes, D. J. S. The collagen superfamily - Diverse structures and assemblies Essays Biochem. 1992, 27, 49
3. Scordino, A.; Grasso, R.; Gulino, M.; Lanzano, L.; Musumeci, F.; Privitera, G.; Tedesco, M.; Triglia, A.; Brizhik, L. Hydration Effects on Photophysical Properties of Collagen. In Self-Organization of Molecular Systems: From Molecules and Clusters to Nanotubes and Proteins; Russo, N.; Antonchenko, V. Y.; Kryachko, E. S., Eds.; Springer: Berlin, 2009; Vol. 14, 359.
4. Exposito, J. Y.; Valcourt, U.; Cluzel, C.; Lethias, C. Int. J. Mol. Sci. 2010, 11, 407
5. Hattori, S. Sen-i Gakkaishi 2009, 65, 453
6. Fullerton, G. D.; Rahal, A. J. Magn. Reson. Imaging 2007, 25, 345
7. Bravo, J. F. Rev. Med. Chile 2009, 137, 1488
8. Bodian, D. L.; Madhan, B.; Brodsky, B.; Klein, T. E. Biochemistry 2008, 47, 5424
9. Persikov, A. V.; Pillitteri, R. J.; Amin, P.; Schwarze, U.; Byers, P. H.; Brodsky, B. Hum. Mutat. 2004, 24, 330
10. Kahan, V.; Andersen, M. L.; Tomimori, J.; Tufik, S. Brain Behavior and Immunity 2009, 23, 1089
11. Brodsky, B.; Baum, J. Nature 2008, 453, 998
12. Baum, J.; Brodsky, B. FASEB J. 1998, 12, 116
13. Li, Y. J.; Brodsky, B.; Baum, J. J. Biol. Chem. 2009, 284, 20660
14. Liu, X. Y.; Kim, S.; Dai, Q. H.; Brodsky, B.; Baum, J. Biochemistry 1998, 37, 15528
15. Battineni, M. L.; Yang, W.; Liu, X. Y.; Baum, J.; Brodsky, B. Matrix Biol. 1996, 15, 174
16. Ramachandran, G. N.; Kartha, G. Nature 1955, 176, 593
17. Rich, A.; Crick, F. H. C. Nature 1955, 176, 915
18. Okuyama, K.; Okuyama, K.; Arnott, S.; Takayanagi, M.; Kakudo, M. J. Mol. Biol. 1981, 152, 427
19. Leikin, S.; Parsegian, V. A.; Yang, W. H.; Walrafen, G. E. Proc. Natl.Acad. Sci. U.S.A. 1997, 94, 11312
20. Bhatnagar, R. S.; Gough, C. A.; Qian, J. J.; Shattuck, M. B. Proc.-Indian Acad. Sci., Chem. Sci. 1999, 111, 301
21. Melacini, G.; Bonvin, A.; Goodman, M.; Boelens, R.; Kaptein, R. J. Mol. Biol. 2000, 300, 1041
22. Xu, Y. J.; Persikov, A.; Jordan, J. A.; Brodsky, B. Biophys. J. 2000, 78, 2504
23. Xu, Y. J.; Bhate, M.; Brodsky, B. Biochemistry 2002, 41, 8143
24. Persikov, A. V.; Ramshaw, J. A. M.; Kirkpatrick, A.; Brodsky, B. J. Am. Chem. Soc. 2003, 125, 11500
25. Simon-Lukasik, K. V.; Persikov, A. V.; Brodsky, B.; Ramshaw, J. A. M.; Laws, W. R.; Ross, J. B. A.; Ludescher, R. D. Biophys. J. 2003, 84, 501
26. Handgraaf, J. W.; Zerbetto, F. Proteins: Struct., Funct., Bioinf. 2006, 64, 711
27. Shoulders, M. D.; Hodges, J. A.; Raines, R. T. J. Am. Chem. Soc. 2006, 128, 8112
28. Bryan, M. A.; Brauner, J. W.; Anderle, G.; Flach, C. R.; Brodsky, B.; Mendelsohn, R. J. Am. Chem. Soc. 2007, 129, 7877
29. Brodsky, B.; Thiagarajan, G.; Madhan, B.; Kar, K. Biopolymers 2008, 89, 345
30. Improta, R.; Berisio, R.; Vitagliano, L. Protein Sci. 2008, 17, 955
31. Madhan, B.; Xiao, J. X.; Thiagarajan, G.; Baum, J.; Brodsky, B. J. Am. Chem. Soc. 2008, 130, 13520
32. Shoulders, M. D.; Raines, R. T. Modulating Collagen Triple Helix Stability with 4-Chloro, 4-Fluoro, and 4-Methylprolines. In Peptides for Youth: The Proceedings of the 20th American Peptide Symposium; DelValle, S.; Escher, E.; Lubell, W. D., Eds.; Springer: New York, 2009; Vol. 611, p 251.
