A Photon-Free Approach to Transmembrane Protein Structure Determination

The structures of membrane proteins are generally solved using samples dissolved in micelles, bicelles, or occasionally phospholipid bilayers using X-ray diffraction or magnetic resonance. Because these are less than perfect mimics of true biological membranes, the structures are often confirmed by evaluating the effects of mutations on the properties of the protein in their native cellular environments. Low-resolution structures are also sometimes generated from the results of site-directed mutagenesis when other structural data are incomplete or not available. Here, we describe a rapid and automated approach to determine structures from data on site-directed mutants for the special case of homo-oligomeric helical bundles. The method uses as input an experimental profile of the effects of mutations on some property of the protein. This profile is then interpreted by assuming that positions that have large effects on structure/function when mutated project toward the center of the oligomeric bundle. Model bundles are generated, and correlation analysis is used to score which structures have inter-subunit Cβ distances between adjoining monomers that best correlate with the experimental profile. These structures are then clustered and refined using energy-based minimization methods. For a set of 10 homo-oligomeric TM protein structures ranging from dimers to pentamers, we show that our method predicts structures to within 1–2 Å backbone RMSD relative to X-ray and NMR structures. This level of agreement approaches the precision of NMR structures solved in different membrane mimetics.

Graphical AbstractFigure optionsDownload high-quality image (203 K)Download as PowerPoint slideHighlights
► Low-resolution biological data can be used to effectively model transmembrane helical bundles.
► Correlation analysis can be used as a filter in modeling transmembrane helical bundles.
► A combination of correlation analysis and a van der Waals clash filter can be used to generate ensembles of low-RMSD (to native) helical bundles.
► The proposed modeling method can be used to complement existing NMR structural determination methods.