High resolution KSCN/CsSCN equilibrium gradients effectively separate a population of density labeled proteins from unlabeled proteins

The persistence of proteins in a number of biological systems has been analyzed by density labeling techniques; however, the utility of this approach has been severely hampered by poor resolution between densitylabeled and unlabeled proteins on equilibrium gradients. A high resolution equilibrium salt gradient composed of KSCN/CsSCN has been developed to effectively separated density-labeled proteins (¹³C-¹⁵N-²H-substituted) from unlabeled proteins. The resolution of this system is approximately twofold greater than that previously achieved with cesium formate/guanidine hydrochloride equilibrium gradients which have been used in many recent protein density labeling studies. In order to examine the extent of cross-contamination between density-labeled and unlabeled proteins in a KSCN/CsSCN gradient system, density-labeled chick epidermal proteins were mixed with unlabeled Drosophila larval proteins and then separated on these equilibrium gradients. From individual gradient fractions, proteins were recovered and fractionated on a sodium dodecyl sulfate-polyacrylamide gel, demonstrating the virtually complete separation between the two populations. The general utility of this system for protein stability studies is also demonstrated.