33. Zhang, W. H.; He, Q.; Liao, X. P.; Shi, B. J. Am. Leather Chem. Assoc. 2009, 104, 244
34. Bronco, S.; Cappelli, C.; Monti, S. J. Phys. Chem. B 2004, 108, 10101
35. Monti, S.; Bronco, S.; Cappelli, C. J. Phys. Chem. B 2005, 109, 11389
36. Janko, M.; Zink, A.; Gigler, A. M.; Heckl, W. M.; Stark, R. W. Proc. R. Soc. B 2010, 277, 2301
37. Ramshaw, J. A. M.; Shah, N. K.; Brodsky, B. J. Struct. Biol. 1998, 122, 86
38. Kar, K.; Ibrar, S.; Nanda, V.; Getz, T. M.; Kunapuli, S. P.; Brodsky, B. Biochemistry 2009, 48, 7959
39. Brodsky, B.; Thiagarajan, G.; Madhan, B.; Kar, K. Biopolymers 2008, 89, 345
40. Bella, J.; Liu, J.; Kramer, R.; Brodsky, B.; Berman, H. M. J. Mol. Biol. 2006, 362, 298
41. Persikov, A. V.; Ramshaw, J. A. M.; Kirkpatrick, A.; Brodsky, B. Biochemistry 2005, 44, 1414
42. Persikov, A. V.; Ramshaw, J. A. M.; Brodsky, B. J. Biol. Chem. 2005, 280, 19343
43. Persikov, A. V.; Pillitteri, R. J.; Amin, P.; Schwarze, U.; Byers, P. H.; Brodsky, B. Hum. Mutat. 2004, 24, 330
44. Persikov, A. V.; Ramshaw, J. A. M.; Kirkpatrick, A.; Brodsky, B. Biochemistry 2000, 39, 14960
45. Persikov, A. V.; Ramshaw, J. A. M.; Kirkpatrick, A.; Brodsky, B. J. Mol. Biol. 2002, 316, 385
46. Persikov, A. V.; Kirkpatrick, A.; Ramshaw, J. A. M.; Brodsky, B. Biophys. J. 2002, 82, 1424
47. Persikov, A. V.; Ramshaw, J. A. M.; Brodsky, B. Biopolymers 2000, 55, 436
48. Doss-Pepe, E.; Deprez, P.; Inestrosa, N. C.; Brodsky, B. Biochemistry 2000, 39, 14884
49. Buevich, A. V.; Dai, Q. H.; Liu, X. Y.; Brodsky, B.; Baum, J. Biochemistry 2000, 39, 4299
50. Kramer, R. Z.; Bella, J.; Mayville, P.; Brodsky, B.; Berman, H. M. Nat. Struct. Biol. 1999, 6, 454
51. Shah, N. K.; Ramshaw, J. A. M.; Kirkpatrick, A.; Shah, C.; Brodsky, B. Biochemistry 1996, 35, 10262
52. Berisio, R.; De Simone, A.; Ruggiero, A.; Improta, R.; Vitagliano, L. J. Pept. Sci. 2009, 15, 131
53. Okuyama, K.; Narita, H.; Kawaguchi, T.; Noguchi, K.; Tanaka, Y.; Nishino, N. Biopolymers 2007, 86, 212
54. Raman, S. S.; Vijayaraj, R.; Parthasarathi, R.; Subramanian, V.; Ramasami, T. J. Mol. Struct. (THEOCHEM) 2008, 851, 299
55. Raman, S. S.; Parthasarathi, R.; Subramanian, V.; Ramasami, T. J. Phys. Chem. B 2008, 112, 1533
