Prediction of transmembrane β‐strands from hydrophobic characteristics of proteins

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Abstract
The assembly of outer-membrane proteins consisting of beta-strands as transmembrane segments is somewhat more complex when compared to the assembly of inner membrane proteins having alpha-helices as transmembrane parts. This is probably due to the difference in the amino acid sequences of the transmembrane part strands and helices. Because of this feature, most predictive schemes which are successful in predicting transmembrane helical segments fail to predict transmembrane strand segments. Here we propose a new predictive scheme for forecasting the transmembrane strand segments in outer-membrane proteins with the use of the general surrounding hydrophobicity scale developed both for the globular and membrane proteins in the preceding article. Two major features of the scheme are (i) that it does not solely depend on the amphipathic character of a sequence segment while identifying it as a transmembrane strand, and it is capable of predicting strands in varied lengths, a facility to reflect the variation in the membrane surfaces. This scheme predicts the transmembrane beta-strands in porin from R. capsulatus at 76% accuracy (giving due weights to over- and under-predictions when compared to X-ray results). The predicted beta-structure contents in OmpA, porin from E. coli and maltoporin compared with the Raman spectroscopic results at 95% level. These accuracy levels are far superior than the levels obtained from other existing methods. Apart from the above four proteins for which experimental informations are available, ten other outer-membrane proteins, for which there is no information about their secondary structure, are considered in the forecast. The results are analysed and the common features in the folds of the set of fourteen outer-membrane proteins are deduced.