Transmembrane helix: simple or complex.

Nucleic Acids Research
Wing-Cheong WongFrank Eisenhaber

Abstract

Transmembrane helical segments (TMs) can be classified into two groups of so-called 'simple' and 'complex' TMs. Whereas the first group represents mere hydrophobic anchors with an overrepresentation of aliphatic hydrophobic residues that are likely attributed to convergent evolution in many cases, the complex ones embody ancestral information and tend to have structural and functional roles beyond just membrane immersion. Hence, the sequence homology concept is not applicable on simple TMs. In practice, these simple TMs can attract statistically significant but evolutionarily unrelated hits during similarity searches (whether through BLAST- or HMM-based approaches). This is especially problematic for membrane proteins that contain both globular segments and TMs. As such, we have developed the transmembrane helix: simple or complex (TMSOC) webserver for the identification of simple and complex TMs. By masking simple TM segments in seed sequences prior to sequence similarity searches, the false-discovery rate decreases without sacrificing sensitivity. Therefore, TMSOC is a novel and necessary sequence analytic tool for both the experimentalists and the computational biology community working on membrane proteins. It is freely acc...Continue Reading

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Feb 18, 2011·Journal of Bioinformatics and Computational Biology·Wing-Cheong WongFrank Eisenhaber

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Citations

Oct 28, 2015·Journal of Bioinformatics and Computational Biology·Westley Arthur ShermanFrank Eisenhaber
Nov 18, 2015·PLoS Computational Biology·Alejandro OchoaMona Singh
Mar 25, 2020·Biochimica Et Biophysica Acta. Biomembranes·Steven C WangMilton H Saier

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Software Mentioned

ClusterX
PSI
DASTM
blast
TMSOC
HMMTOP
Phobius
TMHMM
PhobiusTM
SAPS

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