The size of a protein
determines the rate of its passage through a molecular sieve
. Molecular sieves consist of small particles which have a network
within which particles up to a certain size limit can enter (called gel filtration because the suspension
of particles is tightly packed and jelly like). Proteins, when interacting with these particles, spend part of their time inside the sieve, and part of the time in the bulk solution
. The smaller the protein, the higher the probability
that it can enter one of these pores. If you imagine a column of such a material with liquid flowing through it, pushing a mixture of proteins down the column ... those proteins which are smaller will move slower because they keep jumping in and out of the pores, while the bigger proteins will just flow through. If you add the protein at the top of the column and collect the liquid that comes off the bottom, you will get liquid that contains sequentially smaller and smaller proteins.
The size of a protein that is measured by gel filtration is the average volume it occupies in solution. This volume is characterized by a Stoke's radius, which is sensitive to both the size and the shape of the protein, much the same as in sedimenation analysis. For proteins which are unfolded, the mobility on a gel filtration column is more directly correlated with size because all the proteins are generally in a random coil shape.
See also: SDS-PAGE, Analytical Ultracentrifugation, Mass Spectrometry