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Protein Science (2004), 13:937-945. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Experimentally based topology models for E. coli inner membrane proteins

Mikaela Rapp1, David Drew1, Daniel O. Daley1, Johan Nilsson2,3, Tiago Carvalho1,2, Karin Melén1,2, Jan-Willem De Gier1 and Gunnar Von Heijne1,2

1 Department of Biochemistry and Biophysics, and
2 Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden
3 Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden

(RECEIVED December 8, 2003; FINAL REVISION January 9, 2004; ACCEPTED January 9, 2004)



Abstract

Membrane protein topology predictions can be markedly improved by the inclusion of even very limited experimental information. We have recently introduced an approach for the production of reliable topology models based on a combination of experimental determination of the location (cytoplasmic or periplasmic) of a protein’s C terminus and topology prediction. Here, we show that determination of the location of a protein’s C terminus, rather than some internal loop, is the best strategy for large-scale topology mapping studies. We further report experimentally based topology models for 31 Escherichia coli inner membrane proteins, using methodology suitable for genome-scale studies.

Keywords: membrane proteins; topology; prediction; bioinformatics; fusion protein; PhoA; green fluorescent protein; GFP

Reprint requests to: Gunnar von Heijne, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden; e-mail: gunnar{at}dbb.su.se; fax: 46-8-15-36-79.

Supplemental material: see www.proteinscience.org

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03553804.


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