Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT.
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.
Beuming
Thijs
T
Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.
Weinstein
Harel
H
D000465:Algorithms; D027321:Anion Transport Proteins / Q000737:chemistry*; D001436:Bacteriorhodopsins / Q000737:chemistry; D002462:Cell Membrane / Q000378:metabolism*; D003432:Cross-Linking Reagents / Q000494:pharmacology; D003460:Crystallization; D018360:Crystallography, X-Ray; D025602:Halorhodopsins / Q000737:chemistry; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008565:Membrane Proteins / Q000737:chemistry*; D008854:Microscopy, Electron / Q000379:methods*; D008958:Models, Molecular; D010070:Oxalates / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012243:Rhodopsin / Q000737:chemistry
D027321:Anion Transport Proteins; D003432:Cross-Linking Reagents; D025602:Halorhodopsins; D008565:Membrane Proteins; D010070:Oxalates; D001436:Bacteriorhodopsins; D012243:Rhodopsin