A refinement protocol to determine structure,topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints |
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Authors: | Lei Shi Nathaniel J Traaseth Raffaello Verardi Alessandro Cembran Jiali Gao Gianluigi Veglia |
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Institution: | (1) Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;(2) Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA |
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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, E
z (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.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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Keywords: | Hybrid method Membrane protein Molecular modeling Structural topology PISEMA Solid-state NMR |
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