TM Finder: a prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales

Abstract

Based on the principle of dual prediction by segment hydrophobicity and nonpolar phase helicity, in concert with imposed threshold values of these two parameters, we developed the automated prediction program TM Finder that can successfully locate most transmembrane (TM) segments in proteins. The program uses the results of experiments on a series of host-guest TM segment mimic peptides of prototypic sequence KK AAAXAAAAAXAAWAAXAAAKKKK-amide (where X = each of the 20 commonly occurring amino acids) through which an HPLC-derived hydropathy scale, a hydrophobicity threshold for spontaneous membrane insertion, and a nonpolar phase helical propensity scale were determined. Using these scales, the optimized prediction algorithm of TM Finder defines TM segments by first searching for competent core segments using the combination of hydrophobicity and helicity scales, and then performs a gap-joining operation, which minimizes prediction bias caused by local hydrophilic residues and/or the choice of window size. In addition, the hydrophobicity threshold requirement enables TM Finder to distinguish reliably between membrane proteins and globular proteins, thereby adding an important dimension to the program. A full web version of the TM Finder program can be accessed at http://www.bioinformatics-canada.org/TM/.

Fig. 1.

TM Finder output taken directly from the website (http://www.bioinformatics-canada.org/TM/). The program accepts the primary sequence in FASTA format as input, and generates a dual hydropathy/helicity plot as a function of protein primary sequence. Hydrophobicity values (red line) and helicity values (blue line) are based on input from the scales given in columns 1 and 2 of Table 1. TM segments (yellow bars) are predicted based upon considerations of segment length and gap size, in conjunction with the combined requirements of threshold hydrophobicity (>0.4) and threshold helicity (>1.1); the dual threshold is shown as a horizontal line drawn through the prediction profile. The example presented is chain III of cytochrome C oxidase (SWISSPROT accession number: P00415). The sequence used to generate this plot is ¹MTHQTHAYHM VNPSPWPLTG ALSALLMTSG LTMWFHFNSM TLLMIGLTTN ⁵¹MLTMYQWWRD VIRESTFQGH HTPAVQKGLR YGMILFIISE VLFFTGFFWA ¹⁰¹FYHS SLAPTP ELGGCWPPTG IHPLNPLEVP LLNTSVLLAS GVSITWAH HS ¹⁵¹LMEGDRKHML QALFITITLG VYFTLLQASE YYEAPFTISD GVYGSTFFVA ²⁰¹TGFHGLHVII GSTFLIVCFF RQLKFHFTSN HHFGFEAGAW YWHFVDVVWL ²⁵¹FLYVSIYWWGS²⁶¹. The plot using default parameters is shown for illustration.

Fig. 2.

TM Finder prediction for M13 major coat protein, showing hydrophobicity (red trace) and helicity (blue trace). The sequence of the protein is ¹AEGDDPAKAA ¹¹FNSLQASATE ²¹YIGYAWAMVV ³¹VIVGATIGIK ⁴¹LFKKFTSKAS⁵⁰. M13 major coat protein contains a single transmembrane segment that may extend maximally from 25–45 as deduced from nuclear magnetic resonance studies (Papavoine et al. 1998). Application of window size = 19 AA predicts the TM segment to occur at residues 19–38, while using a smaller window size = 7, the TM segment is identified at 23–42, closer to its experimentally determined location.

Fig. 3.

Transmembrane segment prediction profiles of human elastin (SWISSPROT accession number: P15502). (a) TM Finder profiles of hydrophobicity (red) and helicity (blue) (Liu and Deber 1998a,b), with the dual threshold shown as a horizontal line drawn through the prediction profiles. Hydrophobicity profiles for the same sequence are also shown for (b) the KD scale (Kyte and Doolittle 1982); (c) the GES scale (Engelman et al. 1986); and (d) the Eisenberg scale (Eisenberg et al. 1984). See text for a further discussion.