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PEDS Advance Access originally published online on April 8, 2005
Protein Engineering Design and Selection 2005 18(3):119-125; doi:10.1093/protein/gzi013
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oupjournals.org

Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT

Thijs Beuming1 and Harel Weinstein1,2,3

1Department of Physiology and Biophysics and 2Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA

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

The availability of both EM and high-resolution crystallographic data for several membrane proteins (MPs) permits a detailed evaluation of the ability of molecular modeling techniques to complement EM data in the development of models of MPs. A protocol for this purpose is presented, consisting of (1) identifying transmembrane (TM) domains from sequence; (2) assigning buried and lipid-exposed faces of the TM domains; and (3) assembling the TM domains into a bundle, based on geometric restraints obtained from the EM data. The protocol is validated by predicting the structures of several 7- and 12-TM MPs to within 3–5 Å r.m.s.d. from their crystal structures. The protocol is applied to generate a model of the oxalate transporter OxlT, for which a high-resolution structure is not yet available.

Keywords: electron microscopy/membrane proteins/MFS transporter/molecular modeling

Received July 14, 2004; revised November 22, 2004; accepted February 11, 2005.

Edited by Harold Scheraga


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