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Protein Science (2002), 11:2974-2980.
Copyright © 2002 The Protein Society

FOR THE RECORD

Prediction of partial membrane protein topologies using a consensus approach

Johan Nilsson1,2, Bengt Persson1,2 and Gunnar von Heijne1,3

1 Stockholm Bioinformatics Centre, AlbaNova, SE-106 91 Stockholm, Sweden
2 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
3 Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden

Reprint requests to: Gunnar von Heijne, Stockholm Bioinformatics Centre, AlbaNova, SE-106 91 Stockholm, Sweden; e-mail: gunnar{at}dbb.su.se; fax: 46-8-153679.

We have developed a method to reliably identify partial membrane protein topologies using the consensus of five topology prediction methods. When evaluated on a test set of experimentally characterized proteins, we find that approximately 90% of the partial consensus topologies are correctly predicted in membrane proteins from prokaryotic as well as eukaryotic organisms. Whole-genome analysis reveals that a reliable partial consensus topology can be predicted for ~70% of all membrane proteins in a typical bacterial genome and for ~55% of all membrane proteins in a typical eukaryotic genome. The average fraction of sequence length covered by a partial consensus topology is 44% for the prokaryotic proteins and 17% for the eukaryotic proteins in our test set, and similar numbers are found when the algorithm is applied to whole genomes. Reliably predicted partial topologies may simplify experimental determinations of membrane protein topology.

Keywords: Membrane protein; topology; consensus prediction

Abbreviations: PCT, partial consensus topology • TMH, transmembrane helix


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Copyright © 2002 by The Protein Society.