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Science 27 May 2005:
Vol. 308. no. 5726, pp. 1321 - 1323
DOI: 10.1126/science.1109730
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Reports

Global Topology Analysis of the Escherichia coli Inner Membrane Proteome

Daniel O. Daley,1* Mikaela Rapp,1* Erik Granseth,2 Karin Melén,2 David Drew,1 Gunnar von Heijne1,2{dagger}

The protein complement of cellular membranes is notoriously resistant to standard proteomic analysis and structural studies. As a result, membrane proteomes remain ill-defined. Here, we report a global topology analysis of the Escherichia coli inner membrane proteome. Using C-terminal tagging with the alkaline phosphatase and green fluorescent protein, we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins. By constraining a topology prediction algorithm with this data, we derived high-quality topology models for the 601 proteins, providing a firm foundation for future functional studies of this and other membrane proteomes. We also estimated the overexpression potential for 397 green fluorescent protein fusions; the results suggest that a large fraction of all inner membrane proteins can be produced in sufficient quantities for biochemical and structural work.

1 Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
2 Stockholm Bioinformatics Center, AlbaNova, SE-106 91 Stockholm, Sweden.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: gunnar{at}dbb.su.se

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