56. Raman, S. S.; Parthasarathi, R.; Subramanian, V.; Ramasami, T. J. Phys. Chem. B 2006, 110, 20678
57. Persikov, A. V.; Ramshaw, J. A. M.; Brodsky, B. J. Biol. Chem. 2005, 280, 19343
58. Jenkins, C. L.; Bretscher, L. E.; Raines, R. T. Abstr. Pap.-Am. Chem. Soc. 2001, 222, 230
59. Huang, C. C.; Couch, G. S.; Pettersen, E. F.; Ferrin, T. E.; Howard, A. E.; Klein, T. E. Pac. Symp. Biocomput. 98 1998, 349
60. Park, S.; Klein, T. E.; Pande, V. S. Biophys. J. 2007, 93, 4108-4115
61. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins: Struct., Funct., Bioinf. 2006, 65, 712
62. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Klein, M. L. J. Chem. Phys. 1983, 79, 926
63. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
64. Lobanov, M.; Bogatyreva, N.; Galzitskaya, O. J. Mol. Biol. 2008, 42, 623
65. Shikata, T.; Yoshida, N.; Minakawa, A.; Okuyama, K. J. Phys. Chem. B 2009, 113, 9055
66. Shikata, T.; Minakawa, A.; Okuyama, K. J. Phys. Chem. B 2009, 113, 14504
67. Okuyama, K.; Hongo, C.; Wu, G. H.; Mizuno, K.; Noguchi, K.; Ebisuzaki, S.; Tanaka, Y.; Nishino, N.; Bachinger, H. P. Biopolymers 2009, 91, 361
68. Boudko, S. P.; Engel, J.; Okuyama, K.; Mizuno, K.; Bachinger, H. P.; Schumacher, M. A. J. Biol. Chem. 2008, 283, 32580
69. Stetefeld, J.; Frank, S.; Jenny, M.; Schulthess, T.; Kammerer, R. A.; Boudko, S.; Landwehr, R.; Okuyama, K.; Engel, J. Structure 2003, 11, 339
70. Hongo, C.; Nagarajan, V.; Noguchi, K.; Kamitori, S.; Okuyama, K.; Tanaka, Y.; Nishino, N. Polym. J. 2001, 33, 812
71. Okuyama, K.; Nagarajan, V.; Kamitori, S. Proc.-Indian Acad. Sci., Chem. Sci. 1999, 111, 19
72. Okuyama, K.; Tanaka, N.; Ashida, T.; Kakudo, M.; Sakakibaka, S.; Kishida, Y. J. Mol. Biol. 1972, 72, 571
73. Bansal, M Int. J. Pept. Protein Res. 1977, 9, 224
74. Kramer, R. Z.; Bella, J.; Brodsky, B.; Berman, H. M. J. Mol. Biol. 2001, 311, 131
75. Yang, W.; Chan, V. C.; Kirkpatrick, A.; Ramshaw, J. A. M.; Brodsky, B. J. Biol. Chem. 1997, 272, 28837
76. Persikov, A. V.; Ramshaw, J. A. M.; Kirkpatrick, A.; Brodsky, B. Biochemistry 2005, 44, 1414
77. Bella, J.; Brodsky, B.; Berman, H. M. Structure 1995, 3, 893