I am getting 2 bands in Tris-Tricine SDS PAGE. I am also getting multiple broad bands in MALDI. Additionally only getting peaks in maldi at high laser intensity and reflector with maximum input possible. Thanks in advance
According to UniProt, there is only one sequence for protamine from salmon, but there are several from the related species rainbow trout. The salmon sequence consists largely of arginine residues, so it should be a very good substrate from proteases that cleave at basic residues, such as trypsin, which would result in a multiplicity of products.
The entry for salmon protamine sulfate from Sigma catalog number P4020 gives a range of molecular weights from 5,000-10,000, indicating that it is, in fact, a heterogeneous material.
Phosphorylation also occurs, adding to the heterogeneity.
Protamine seems to be a mix, but you will get a clear picture by running it on a Native PAGE gel. Perform it to get a perfect answer.
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