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, tau (c), and no effect of the compression ratio on tau (c) could be discerned over the range studied (d(o)/d(N) less than or equal to 1.4). Application is demonstrated for a sample containing the first Ig-binding domain of protein G, and for a detergent-solubilized peptide.