The classical procedure for estimating the approximate size of a protein is by its sedimentation coefficient, determined either using an analytical ultracentrifuge, or sucrose gradient centrifugation. Under a given set of conditions, the speed of sedimentation of a protein (how fast it collects at the bottom of a tube spun in a centrifuge) is determined by its weight, density, shape and how it interacts with the solvent (solvation). Consequently, it is dangerous to estimate size based on the sedimentation coefficient alone.

This problem can be overcome by measuring the sedimentation equilibrium instead of the rate of sedimentation. At a lower centrifugal force, the tendency of a molecule to sediment is opposed by its tendency to diffuse. Consequently, a gradient of protein will be established over time as it is spun in a centrifuge.

opposing forces on a particle in a centrifuge tube
       /\				    \
       || diffusion <-- O --> sedimentation |

The steepness of this gradient depends only on the molecular weight and the density of the protein. The density can be calculated based on its amino acid composition.

This technique can be used to measure the weight of a protein, determine how many units assemble together (quaternary structure) and look for molecular interactions such as protein-DNA complexes.

Other techniques that can determine molecular size include: