Abstract
A method is proposed for rapidly, quantitatively comparing protein structures of arbitrary sizes, based on the differential geometric representation. The method is applied to a group of 22 protein x-ray structures, and the resulting network of closest relationships is delineated. Several well-known fold types are automatically detected as groupings of related structures, even when the constituent proteins are of different lengths. A complete gradation of types is shown to be detected, ranging from all-helical to all-beta-structure proteins. A relationship among functionally similar proteins is shown in several cases, even where their three-dimensional structures differ. It is suggested that the positions of proteins within the network of relationships correspond with their folding mechanisms.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Levitt M., Chothia C. Structural patterns in globular proteins. Nature. 1976 Jun 17;261(5561):552–558. doi: 10.1038/261552a0. [DOI] [PubMed] [Google Scholar]
- Matthews B. W., Rossmann M. G. Comparison of protein structures. Methods Enzymol. 1985;115:397–420. doi: 10.1016/0076-6879(85)15029-9. [DOI] [PubMed] [Google Scholar]
- Rackovsky S., Scheraga H. A. Intermolecular anti-parallel beta sheet: Comparison of predicted and observed conformations of gramicidin S. Proc Natl Acad Sci U S A. 1980 Dec;77(12):6965–6967. doi: 10.1073/pnas.77.12.6965. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rao S. T., Rossmann M. G. Comparison of super-secondary structures in proteins. J Mol Biol. 1973 May 15;76(2):241–256. doi: 10.1016/0022-2836(73)90388-4. [DOI] [PubMed] [Google Scholar]
- Remington S. J., Matthews B. W. A systematic approach to the comparison of protein structures. J Mol Biol. 1980 Jun 15;140(1):77–99. doi: 10.1016/0022-2836(80)90357-5. [DOI] [PubMed] [Google Scholar]
- Richardson J. S. The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981;34:167–339. doi: 10.1016/s0065-3233(08)60520-3. [DOI] [PubMed] [Google Scholar]
- Rossmann M. G., Argos P. The taxonomy of protein structure. J Mol Biol. 1977 Jan 5;109(1):99–129. doi: 10.1016/s0022-2836(77)80048-x. [DOI] [PubMed] [Google Scholar]