Hi Debajyoti, Migration of proteins in SDS containing gels is dependent on hydrophobicity, the amount of SDS that your protein binds (despite the fact that in theory all proteins should behave the same way under these conditions) and charge. Highly basic or acidic proteins will migrate anomalously, thermophilic proteins (which are usually more highly charged and hydrophobic) also tend to migrate anomalously..membrane proteins also because they usually tend to interact differently with the detergent; it is not unusual to observe stable non-covalent homo-oligomers of membrane proteins even in an SDS-PAGE gel. Phosphorylation and glycosylation will also affect the apparent MW as estimated from the SDS-PAGE experiment.
What you observe is not unusual at all. If you want to be sure of your MW, Mass Spec will tell you what you want to know. Hope this helps, good luck -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu
