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Protein Engineering, Vol. 12, No. 7, 557-561, July 1999
© 1999 Oxford University Press

A simple method for predicting transmembrane {alpha} helices with better accuracy

M. Michael Gromiha

Tsukuba Life Science Center, The Institute of Physical and Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan

The prediction of a protein's structure from its amino acid sequence has been a long-standing goal of molecular biology. In this work, a new set of conformational parameters for membrane spanning {alpha} helices was developed using the information from the topology of 70 membrane proteins. Based on these conformational parameters, a simple algorithm has been formulated to predict the transmembrane {alpha} helices in membrane proteins. A FORTRAN program has been developed which takes the amino acid sequence as input and gives the predicted transmembrane {alpha}-helices as output. The present method correctly identifies 295 transmembrane helical segments in 70 membrane proteins with only two overpredictions. Furthermore, this method predicts all 45 transmembrane helices in the photosynthetic reaction center, bacteriorhodopsin and cytochrome c oxidase to an 86% level of accuracy and so is better than all other methods published to date.

Keywords: conformational parameter/prediction/topology/transmembrane {alpha} helices


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