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Updated: Jun 23, 2026

Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)
Published on: April 20, 2015
Prediction of membrane spanning segments and topology in beta-barrel membrane proteins at better accuracy
Yu-Yen Ou1, Shu-An Chen, M Michael Gromiha
1Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan.
Abstract:
Prediction of membrane spanning segments in beta-barrel outer membrane proteins (OMP) and their topology is an important problem in structural and functional genomics. In this work, we propose a method based on radial basis networks for predicting the number of beta-strands in OMPs and identifying their membrane spanning segments. Our method showed a leave-one-out cross validation accuracy of 96% in a set of 28 OMPs, which have the range of 8-22 beta-strand segments. The beta-strand segments in OMPs and the residues in membrane spanning segments are correctly predicted with the accuracy of 96% and 87%, respectively. We have developed a web server, TMBETAPRED-RBF for predicting the transmembrane beta-strands from amino acid sequence and it is available at http://rbf.bioinfo.tw/~sachen/tmrbf.html. We suggest that our method could be an effective tool for predicting the membrane spanning regions and topology of beta-barrel membrane proteins.
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