Multiple alignment of membrane proteins for measuring residual dipolar couplings using lanthanide ions bound to a small metal chelator

NMR structure determination of helical integral membrane proteins is one of the most challenging undertakings in modern structural biology. The solubilizing detergent micelle or phospholipid bicelle adds significantly to the overall size of the system, often requiring perdeuteration to obtain useable spectra. However, perdeuteration prevents structure determination using traditional NOE analysis. Residual dipolar coupling constraints are an attractive complement to NOE distance constraints, but alignment methods are limited to strained polyacrylamide gels due to the incompatibility of the solubilizing detergent or lipid with alignment media such as bicelles or phage particles. We demonstrate the use of lanthanide ions bound to the protein through a small thiol-linked metal chelator as a robust method for partial alignment of membrane proteins. This method provides multiple alignment orientations depending on the ion bound and permits RDC measurement of multiple bond vectors. We demonstrate that using this method a large number of RDCs can be measured using three-dimensional NMR methods where alignment using strained polyacrylamide gels results in fewer peaks due to drastic line-broadening.