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 language||English (US)|
|Number of pages||11|
|Journal||Journal of biomolecular NMR|
|State||Published - 2009|
Bibliographical noteFunding Information:
Acknowledgments We would like to thank J. Hoch and B. Roux for helpful discussions, R. Bertram for sharing the DC and CSA python modules, C. Schwieters for help with the XPLOR-NIH code, and P. Gor’kov and others at the National High Magnetic Field Laboratory. This work was supported by grants to G.V. from the NIH (GM64742, HL80081, GM072701). This work was carried out in part using hardware and software provided by the University of Minnesota Supercomputing Institute.
- Hybrid method
- Membrane protein
- Molecular modeling
- Solid-state NMR
- Structural topology