Analysis of protein complex formation, microtubules and cytoskeleton
Determination of the sedimentation coefficient of a protein, traditionally in a 5-20% sucrose gradient, in order to determine its molecular mass, is a technique that was developed many years ago.
Although alternative methods, notably polyacrylamide gel electrophoresis, have achieved a wide popularity, there are certain situations that are better suited to density gradients, for example the analysis of heavily glycosylated proteins, which run anomalously on gels. Another area that may be better suited to density gradient analysis is the study of protein-protein interactions.
The standard sucrose gradient analysis, which is carried out in swinging-bucket rotors for 4-16 h, may be less than ideal for determining protein-protein interactions. Macromolecular complexes may be insufficiently stable to survive these long centrifugation times and they may be intolerant of the high hydrostatic pressures generated in a swinging-bucket rotor [1,2].
In addition Timasheff  pointed out that solutions of low water activity (high osmolality) can remove bound water from proteins and could cause changes in stability of the protein and its propensity to aggregate.
The use Nycodenz will reduce the osmolality (raise the water activity) of gradients considerably, while with iodixanol gradients can be made isoosmotic throughout the entire useful density range.
Gradient made from one
or other of these solutes may therefore be an important advantage in studying protein-protein
interactions in density gradients. Some reports also highlight the functional problems associated with
sucrose gradients; for example these caused proteolysis of a kinesin-related motor protein, while in
iodixanol gradients there was no proteolysis whatsoever .