Why do all proteins given a negative charge prior to electrophoresis?
Answer:
The principle for native gels when Coomassie is not added to the sample is that proteins are separated by a combination of size and charge. The charge in general depends on the number of amino acid residues that bear a positive or negative charge at the pH of the gel. So if running the gel at pH from 8.3 / 8.9, Asp and Glu will be negatively charged, Lys and Arg and His will be protonated and have a positive charge. The N- terminus would have a positive charge while the C terminus would have a negative charge. There might be exceptions depending upon the micro environment of each residue. Native gels can be run at acidic pH as well, to give another way of resolving proteins. Smaller proteins migrate faster than larger proteins. Also, quaternary structure is preserved, so a dimer will run as a dimer so the percentage of total acrylamide monomer used is usually lower than what is used for SDS-PAGE, e.g. 7.5% acrylamide
