Abstract
Most known structures have been derived by X-ray crystallographic means. This technique requires good quality crystals of the protein and almost all structures are of globular proteins. Because of the difficulty of crystallising membrane bound proteins, there is a paucity of structures for these (Eisenberg, 1984). 2D NMR is a relatively new technique producing distance or angle constraints which may be used to determine structures for small proteins in solution (polypeptides of up to around 100 residues have been attempted). Both methods have the practical limitation of requiring samples of the material in appropriate form and purity.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Abagyan, R. A. and Maiorov, V. N. (1988). A simple qualitative representation of polypeptide chain folds: Comparison of protein tertiary structures. J. Biomol. Structure & Dynamics, 5 (6): 1267–1279.
Bowie, J. U., Reidhaar-Olson, J. E, Lim, W. A., and Sauer, R. T. (1990). Deciphering the message in protein sequences: Tolerance to amino acid substitutions. Science, 247: 1306–1310.
Chatfield, C. and Collins, A. J. (1989). Introduction to Multivariate Analysis. Chapman and Hall.
Chothia, C. and Janin, J. (1981). Relative orientation of close-packed β-sheets in proteins. Proc. Natl. Acad. Sci. USA, 78 (7): 4146–4150.
Chothia, C., Levitt, M., and Richardson, D. (1977). Structure of proteins: Packing of a-helices and pleated sheets. Proc. Natl. Acad. Sci. USA, 74: 4130–4134.
Chothia, C., Levitt, M., and Richardson, D. (1981). Helix to helix packing in proteins. J. Mol. Biol, 145: 215–250.
Chothia, C. (1984). Principles that determine the structure of proteins. Ann. Rev. Biochem., 53: 537–572.
Eisenberg, D. (1984). Three-dimensional structure of membrane and surface proteins. Ann. Rev. Biochem., 53: 595–623.
Finkelstein, A. V. and Ptitsyn, O. B. (1987). Why do globular proteins fit the limited set of folding patterns? Prog. Biophys. Mol. Biol., 50: 171–190.
Gray, P., Paton, N., Kemp, G., and Fothergill, J. E. (1990). An object-oriented database for protein structure analysis. Prot. Eng., 3 (4): 235–243.
Islam, S. A. and Sternberg, M. J. E. (1989). A relational database of protein structures designed for flexible enquiries about conformation. Prot. Eng., 2 (6): 431–442.
Jaenicke, R. (1987). Folding and association of proteins. Prog. Biophys. Mol. Biol., 49 (23): 117–237.
Janin, J. and Chothia, C. (1980). Packing of a-helices onto β–pleated sheets and the anatomy of aβ proteins. J. Mol. Biol., 143: 95–128.
Kabsch, W. and Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22: 2577–2637.
Lee, B. and Richards, F. M. (1971). The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol., 55: 379–40.
Murzin, A. G. and Finkelstein, A. V. (1988). General architecture of the a-helical globule. J. Mol. Biol., 204: 749–769.
Needleman, S. B. and Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48: 443–453.
Orengo, C. A. and Taylor, W. R. (1990). A rapid method of protein structure alignment. J. Theor. Biol., 147: 517–551.
Rawlings, C. J., Taylor, W. R., Nyakairu, J., Fox, J., and Sternberg, M. J. E. (1985). Reasoning about protein topology using the logic programming language PROLOG. J. Mol. Graph., 3 (4): 151–157.
Richards, F. M. and Kundrot, C. E. (1988). Identification of structural motifs from protein coordinate data: Secondary structure and first level supersecondary structure. PROTEINS: Structure, Function, & Genetics, 3: 71–84.
Richards, F. M. (1977). Areas, volumes, packing, and protein structure. Ann. Rev. Biophys. Bioeng., 6: 151–176.
Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Adv. Prot. Chem., 34: 167–339.
Richardson, J. S. (1985). Describing patterns of protein tertiary structure. Methods Enzymol., 115: 341–358.
Richmond, T. J. and Richards, F. M. (1978). Packing of a-helices: Geometrical constraints and contact areas. J. Mol. Biol., 119: 537–555.
Schulz, G. E. and Schirmer, R. H. (1979). Principles of Protein Structure. Springer-Verlag.
Taylor, W. R. and Orengo, C. (1989). Protein structure alignment. J. Mol. Biol., 208: 1–22.
Taylor, W. R. (1988). Pattern matching methods in protein sequence comparison and structure prediction. Prot. Eng., 2 (2): 77–86.
von Heijne, G. (1987). Sequence Analysis in Molecular Biology (Treasure Trove or Trivial Pursuit). Academic Press Inc.
Zvelebil, M. J., Barton, G. J., Taylor, W. R., and Sternberg, M. J. E. (1987). Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J. Mol. Biol., 195: 957–961.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1992 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Brown, N.P. (1992). Patterns in Secondary Structure Packing — a Database for Prediction. In: Taylor, W.R. (eds) Patterns in Protein Sequence and Structure. Springer Series in Biophysics, vol 7. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-76637-4_13
Download citation
DOI: https://doi.org/10.1007/978-3-642-76637-4_13
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-76639-8
Online ISBN: 978-3-642-76637-4
eBook Packages: Springer Book Archive