Abstract
The average crystal structure of a collagen-model peptide, (Pro-Pro-Gly)9 has been determined at 1.0Å resolution. Crystals belong to an orthorhombic system (P212121) with cell parameters of a=26.82(2), b=26.33(2), and c=20.25(2)Å. The X-Ray oscillation photograph clearly showed satellite spots with an 80 Å axial repeat on both sides of the strong spots on the layer lines corresponding to c=20Å. The existence of c=80Å axial repeat suggests that the longer repeat along the c-axis is the shortest integral multiply of the helical repeat (20Å) enough to accommodate one (Pro-Pro-Gly)9 molecule and an appropriate gap between adjacent molecules. According to the reflection data with c=20Å axial repeat, the overall peptide structure is very close to the left-handed 7/2-helical model for collagen. Based on the difference Fourier map, 34 water molecules were added in the asymmetric unit of seven triplets. Of which 14 water molecules make hydrogen bonds with peptide chains and rest of them participate in hydrogen bonds only with other water molecules.
Similar content being viewed by others
Article PDF
References
A. Rich and F. H. C. Crick, J. Mol. Biol., 3, 483 (1961).
K. Okuyama, M. Takayanagi, T. Ashida, and M. Kakudo, Polym. J., 9, 341 (1977).
K. Okuyama, N. Tanaka, T. Ashida, and M. Kakudo, Bull. Chem. Soc. Jpn., 49, 1805 (1976).
K. Okuyama, K. Okuyama, S. Arnott, M. Takayanagi, and M. Kakudo, J. Mol. Biol., 152, 427 (1981).
P. J. C. Smith and S. Arnott, Acta Crystallogr., Sect. A, 34, 3 (1978).
V. Nagarajan, S. Kamitori, and K. Okuyama, J. Biochem., 124, 1117 (1998).
R. Z. Kramer, L. Vitagliano, J. Bella, R. Berisio, L. Mazzarella, B. Brodsky, A. Zagari, and H. M. Berman, J. Mol. Biol., 280, 623 (1998).
V. Nagarajan, S. Kamitori, and K. Okuyama, J. Biochem., 125, 310 (1999).
J. Bella, M. Eaton, B. Brodsky, and H. M. Berman, Science, 266, 75 (1994).
R. Z. Kramer, J. Bella, P. Mayville, B. Brodsky, and H. M. Berman, Nat. Struct. Biol., 6, 454 (1999).
R. Z. Kramer, M. G. Venugopal, J. Bella, P. Mayville, B. Brodsky, and H. M. Berman, J. Mol. Biol., 301, 1191 (2000).
R. Berisio, L. Vitagliano, G. Sorrentino, L. Carotenuto, C. Piccolo, L. Mazzararella, and A. Zagari, Acta Crystallogr., Sect. D, 56, 55 (2000).
L. Vitagliano, R. Berisio, L. Mazzarella, and A. Zagari, Biopolymers, 58, 459 (2001).
A. R. Mitchell, B. W. Erickson, M. N. Ryabtsev, R. S. Hodges, and R. B. Merrifield, J. Am. Chem. Soc., 98, 7357 (1976).
S. Sakakibara, Y. Kishida, Y. Kikuchi, R. Sakai, and K. Kakiuchi, Bull. Chem. Soc. Jpn., 41, 1273 (1968).
E. Kaiser, R. L. Colescott, C. D. Rossingor, and P. I. Cook, Anal. Biochem., 34, 595 (1970).
A. T. Brunger, “A System for X-Ray Crystallography and NMR, X-PLOR Version 3.1”, Yale University Press, New Haven, CT, 1992.
G. M. Sheldric and T. R. Schneidern, “In Methods in Enzymology”, R. M. Sweet and C. W. Cater, Jr., Ed., Academic Press, Inc., Orlando, FL, 1997, vol. 277, pp 319–343.
E. M. Duncan, “Practical Protein Crystallography”, Academic Press, Inc., New York, N.Y., 1993.
G. N. Ramachandran and V. Sasisekuharan, Biochim. Biophys. Acta, 109, 314 (1965).
H. Sugeta and T. Miyazawa, Biopolymers, 5, 673 (1967).
K. Okuyama, Y. Saga, M. Nakayama, and M. Narita, Biopolymers, 31, 975 (1991).
A. Yonath and W. Traub, J. Mol. Biol., 43, 461 (1969).
Y. Obata and K. Okuyama, Kobunshi Ronbunshu, 51, 371 (1994).
M. H. Li, P. Fan, B. Brodosky, and J. Baum, Biochemistry, 32, 7377 (1993).
B. Grunbaum and G. C. Shephard, “Tilings and Patterns”, Freeman, New York, N.Y., 1987.
S. Sakakibara, Y. Kishida, K. Okuyama, N. Tanaka, T. Ashida, and M. Kakudo, J. Mol. Biol., 65, 371 (1972).
K. Okuyama, C. Hongo, K. Noguchi, G. Wu, and T. Ohuchi, unpublished data.
K. Okuyama, V. Nagarajan, and S. Kamitori, Proc. -Indian Acad. Sci., Chem. Sci., 111, 19 (1999).
C. K. Johnson, ORTEP II. Report ORNL-5138, Oak Ridge National Laboratory, Oak Ridge, TN, 1976.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Hongo, C., Nagarajan, V., Noguchi, K. et al. Average Crystal Structure of (Pro-Pro-Gly)9 at 1.0Å Resolution. Polym J 33, 812–818 (2001). https://doi.org/10.1295/polymj.33.812
Issue Date:
DOI: https://doi.org/10.1295/polymj.33.812
Keywords
This article is cited by
-
Parallels between DNA and collagen – comparing elastic models of the double and triple helix
Scientific Reports (2017)