Computational investigations of structural changes resulting from point mutations in a collagen-like peptide

Biopolymers

Volumn 49, Issue 2, 1999, Pages 167-183

  Klein, Teri E ^a   Huang, Conrad C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Collagen like peptides; Hydrogen bonding; Molecular dynamics; Triple helix

Indexed keywords

COMPUTER SIMULATION; CRYSTAL STRUCTURE; HYDROGEN BONDS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; NUCLEIC ACIDS; SOLVENTS; X RAY CRYSTALLOGRAPHY;

PROLINE HYDROXYPROLINE GLYCINE;

PROTEINS;

COLLAGEN; GLOBULAR PROTEIN; GLYCINE; HYDROGEN; HYDROXYPROLINE; NUCLEIC ACID; PEPTIDE; PROLINE; WATER;

ARTICLE; HYDROGEN BOND; MOLECULAR DYNAMICS; POINT MUTATION; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY;

COLLAGEN; COMPUTER SIMULATION; HYDROGEN BONDING; MATHEMATICAL COMPUTING; MODELS, MOLECULAR; PEPTIDES; POINT MUTATION; THERMODYNAMICS; WATER;

POA;

EID: 0033081673     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0282(199902)49:2<167::AID-BIP5>3.0.CO;2-5     Document Type: Article

References (51)

