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Protein Science (2006), 15:1987-2001. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: Relationship to biological hydrophobicity

Gang Zhao

Erwin London

Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA

(RECEIVED April 12, 2006; FINAL REVISION May 19, 2006; ACCEPTED May 19, 2006)

Hydrophobicity analyses applied to databases of soluble and transmembrane (TM) proteins of known structure were used to resolve total genomic hydrophobicity profiles into (helical) TM sequences and mainly "subhydrophobic" soluble components. This information was used to define a refined "hydrophobicity"-type TM sequence prediction scale that should approach the theoretical limit of accuracy. The refinement procedure involved adjusting scale values to eliminate differences between the average amino acid composition of populations TM and soluble sequences of equal hydrophobicity, a required property of a scale having maximum accuracy. Application of this procedure to different hydrophobicity scales caused them to collapse to essentially a single TM tendency scale. As expected, when different scales were compared, the TM tendency scale was the most accurate at predicting TM sequences. It was especially highly correlated (r = 0.95) to the biological hydrophobicity scale, derived experimentally from the percent TM conformation formed by artificial sequences passing though the translocon. It was also found that resolution of total genomic sequence data into TM and soluble components could be used to define the percent probability that a sequence with a specific hydrophobicity value forms a TM segment. Application of the TM tendency scale to whole genomic data revealed an overlap of TM and soluble sequences in the "semihydrophobic" range. This raises the possibility that a significant number of proteins have sequences that can switch between TM and non-TM states. Such proteins may exist in moonlighting forms having properties very different from those of the predominant conformation.

Keywords: Kyte-Doolittle scale; hydrophobicity; hydropathy; transmembrane helix; transmembrane sequence prediction; transmembrane tendency; transmembrane propensity


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