A statistically derived parameterization for the collagen triple-helix

Protein Science

Volumn 11, Issue 11, 2002, Pages 2748-2754

  Rainey, Jan K ^a   Cynthia Goh, M ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Bioinformatics; Collagen; Helical wheel; Protein structure prediction; Triple helix

Indexed keywords

COLLAGEN;

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STEREOCHEMISTRY; STRUCTURE ANALYSIS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; STATISTICAL ANALYSIS;

HOMO;

AMINO ACID SEQUENCE; COLLAGEN; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY;

EID: 0036838777     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0218502     Document Type: Article

References (31)

1. Barnett, V. and Lewis, T. 1994. Outliers in statistical data, 3rd ed. John Wiley & Sons, Chichester, United Kingdom.
2. Beck, K. and Brodsky, B. 1998. Supercoiled protein motifs: The collagen triple-helix and the α-helical coiled coil. J. Struct. Biol. 122: 17-29.
3. Bella, J., Eaton, M., Brodsky, B., and Berman, H.M. 1994. Crystal and molecular structure of a collagen-like peptide at 1.9 Å resolution. Science 266: 75-81.
4. Bella, J., Brodsky, B., and Berman, H.M. 1995. Hydration structure of a collagen peptide. Structure 3: 893-906.
5. 3. Protein Sci. 11: 262-270.
6. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
7. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, Jr., E.E., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures, J. Mol. Biol. 112: 535-542.
8. Bower, M.J., Cohen, F.E., and Dunbrack, Jr., R.L. 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool. J Mol. Biol. 267: 1268-1282.
9. Brodsky, B. and Shah, N.K. 1995. Protein motifs, 8: The triple-helix motif in proteins. FASEB J. 9: 1537-1546.
10. Engh, R.A. and Huber, R. 1991. Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Crystallogr. A 47: 392-400.
11. Harbury, P.B., Tidor, B., and Kim, P.S. 1995. Repacking protein cores with backbone freedom: Structure prediction for coiled coils. Proc. Natl. Acad. Sci. 92: 8408-8412.
12. Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
13. Kajava, A.V. 2001. Proteins with repeated sequence: Structural prediction and modeling. J. Struct, Biol. 134: 132-144.
14. Klein, T.E. and Huang, C.C. 1999. Computational investigations of structural changes resulting from point mutations in a collagen-like peptide. Biopolymers 49: 167-183.
15. Kramer, R.Z., Vitagliano, L., Bella, J., Berisio, R., Mazzarella, L., Brodsky, B., Zagari, A., and Berman, H.M. 1998. X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly). J. Mol. Biol. 280: 623-638.
16. Kramer, R.Z., Bella, J., Mayville, P., Brodsky, B., and Berman, H.M. 1999. Sequence-dependent conformational variations of collagen triple-helical structure. Nat. Struct. Biol. 6: 454-457.
17. Kramer, R.Z., Venugopal, M.G., Bella, J., Mayville, P., Brodsky, B., and Berman, H.M. 2000. Staggered molecular packing in crystals of a collagen-like peptide with a single charged pair. J. Mol. Biol. 301: 1191-1205.
18. Mayo, K.H. 1996. NMR and X-ray studies of collagen model peptides. Biopolymers 40: 359-370.
19. McLachlan, A.D. 1982. Rapid comparison of protein structures. Acta Crystallogr. A 38: 871-873.
20. 10. J. Biochem. (Tokyo) 124: 1117-1123.
21. Nagarajan, V., Kamitori, S., and Okuyama, K. 1999. Structure analysis of a collagen-model peptide with a (Pro-Hyp-Gly) sequence repeat. J. Biochem. (Tokyo) 125: 310-318.
22. Okuyama, K., Takayanagi, M., Ashida, T., and Kakudo, M. 1977. New structural model for collagen. Polym. J. 9: 341-343.
23. Paige, M.F. and Goh, M.C. 2001. Ultrastructure and assembly of segmental long spacing (SLS) collagen studied by atomic force microscopy. Micron 32: 355-361.
24. Paige, M.F., Rainey, J.K., and Goh, M.C. 2001. A study of fibrous long spacing collagen ultrastructure and assembly by atomic force microscopy. Micron 32: 341-353.
25. Persikov, A.V., Ramshaw, J.A., Kirkpatrick, A., and Brodsky, B. Amino acid propensities for the collagen triple-helix. Biochemistry 39: 14960-14967.
26. 2002. Peptide investigations of pairwise interactions in the collagen triple-helix. J. Mol. Biol. 316: 385-394.
27. Rich, A. and Crick, F.H.C. 1961. Molecular structure of collagen. J. Mol. Biol. 3: 483-506.
28. Schiffer, M. and Edmundson, A.B. 1967. Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys. J. 7: 121-135.
29. Skolnick, J., Kolinski, A., and Mohanty, D. 1999. De novo predictions of the quaternary structure of leucine zippers and other coiled coils. Int. J. Quantum Chem. 75: 165-176.
30. Vitagliano, L., Berisio, R., Mazzarella, L., and Zagari, A. 2001. Structural bases of collagen stabilization induced by proline hydroxylation. Biopolymers 58: 459-464.
31. Yang, P.K., Tzou, W.S., and Hwang, M.J. 1999. Restraint-driven formation of α-helical coiled coils in molecular dynamics simulations. Biopolymers 50: 667-677.