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FOR THE RECORD

Asymmetric amino acid compositions of transmembrane -strands

Department of Chemistry and Biochemistry, University of California, Los Angeles-Department of Energy Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California 90095-1570, USA

(RECEIVED March 30, 2004; FINAL REVISION May 11, 2004; ACCEPTED May 12, 2004)

In contrast to water-soluble proteins, membrane proteins reside in a heterogeneous environment, and their surfaces must interact with both polar and apolar membrane regions. As a consequence, the composition of membrane proteins’ residues varies substantially between the membrane core and the interfacial regions. The amino acid compositions of helical membrane proteins are also known to be different on the cytoplasmic and extracellular sides of the membrane. Here we report that in the 16 transmembrane -barrel structures, the amino acid compositions of lipid-facing residues are different near the N and C termini of the individual strands. Polar amino acids are more prevalent near the C termini than near the N termini, and hydrophobic amino acids show the opposite trend. We suggest that this difference arises because it is easier for polar atoms to escape from the apolar regions of the bilayer at the C terminus of a -strand. This new characteristic of -barrel membrane proteins enhances our understanding of how a sequence encodes a membrane protein structure and should prove useful in identifying and predicting the structures of trans-membrane -barrels.

Keywords: barrel; membrane protein; snorkeling; membrane polarity; protein structure; genome

Reprint requests to: James U. Bowie, Department of Chemistry and Biochemistry, University of California, Los Angeles-DOE Center for Genomics and Proteomics, Molecular Biology Institute, Boyer Hall, University of California, Los Angeles, 611 Charles E. Young Drive E., Los Angeles, CA 90095-1570, USA; e-mail: bowie{at}mbi.ucla.edu; fax: (310) 206-4749.

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04777304.

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