A theoretical study of the substituent effect on the stability of collagen

Journal of Theoretical and Computational Chemistry

Volumn 3, Issue 2, 2004, Pages 225-243

  Quan, Jun Min ^a   Wu, Yun Dong ^a,b  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

^b PEKING UNIVERSITY   (China)

Author keywords

Collagen; Computation; Stability; Substituent effect

Indexed keywords

AMIDE; COLLAGEN; GLYCINE; HYDROGEN; PROLINE; TRIPEPTIDE;

AQUEOUS SOLUTION; ARTICLE; CALCULATION; CONFORMATION; DENSITY FUNCTIONAL THEORY; ELECTRICITY; ENERGY; THEORETICAL MODEL; THEORETICAL STUDY;

EID: 84962426703     PISSN: 02196336     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219633604001008     Document Type: Article

References (63)

1. (a) Nimni ME (ed.), Collagen, Vols. 1-4, CRC Press, Boca Raton, FL, 1988.
2. (b) Ramachandran GN, Reddi AH (eds.), Biochemistry of Collagen, Plenum Press, New York, 1976.
3. Fraser RDB, MacRae TP, Suzuki E, J Mol Biol 129:463, 1979.
4. +).
5. (a) Engel J, Chen H-T, Prockop DJ, Klup H, Biopolymers 16:601, 1977.
6. (b) Tumanyan VG, Esipova NG, Biopolymers 21:475, 1982.
7. (c) Bansal M, Ananthanarayanan VS, Biopolymers 27:299, 1988.
8. Fietzek PP, Kuhn K, Mol Cell Biochem 8:141, 1975.
9. (a) Van der Rest M, Garrone R, FASEB J 5:2814, 1991.
10. (b) Van der Rest M, Garrone R, Herbage D, Adv Mol Cell Biol 6:1, 1993.
11. (c) Prockop DJ, Kivirikko KI, Ann Rev Biochem 64:403, 1995.
12. (a) Chopra RK, Ananthanarayanan VS, Proc Natl Acad Sci USA, 79:7180, 1982.
13. (b) Privalov PL, Adv Prot Chem, 35:1, 1982.
14. (c) Berg RA, Prockop DJ, Biochem Biophys Res Commun 52:115, 1973.
15. (d) Michael SA, Manjiri B, Nigel S, Konrad B, John AMR, Barbara B, J Biol Chem 274:7668-7673, 1999.
16. (a) Woodruff CW, Ascorbic acid-scurvy, Prog Food Nutr Sci 1:493-506, 1975.
17. (b) Prockop DJ, Kivirikko KI, Ann Rev Biochem 64:403, 1995.
18. Inouye K, Kobayashi Y, Kyogoku Y, Kishida Y, Sakakibara S, Prockop DJ, Arch Biochem Biophys 219:198, 1982.
19. Inouye K, Sakakibara S, Prockop DJ, Biochim Biophys Acta 420:133, 1976.
20. (a) Bella J, Eaton M, Brodsky B, Berman HM, Science 266:75, 1994.
21. (b) Bella J, Brodsky B, Berman HM, Structure 3:893, 1995.
22. (c) Kramer RZ, Berman HM, J Biomol Struct Dynam 16:367, 1998.
23. Nagarajan V, Kamitori S, Okuyama K, J Biochem 125:310, 1999.
24. (a) Holmgrem SK, Taylor KM, Bretscher LE, Raines RT, Nature 392:666, 1998.
25. (b) Eberhardt ES, Panasik N, Jr., Raines RT, J Am Chem Soc 118:2261, 1996.
26. (c) Holmgrem SK, Bretscher LE, Taylor KM, Raines RT, Chem Biol 6:63, 1999.
27. (a) Kramer RZ, Vitagliano L, Bella J, Berisio R, Mazzarella L, Brodsky B, Zagari A, Berman HM, J Mol Biol 280:623, 1998.
28. (b) Berisio R, Vitagliano L, Sorrentino G, Carotenuto L, Piccolo C, Mazzarella L, Acta Crystallogr, Sect D 56:55, 2000.
29. (c) Vitagliano L, Berisio R, Mazzarella L, Zagari A, Biopolymers 58:459, 2001.
30. (d) Berisio R, Vitagliano L, Mazzarella L, Zagari A, Prot Sci 11:262, 2002.
31. (a) Li M-H, Fan P, Brodsky B, Baum J, Biochemistry 32:7377-7387, 1993.
