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Bioinformatics 2005 21(Suppl 1):i378-i386; doi:10.1093/bioinformatics/bti1035
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains

Tali Sadka 1 and Michal Linial 2,*,{dagger}

1School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem 91904, Israel
2Department of Biological Chemistry, The Hebrew University of Jerusalem 91904, Israel

*To whom correspondence should be addressed.

Summary: In eukaryotes, membranous proteins account for 20–30% of the proteome. Most of these proteins contain one or more transmembrane (TM) domains. These are short segments that transverse the bilayer lipid membrane. Various properties of the TM domains, such as their number, their topology and their arrangement within the membrane, are closely related to the protein's cellular functions. The properties of the TM domains also determine the cellular targeting and localization of these proteins. It is not known, however, whether the information encoded by TM domains suffices for the purpose of classifying proteins into their functional families. This is the question we address here. We introduce an algorithm that creates a profile of each functional family of membranous proteins based only on the amino acid composition of their TM domains. This is complemented by a classifier program for each such family (to determine whether a given protein belongs to it or not). We find that in most instances TM domains contain enough information to allow an accurate discrimination of ~80% sensitivity and ~90% specificity among unrelated polytopic functional families with the same number of TM domains.

Contact: michall{at}cc.huji.ac.il

Supplementary information: Available at www.protonet.cs.huji.ac.il/TM/

Received on January 15, 2005; accepted on March 27, 2005

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