Protein Engineering vol. 16 no. 7 pp. 479-488, 2003
© 2003 Oxford University Press
Identification of transmembrane protein functions by binary topology patterns
1Department of Electronic and Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan 2Present address: Graduate School of Humanity and Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
3 To whom correspondence should be addressed. e-mail: slsimi{at}si.hirosaki-u.ac.jp
We propose a novel method for identifying and classifying the functions of transmembrane (TM) proteins based on their TM topology [the number of TM segments (tms), the loop length and the N-terminus location]. In this method, the TM topology is expressed as a string of ‘0’ and ‘1’, and this is designated the binary topology pattern (BTP). We focused on TM proteins with up to 12 tms, with the exception of 1 and 9 tms, and classified them into 37 functional groups by the number of tms and the functional annotation. These grouped TM protein sequences were used to determine BTPs which are specific to the individual functional groups. Since the evaluated accuracies (sensitivity, specificity and self-consistency) of these patterns in functional identification were quite high overall, i.e. 0.940, 0.934 and 0.935, respectively, as averaged over the 37 functional groups, we confirmed that TM protein function can be identified by the number of tms and the characteristics of loop lengths, i.e. BTPs.
Received December 28, 2002; revised May 31, 2003; accepted June 8, 2003.
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