- Article -
| In Silico Biology 6, 0025 (2006); ©2006, Bioinformation Systems e.V. |
Basic faced α-helices are widespread in the peptide extensions of the eukaryotic aminoacyl-tRNA synthetases
Steven E. Massey
Biology Dept., University of South Florida, 4202E Fowler Ave, Tampa, Florida, USA
* Corresponding author
Email: semassey@chuma1.cas.usf.edu
Edited by E. Wingender; received December 12, 2005; revised March 24, 2006; accepted April 22, 2006; published May 06, 2006
Abstract
Three aminoacyl-tRNA synthetases from yeast, one from plants and one from mammals possess unusual structures at their N termini, namely α helices with basic residues distributed asymmetrically, on a single face of the helix. It is unknown if these 'basic faced' α helices (BFAHs) are unique to the aminoacyl-tRNA synthetases. Analysis of the amino acid sequences of these five aminoacyl-tRNA synthetases using the hydrophobic moment algorithm failed to accurately identify the BFAHs. A new algorithm was therefore developed, called the 'basic moment'. This is a Fourier analysis procedure that predicts the distribution of basic residues within protein secondary structure. The basic moment identifies with a high degree of accuracy the five known BFAHs and also identifies further potential BFAHs at evolutionarily conserved positions in the peptide extensions of aspartyl-, lysyl- and valyl- tRNA synthetases from a range of eukaryotic species. In addition, the algorithm identifies the two-helix pair tRNA binding domain of alanyl-tRNA synthetase, implying that the domain includes a BFAH. The functional and evolutionary aspects of these structural features are discussed.
Keywords: aminoacyl-tRNA synthetase, basic moment, α-helix, hydrophobic moment, Fourier analysis