1. Bornstein, P.; Traub, W. In The Proteins; Neurath, H., Hill, R. L., Boeder, C. L., Eds.; Academic Press: New York, 1979; Vol 4, pp 412-630.
2. Kielty, C. M.; Hopkinson, I.; Grant, M. E. In Connective Tissue and its Heritable Disorders: Molecular, Genetic and Medical Aspects; Royce, P. M., Steinmann, B., Eds.; Wiley - Liss: New York, 1993; 104-147.
3. Byers, P. H. In The Metabolic and Molecular Bases of Inherited Disease: Scriver, C. R., Beaudet, A. L., Sly, W. S., Valle, D., Eds.; McGraw-Hill: New York, 1995; pp 4029-4077.
4. Vuorio, E.; de Crombrugghe, B. Ann Rev Biochem 1990, 59, 837-872.
5. Byers, P. H. In McKusick's Heritable Disorders of Connective Tissue; Beighton, P., Ed.; Mosby: St. Louis, MO, 1993; pp 33-50.
6. Piez, K. A. In Extracellular Matrix Biochemistry; Piez, K. A., Reddi, A. H., Eds.; Elsevier: New York, 1984; Chapter 1.
7. Bailey, A. J.; Robins, S. P.; Balian, G. Nature 1974, 251, 105-109.
8. Olsen, B. R. Z Zellforsch 1963, 59, 184-198.
9. Dölz, R.; Engel, J. Ann NY Acad Sci 1990, 580, 421-424.
10. Privalov, P. L. Adv Protein Chem 1982, 35, 1-104.
11. Bella, J.; Eaton, M.; Brodsky, B.; Berman, H. Science 1994, 266, 75-81.
12. Bella, J.; Brodsky, B.; Berman, H. Structure 1995, 3, 893-906.
13. Piez, K. A.; Trus, B. L. J Mol Biol 1978, 122, 419-432.
14. Cunningham, L. W.; Davies, H. A.; Hammonds, R. G., Jr. Biopolymers 1976, 15, 483-502.
15. Jones, E. Y.; Miller, A. J Mol Biol 1991, 218, 209-219.
16. Fraser, R. D. B.; MacRae, T. P.; Miller, A.; Suzuki, E. J Mol Biol 1983, 167, 497-521.
17. Némethy, G.; Scheraga, H. A. Biopolymers 1984, 23, 2781-2799.
18. Némethy, G.; Scheraga, H. A. Biochemistry 1986, 25, 3184-3188.
19. Vitagliano, L.; Némethy, G.; Zagari, A.; Scheraga, H. A. Biochemistry 1993, 32, 7354-7359.
20. Miller, M. H.; Némethy, G.; Scheraga, H. A. Macromolecules 1980, 13, 470-478.
21. Nemethy, G.; Scheraga, H. A. Bull Inst Chem Res Kyoto Univ 1989, 66, 398-408.
22. Miller, M. H.; Scheraga, H. A. J Polym Sci Polym Symp 1976, 54, 171-200.
23. Némethy, G. Biochimie 1961, 63, 125-130.
24. Némethy, G.; Givson, K. D.; Palmer, K. A.; Yoon, C. N.; Paterlini, G.; Zagari, A.; Rumsey, S.; Scheraga, H. A. J Phys Chem 1992, 96, 6472-6484.
25. Bhatnagar, R. S.; Pattabiraman, N.; Sorensen, K. R.; Langridge, R.; MacElroy, R. D.; Renugopalakrishnan, V. J Biomol Struct Dynam 1988, 6, 223-233.
26. Brodsky, B.; Li, M. H.; Long, C. G.; Apigo, J.; Baum, J. Biopolymers 1992, 32, 447-451.
27. Long, C. G.; Li, M. H.; Baum, J.; Brodsky, B. J Mol Biol 1992, 225, 1-4.
28. Long, C. G.; Braswell, E.; Zhu, D.; Apigo, J.; Baum, J.; Brodsky, B. Biochemistry 1993, 32, 11688-11695.
29. Fan, P.; Li, M. H.; Brodsky, B.; Baum, J. Biochemistry 1993, 32, 13299-13309.
30. Venugopal, M. G.; Ramshaw, J. A.; Braswell, E.; Zhu, D.; Brodsky, B. Biochemistry 1994, 33, 7948-7956.
31. Fields, C. G.; Loudahl, C. M.; Miles, A. J.; Matthias Hagen, V. L.; Fields, G. B. Biopolymers 1993, 33, 1695-1707.
32. Fields, G. B.; Prockop, D. J. Biopolymers 1996, 40, 345-357.
33. Melacini, G.; Feng, Y.; Goodman, M. Biochemistry 1997, 36, 8725-8732.
34. Goodman, M.; Melacini, G.; Feng, Y. J Am Chem Soc 1996, 118, 10928-10929.
35. Huang, C. C.; Pettersen, E. F.; Couch, G. S.; Ferrin, T. E.; Howard, A. E.; Klein, T. E. Pacific Symposium on Biocomputing 1998, 349-361.
36. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F., Jr.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. J Mol Biol 1977, 112, 535-542.
37. Abola, E. F.; Bernstein, F. C.; Bryant, S. H.; Koetzle, T. F.; Weng, J. In Crystallographic Databases - Information Content, Software Systems, Scientific Applications; Allen, F. H., Bergerhoff, G., Sievers, R., Eds.; Data Commission of the International Union of Crystallography: Bonn/Cambridge/Chester, 1987; pp 107-132.
38. Couch, G. S.; Pettersen, E. F.; Huang, C. C.; Ferrin, T. E. J Mol Graph 1995, 13, 153-158.
39. Pearlman, D. A.; Case, D. A.; Caldwell, J. C.; Seibel, G. L.; Singh, U. C.; Weiner, P.; Kollman, P. A. AMBER 4.1, University of California, San Francisco, 1995.
40. Sugeta, H.; Miyazawa, T. Biopolymers 1967, 5, 673-679.
41. Dunbrack, R. L., Jr.; Karplus, M. J Mol Biol 1993, 230, 543-574.
42. Ponder, J. W.; Richards, F. M. J Mol Biol 1987, 193, 775-791.
43. Cornell, W.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Fergueson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179-5197.
44. Bayly, C. L; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J Phys Chem 1993, 97, 10269-10280.
45. Ferrin, T. E.; Huang, C. C.; Jarvis, L. E.; Langridge, R. J Mol Graphics 1998, 6, 13-27.
46. Huang, C. C.; Pettersen, E. F.; Klein, T. E.; Ferrin, T. E.; Langridge, R. J Mol Graphics 1991, 9, 230-236.
47. Rich, A.; Crick, F. H. C. J Mol Biol 1961, 3, 483.
48. Engel, J.; Chen, H.-T.; Prockop, D. J. Biopolymers 1977, 16, 601-622.
49. Berg, R. A.; Prockop, D. J. Biochem Biophys Res Commun 1973, 52, 115-120.
50. Panaski, N., Jr.; Eberhardt, E. S.; Edison, A. S.; Powell, D. R.; Raines, R. T. Int J Peptide Protein Res 1994, 44, 262-269.
51. Homgren, S. K.; Taylor, K. M.; Bretscher, L. E.; Raines, R. T. Nature 1998, 392, 666-667.