Journal article
Variation in structural location and amino acid conservation of functional sites in protein domain families
- Abstract:
- Background: The functional sites of a protein present important information for determining its cellular function and are fundamental in drug design. Accordingly, accurate methods for the prediction of functional sites are of immense value. Most available methods are based on a set of homologous sequences and structural or evolutionary information, and assume that functional sites are more conserved than the average. In the analysis presented here, we have investigated the conservation of location and type of amino acids at functional sites, and compared the behaviour of functional sites between different protein domains. Results: Functional sites were extracted from experimentally determined structural complexes from the Protein Data Bank harbouring a conserved protein domain from the SMART database. In general, functional (i.e. interacting) sites whose location is more highly conserved are also more conserved in their type of amino acid. However, even highly conserved functional sites can present a wide spectrum of amino acids. The degree of conservation strongly depends on the function of the protein domain and ranges from highly conserved in location and amino acid to very variable. Differentiation by binding partner shows that ion binding sites tend to be more conserved than functional sites binding peptides or nucleotides. Conclusion: The results gained by this analysis will help improve the accuracy of functional site prediction and facilitate the characterization of unknown protein sequences.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(bin, 1.0MB, Terms of use)
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- Publisher copy:
- 10.1186/1471-2105-6-210
Authors
- Publisher:
- BioMed Central
- Journal:
- BMC Bioinformatics More from this journal
- Volume:
- 6
- Article number:
- 210
- Publication date:
- 2005-01-01
- Edition:
- Publisher's version
- DOI:
- ISSN:
-
1471-2105
- Language:
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English
- Subjects:
- UUID:
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uuid:ed0a1189-d699-4839-b227-c49308b43385
- Local pid:
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ora:2285
- Deposit date:
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2008-09-04
- ARK identifier:
Terms of use
- Copyright holder:
- Pils et al
- Copyright date:
- 2005
- Notes:
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Citation: Pils, B. & Copley, R. R. & Schultz, J. (2005). 'Variation in structural location and amino acid conservation of functional sites in protein domain families', BMC Bioinformatics, 6:210. [Available at http://www.biomedcentral.com/1471-2105/6/210]
Copyright 2005 Pils et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- Licence:
- CC Attribution (CC BY)
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