A simple apparatus for generating stretched polyacrylamide gels, yielding uniform alignment of proteins and detergent micelles*

Compressed and stretched polyacrylamide hydrogels previously have been shown to offer a robust method for aligning proteins. A simple, funnel-like apparatus is described for generating uniformly stretched hydrogels. For prolate-shaped proteins, gels stretched in the direction of the magnetic field yield two-fold larger alignment than gels compressed to the same aspect ratio in this direction. Empirically, protein alignment is found to be proportional to (c–2.3)² [(d_o/d_N)³-1], where d_o and d_N are the diameters of the cylindrical gels before and after stretching, respectively, and c is the polyacrylamide weight fraction in percent. Low gel densities, in the 4–7% range, are found to have minimal effects on macromolecular rotational correlation times, _c, and no effect of the compression ratio on _c could be discerned over the range studied (d_o/d_Nle1.4). Application is demonstrated for a sample containing the first Ig-binding domain of protein G, and for a detergent-solubilized peptide.