Journal of Computer Science & Systems Biology

Detection of Key Residues Involving Functional Divergence into the Translation Elongation Factor Tu/1A Family Using Quantitative Measurements for Specific Conservation of Protein Subfamilies

Abstract

Yosuke Kondo

Delivery of an aminoacyl-tRNA to the ribosomal A-site during protein biosynthesis is mediated by elongation factor Tu/1A (EF-Tu/1A). This function is inferred as a common function of the EF-Tu/1A family. Moonlighting functions and several functional divergences are speculated in the EF-Tu/1A molecules such as actin and fibronectin binding functions. Two variant eEF1A forms, referred to as eEF1A1 and eEF1A2, are surmised to have different actin binding affinities. Mycoplasma pneumoniae EF-Tu has higher fibronectin binding affinity than M. genitalium EF-Tu. Incidentally; quantitative description for specific conservation of protein subfamilies could be helpful for assessment of the functional differences. Our paper defines two types of variability measurements of a multiple sequence alignment site. One is based upon a substitution matrix and sequence weights. The other is based upon information entropy. These variabilities are converted into a specific conservation score by the comparison of different two groups in the evolutionary branches including a target protein. Our paper describes whether the conservation score can divide different residues between two sequences with functional differences into the actin or fibronectin binding residues and the others. The result shows that the functional divergence involving the actin and fibronectin binding functions of the EF-Tu/1A molecules highly correlates with the evolutionary branches supposedly dividing their sequences. This implies that an inherent property of amino acids is an essential factor for the functional differences of the actin and fibronectin binding residues. Our paper describes one possible story for identification of key residues involving functional divergences of the human eEF1A1 and eEF1A2 molecules under the conjecture that the property of amino acids is critical. We expect that such quantitative approach is effective for further assessment of functional differences of the EF-Tu/1A subfamilies and helpful for detection of key residues involving functional divergence of protein families.