A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints

Lei Shi, Nathaniel J. Traaseth, Raffaello Verardi, Alessandro Cembran, Jiali Gao, Gianluigi Veglia

Research output: Contribution to journalArticle

Abstract

To fully describe the fold space and ultimately the biological function of membrane proteins, it is necessary to determine the specific interactions of the protein with the membrane. This property of membrane proteins that we refer to as structural topology cannot be resolved using X-ray crystallography or solution NMR alone. In this article, we incorporate into XPLOR-NIH a hybrid objective function for membrane protein structure determination that utilizes solution and solid-state NMR restraints, simultaneously defining structure, topology, and depth of insertion. Distance and angular restraints obtained from solution NMR of membrane proteins solubilized in detergent micelles are combined with backbone orientational restraints (chemical shift anisotropy and dipolar couplings) derived from solid-state NMR in aligned lipid bilayers. In addition, a supplementary knowledge-based potential, Ez (insertion depth potential), is used to ensure the correct positioning of secondary structural elements with respect to a virtual membrane. The hybrid objective function is minimized using a simulated annealing protocol implemented into XPLOR-NIH software for general use.

Original languageEnglish (US)
Pages (from-to)195-205
Number of pages11
JournalJournal of Biomolecular NMR
Volume44
Issue number4
DOIs
StatePublished - Jul 15 2009

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Keywords

  • Hybrid method
  • Membrane protein
  • Molecular modeling
  • PISEMA
  • Solid-state NMR
  • Structural topology

ASJC Scopus subject areas

  • Biochemistry
  • Spectroscopy

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