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

Thijs Beuming·Harel Weinstein
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Abstract

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 A 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.

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AlgorithmsAnion Transport ProteinsBacteriorhodopsinsCell MembraneCross-Linking ReagentsCrystallizationCrystallography, X-RayHalorhodopsinsImage Processing, Computer-AssistedMembrane ProteinsMicroscopy, ElectronModels, MolecularOxalatesProtein ConformationProtein Structure, SecondaryProtein Structure, TertiaryRhodopsinJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, U.S. Gov't, P.H.S.

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Thijs Beuming, Harel Weinstein. 2005-04-08. Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT.. https://doi.org/10.1093/protein%2Fgzi013

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