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

Thijs Beuming | Zendy; Harel Weinstein | Zendy

Open Access

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

Author(s) -

Thijs Beuming,

Harel Weinstein

Publication year - 2005

Publication title -

protein engineering design and selection

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.627

H-Index - 109

eISSN - 1741-0134

pISSN - 1741-0126

DOI - 10.1093/protein/gzi013

Subject(s) - resolution (logic) , transporter , oxalate , cryo electron microscopy , electron microscope , membrane , membrane protein , chemistry , biophysics , nanotechnology , computational biology , materials science , crystallography , biochemistry , biology , computer science , physics , artificial intelligence , optics , inorganic chemistry , gene

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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