A method to detect transmembrane helical segments at the nucleotide level.
The analysis of base distributions at the three codon positions, in sequences coding for integral inner membrane proteins from Bacteria, reveal a global excess of thymine and a depletion of adenine, at codon position two. These genes were scanned using a sliding window, in which the average ratio of T to A at the second position of codons, TA(2) (converted to a logarithm, the LTA2 ratio) was computed. The profiles obtained reveal sharp and local peaks of the LTA2 ratio, which account for the high mean values of this parameter. For inner membrane proteins of known structure, the position and extent of these peaks correlate with the location of transmembrane alpha-helices. The prediction accuracy of the detection of such structures using the LTA2 ratio compares to that obtained using algorithms based on an hydrophobicity index of amino-acids. This new criterion presents several advantages, as it deals directly with the nucleotide sequence, does not rely on the values of empirical parameters and finds direct applications in molecular biology studies. Since the nucleotide sequences of transmembrane beta-strands do not give rise to peaks in the LTA2 ratio profile, the criterion appears to characterize exclusively alpha-helical segments in transmembrane proteins.
Lesnik
T
T
Centre de Genetique Moleculaire, France. THIERRY.LESNIK@CGM.CNRS-GIF.FR
Reiss
C
C
D001419:Bacteria / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D004269:DNA, Bacterial / Q000032:analysis* / Q000235:genetics; D005798:Genes, Bacterial; D008565:Membrane Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D008565:Membrane Proteins