Considering discrete protein pools when measuring the dynamics of nuclear membrane proteins

Measuring dynamics of nuclear proteins is complicated by the fact that many DNA- and chromatin-binding proteins have separate nucleoplasmic and nuclear membrane pools with distinct mobilities. Moreover, when measuring recoveries in FRAP experiments, it is important to be aware that the continuous transport of new protein through the nuclear pore complexes means that fluorescence recovery comes from both dynamic exchange of protein already within the nucleus and newly imported protein. Here we describe fluorescence recovery after photobleaching and photoactivation techniques designed to track nuclear membrane proteins and some methods we have developed that may help to distinguish these various pools. A combination of these approaches with standard FRAP approaches is necessary to understand the true dynamics of nuclear proteins.