Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins

Ashkenazi, S. , Snir, R. and Ofran, Y. (2012) Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins. Bioinformatics, 28(24), pp. 3203-3210. (doi: 10.1093/bioinformatics/bts608) (PMID:23080118)

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Abstract

Motivation: Assessing the false positive rate of function prediction methods is difficult, as it is hard to establish that a protein does not have a certain function. To determine to what extent proteins with similar sequences have a common function, we focused on photosynthesis-related proteins. A protein that comes from a non-photosynthetic organism is, undoubtedly, not involved in photosynthesis. Results: We show that function diverges very rapidly: 70% of the close homologs of photosynthetic proteins come from non-photosynthetic organisms. Therefore, high sequence similarity, in most cases, is not tantamount to similar function. However, we found that many functionally similar proteins often share short sequence elements, which may correspond to a functional site and could reveal functional similarities more accurately than sequence similarity. Conclusions: These results shed light on the way biological function is conserved in evolution and may help improve large-scale analysis of protein function.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Ashkenazi, Shaul
Authors: Ashkenazi, S., Snir, R., and Ofran, Y.
College/School:College of Science and Engineering > School of Computing Science
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Published Online:18 October 2012

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