Detection of transmembrane helical segments at the nucleotide level in eukaryotic membrane protein genes

The analysis of base distributions at the three codon positions, in sequences coding for polytopic membrane proteins from Eukaryotes, reveals a global excess of thymine and a depletion of adenine, at the second codon position. These genes were scanned using a sliding window, in which the average ratio of T over A at the second position of codons was computed. The scan shows that sharp peaks of this ratio, which are responsible for the high mean value of this parameter in the genes, correlate closely with the transmembrane segments of the membrane proteins. These results are quite similar to our previous findings for bacterial polytopic inner membrane proteins. This establishes the ratio of T over A at codon position two as a universal parameter for both the characterization of the genes of polytopic membrane proteins, and for the location of alpha-helical, transmembrane segments of these proteins.