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Bioinformatics Advance Access published online on March 3, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti369
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 2, 2004
Revised February 15, 2005
Accepted March 1, 2005

Article

A periodicity analysis of transmembrane helices

Hadas Leonov 1 and Isaiah T. Arkin 1*

1 The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Givat-Ram, Jerusalem, 91904, Israel

* To whom correspondence should be addressed.
Isaiah T. Arkin, E-mail: arkin{at}cc.huji.ac.il


  Abstract

Transmembrane helices and the helical bundles which they form are the major building blocks of membrane proteins. Since helices are characterized by a given periodicity it is possible to search for patterns of traits which typify one side of the helix andnot the other (e.g. amphipathic helices contain a polar and apolar sides). Using Fourier transformation we have analyzed solved membrane protein structures as well as sequences of membrane proteins from the Swiss-Prot data base. The traits searched included aromaticity, volume and ionization. While a number of motifs were already recognized in the literature, many were not. One particular example involved helix VII of Lactose permease which contains seven aromatic residues on six helical turns. Similarly six glycine residues in four consecutive helical turns were identified as forming a motif in the chloride channel. A tabulation of all the findings is presented as well as possible rationalization of the function of the motif.


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