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Updated: May 17, 2026

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry
Published on: March 13, 2014
Assessing the relationship between conservation of function and conservation of sequence using photosynthetic
Shaul Ashkenazi1, Rotem Snir, Yanay Ofran
1The Goodman faculty of life sciences, Bar Ilan University, Ramat Gan 52900, Israel.
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.
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