Determining the subunit structure of phosphodiesterases using gel filtration and sucrose density gradient centrifugation.

Size-exclusion chromatography (gel filtration) is a widely used method to determine the molecular weight of a protein. Often, the elution volume of several standard proteins is plotted against their known molecular weight to generate a standard curve, which is then used to determine the molecular weight of the protein of interest by its elution volume. However, gel filtration does not measure the mass of a particle as such, but the Stokes radius (Rs), a property dependent on mass, shape, and hydration of a protein. Thus, this method works well only if the protein of interest has a spherical symmetrical shape and an average hydration level. For all other proteins, the use of gel filtration as the sole means to determine the molecular weight will be misleading. The molecular weight of any given protein can be calculated, however, using the method of Siegel and Monty. This method combines Stokes radii obtained from gel filtrations and sedimentation coefficients derived from density gradient centrifugations to calculate the mass of a protein independently of its shape or hydration. It has been shown previously that PDE4D3, a representative of the long PDE4 splice forms, behaves as a dimer, whereas PDE4D2, a prototype of the short PDE4 splice forms, is a monomer. Both proteins exhibit an anomalous behavior on gel filtration columns. For this reason, they are used in this study to demonstrate the necessity of performing both gel filtration and density gradient centrifugation to determine the molecular weight of a protein.