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

Overview

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.

publication date

  • April 8, 2005

Research

keywords

  • Anion Transport Proteins
  • Cell Membrane
  • Image Processing, Computer-Assisted
  • Membrane Proteins
  • Microscopy, Electron

Identity

Scopus Document Identifier

  • 18344369377

Digital Object Identifier (DOI)

  • 10.1093/protein/gzi013

PubMed ID

  • 15820982

Additional Document Info

volume

  • 18

issue

  • 3