High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data

J Biomol NMR. 2011 Nov;51(3):227-33. doi: 10.1007/s10858-011-9565-6. Epub 2011 Sep 22.

Abstract

X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.

Publication types

  • Research Support, American Recovery and Reinvestment Act
  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Crystallography, X-Ray
  • Escherichia coli Proteins / chemistry
  • Membrane Proteins / chemistry*
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Conformation
  • Protein Disulfide-Isomerases / chemistry
  • X-Ray Diffraction

Substances

  • Bacterial Proteins
  • DsbB protein, Bacteria
  • Escherichia coli Proteins
  • Membrane Proteins
  • Protein Disulfide-Isomerases
  • dsbA protein, E coli

Associated data

  • PDB/2LEG