32. (b) Nagarajan V, Kamitori S, Okuyama K, J Biochem 124:1117-1123, 1998.
33. (a) O'Hagan D, Bilton C, Howard JAK, Knight L, Tozer DJ, J Chem Soc, Perkin Trans 2:605-607, 2000.
34. (b) Murcko MA, DiPaola RA, J Am Chem Soc 114: 10010-10018, 1992.
35. (c) Olson WK, Sussman JL, J Am Chem Soc 104:270-278, 1982.
36. Babu R, Ganesh KN, J Am Chem Soc 123:2079, 2001.
37. (a) Improta R, Benzi C, Barone V, J Am Chem Soc 123:12568-12577, 2001.
38. (b) DeRider ML, Wilkens SJ, Waddell MJ, Bretscher LE, Weinhold F, Raines RT, Markley JL, J Am Chem Soc 124:2497-2505, 2002.
39. (c) Improta R, Mele F, Crescenzi O, Benzi C, Barone V, J Am Chem Soc 124:7857, 2002.
40. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson BG, Chen W, Wong MW, Andres JL, Head-Gordon M, Replogle ES, Pople JA, Gaussian 98 (Revision A.9), Gaussian, Inc., Pittsburgh, PA, 1998.
41. (a) Becke AD, J Chem Phys 98:5648, 1993.
42. (b) Lee C, Yang W, Parr R, Phys Rev B 37:785, 1988.
43. Foresman JB, Keith TA, Wiberg KB, Snoonian J, Frisch MJ, J Phys Chem 100:16098, 1996.
44. Frisch MJ, Trucks GW, Schlegel HB, Gill PMW, Johnson BG, Robb MA, Cheeseman JR, Keith TA, Petersson GA, Montgomery JA, Raghavachari K, Al-Laham MA, Zakrzewski VG, Ortiz JV, Foresman JB, Cioslowski J, Stefanov BB, Nanayakkara A, Challacombe M, Peng CY, Ayala PY, Chen W, Wong MW, Andres JL, Replogle ES, Gomperts R, Martin RL, Fox DJ, Binkley JS, Defrees DJ, Baker J, Stewart JP, Head-Gordon M, Gonzalez C, Pople JA, Gaussian 94 (Revision B.3), Gaussian, Inc.: Pittsburgh, PA, 1995.
45. (a) Kramer RZ, Vitagliano L, Bella J, Berisio R, Mazzarella, L, Brodsky B, Zagari A, Berman HM, J Mol Biol 280:623-638, 1998.
46. (b) Nemethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA, J Phys Chem 96:6472, 1992.
47. (a) Wu Y-D, Zhao Y-L, J Am Chem Soc 123:5313, 2001.
48. (b) Zhao Y-L, Wu Y-D, J Am Chem Soc 124:1570, 2002.
49. (c) Wu Y-D, Lin J-Q, Zhao Y-L, Helv Chim Acta 85: 3144, 2002.
50. (d) Lin J-Q, Luo S-W, Wu Y-D, J Comput Chem 23:1551, 2002.
51. (a) Boys SF, Bernardi F, Mol Phys 19:553, 1970.
52. (b) Meunier A, Levy B, Berthier G, Theor Chim Acta 29:49, 1973.
53. (c) Jansen HB, Ros P, Chem Phys Lett 3:40, 1969.
54. (a) Bretscher LE, Jenkins CL, Taylor KM, DeRider ML, Raines RT, J Am Chem Soc 123:777-778, 2001.
55. (b) Renner C, Alefelder S, Bae JH, Budisa N, Huber R, Moroder L, Angew Chem Int Ed 40:923-925, 2001.
56. (a) Deslongchamp P, Stereoelectronic Effects in Organic Chemistry, Perganon Press, New York, 1983.
57. (b) Thatcher GRJ (ed.), The Anomeric Effect and Associated Stereoelectronic Effects, American Chemical Society, Washington, DC, 1993.
58. (a) Miertu S, Scrocco E, Tomasi J, Chem Phys 55:117, 1981.
59. (b) Amovilli C, Barone V, Cammi R, Cances E, Cossi M, Mennucci B, Pomelli CS, Tomasi J, Adv Quant Chem 32:227, 1998.
60. (c) Barone V, Cossi M, Tomasi, J Chem Phys 107:3210, 1997.
61. Nagarajan V, Kamitori S, Okuyama K, J Biochem 124:1117, 1998.
62. Okuyama K, Nagarajan V, Kamitori S, Proc Indian Acad Sci (Chem Sci) 111:19, 1999.
63. We thank one of the referees for the suggestion.