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Bioinformatics Advance Access published online on February 26, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth143
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 20, 2003
Revised January 10, 2004
Accepted January 11, 2004

Article

A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins

Thijs Beuming 1 Harel Weinstein 2*

1 1Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY 10029
2 1Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY 10029; 2Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY 10021

* To whom correspondence should be addressed. E-mail: haw2002{at}med.cornell.edu.


  Abstract

Motivation: The dearth of structural data on {alpha}-helical membrane proteins (MPs) has hampered thus far the development of reliable knowledge-based potentials that can be used for automatic prediction of transmembrane (TM) protein structure. While algorithms for identifying TM segments are available, modeling of the TM domains of {alpha}-helical MPs involves assembling the segments into a bundle. This requires the correct assignment of the buried and lipid-exposed faces of the TM domains.

Results: A recent increase in the number of crystal structures of {alpha}-helical MPs has enabled an analysis of the lipid-exposed surfaces and the interiors of such molecules on the basis of structure, rather than sequence alone. Together with a conservation criterion that is based on previous observations that conserved residues are mostly found in the interior of MPs (Stevens and Arkin 2001), the bias of certain residue types to be preferably buried or exposed is proposed as a criterion for predicting the lipid-exposed and interior faces of TMs. Applications to known structures demonstrates 80% accuracy of this prediction algorithm.

Availability: The algorithm used for the predictions is implemented in the ProperTM web-server (http://icb.med.cornell.edu/services/propertm/start).


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