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This article is part of the supplement: The 2007 International Conference on Bioinformatics & Computational Biology (BIOCOMP'07)

Open Access Research

Investigation of transmembrane proteins using a computational approach

Jack Y Yang1, Mary Qu Yang2, A Keith Dunker3, Youping Deng4* and Xudong Huang1*

Author Affiliations

1 Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA

2 National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA

3 Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, 410 W. 10th Street, Indianapolis, IN 46202, USA

4 Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, 39406, USA

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BMC Genomics 2008, 9(Suppl 1):S7  doi:10.1186/1471-2164-9-S1-S7

Published: 20 March 2008

Abstract

Background

An important subfamily of membrane proteins are the transmembrane α-helical proteins, in which the membrane-spanning regions are made up of α-helices. Given the obvious biological and medical significance of these proteins, it is of tremendous practical importance to identify the location of transmembrane segments. The difficulty of inferring the secondary or tertiary structure of transmembrane proteins using experimental techniques has led to a surge of interest in applying techniques from machine learning and bioinformatics to infer secondary structure from primary structure in these proteins. We are therefore interested in determining which physicochemical properties are most useful for discriminating transmembrane segments from non-transmembrane segments in transmembrane proteins, and for discriminating intrinsically unstructured segments from intrinsically structured segments in transmembrane proteins, and in using the results of these investigations to develop classifiers to identify transmembrane segments in transmembrane proteins.

Results

We determined that the most useful properties for discriminating transmembrane segments from non-transmembrane segments and for discriminating intrinsically unstructured segments from intrinsically structured segments in transmembrane proteins were hydropathy, polarity, and flexibility, and used the results of this analysis to construct classifiers to discriminate transmembrane segments from non-transmembrane segments using four classification techniques: two variants of the Self-Organizing Global Ranking algorithm, a decision tree algorithm, and a support vector machine algorithm. All four techniques exhibited good performance, with out-of-sample accuracies of approximately 75%.

Conclusions

Several interesting observations emerged from our study: intrinsically unstructured segments and transmembrane segments tend to have opposite properties; transmembrane proteins appear to be much richer in intrinsically unstructured segments than other proteins; and, in approximately 70% of transmembrane proteins that contain intrinsically unstructured segments, the intrinsically unstructured segments are close to transmembrane segments.