Protein Science, Vol 7, Issue 11 2413-2420, Copyright © 1998 by Cold Spring Harbor Laboratory Press

ARTICLE

Prediction by a neural network of outer membrane {beta}-strand protein topology

K. DIEDERICHS, J. FREIGANG, S. UMHAU, K. ZETH and J. BREED
Universitat Konstanz, Fakultat fur Biologie (M656), D-78457 Konstanz, Germany

An artificial neural network (NN) was trained to predict the topology of bacterial outer membrane (OM) {beta}-strand proteins. Specifically, the NN predicts the z-coordinate of C{alpha} atoms in a coordinate frame with the outer membrane in the xy-plane, such that low z-values indicate periplasmic turns, medium z-values indicate transmembrane {beta}-strands, and high z-values indicate extracellular loops. To obtain a training set, seven OM proteins (porins) with structures known to high resolution were aligned with their pores along the z-axis. The relationship between C{alpha} z-values and topology was thereby established. To predict the topology of other OM proteins, all seven porins were used for the training set. Z-values (topologies) were predicted for two porins with hitherto unknown structure and for OM proteins not belonging to the porin family, all with insignificant sequence homology to the training set. The results of topology prediction compare favorably with experimental topology data.
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