Detection of an ancient principle and an elegant solution to the protein classification problem

Details Detection of an ancient principle and an elegant solution to the protein classification problem Detection of an ancient principle and an elegant solution to the protein classification problem

2007-08-16

arxiv.org/abs/0708.2121v1

Biology

Quantitative Biology

Genomics

13p

Scientific paper

This work is concerned with the development of a well-founded, theoretically justified, and least complicated metric for the classification of proteins with reference to enzymes. As the signature of an enzyme family, a catalytic domain is easily fingerprinted. Given that the classification problem has so far seemed intractable, a classification schema derived from the catalytic domain would be satisfying. Here I show that there exists a natural ab initio if nonobvious basis to theorize that the catalytic domain of an enzyme is uniquely informative about its regulation. This annotates its function. Based on this hypothesis, a method that correctly classifies potassium ion channels into their respective subfamilies is described. To put the principle on firmer ground, extra validation was sought and obtained through co-evolutionary analyses. The co-evolutionary analyses reveal a departure from the notion that potassium ion channel proteins are functionally modular. This finding is discussed in light of the prevailing notion of domain. These studies establish that significant co-evolution of the catalytic domain of a gene with its conjoint domain is a specialized, necessary process following fusion and swapping events in evolution. Instances of this discovery are likely to be found pervasive in protein science.

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