Hey guys,
I have been working with breast cancer biomarkers HER2, ER, and PR. I have tried to look up charges for those proteins. Just wondering if anyone knows if HER2, ER or PR are positively or negatively charged proteins. Thanks!
Diya
Hi,
Depending on the solution pH, the ionizable groups on the proteins could be deprotonated or protonated, hence altering the protein charges. Therefore you need to know the pI value (the pH at which a molecule has no net charge) of the proteins. More detail information of those proteins could be obtained from UniProtKb protein database and also ExPAsy (Compute pI/Mw tool).
If the pH < pI → protein positively charged
If the pH > pI → protein negatively charged
pH = pI → net charge on the protein is zero
Similar concept also used for ion exchange chromatography.
Hope that helps!
The best thing is: take the sequences. Go to the chapter of any university biochemical textbook that deals with the amino acid pka and / or the isoelectric point calculation of proteins and you will find out how to calculate the net charge of a protein even at different pHs. Since I imagine that you are referring to the physiological environment with a pH around 7, you simply have to count the residues of arginine, lysine and histidine (the latter must be considered very carefully because around 7 changes easily charge) to which you will assign charge +1. Then you will calculate the total number of aspartic and glutamic to which you will assign the value of -1. Make the algebraic sum and you will have the net charge of the protein at pH 7. The net charge for globular proteins should be around 0 but if you find strong differences from pH 7 you have to suspect that you are dealing with IDPs or non-globular proteins. Good job.
Just a small clarification.
The absolute numerical value of the net charge at pH 7 is important because it tells us what kind of protein we are dealing with. If the net charge is close to zero, we have a good chance that the protein is globular. If the net charge is different from zero for at least 2 units we must suspect that we are in the presence of a polyelectrolyte (polycation or polyanion). The greater the numerical difference, the more reliable the suspect is.
In this case we have a good chance that our protein is an IDP (Intrinsically Disordered Protein) or has large disordered segments (IDR). In both cases the protein behaves completely opposite to globular proteins (enough rigid with only very few conformers) because an IDP is extremely flexible and in physiological conditions behaves like a set of numerous different conformers. This population of conformers has the ability to interact with many (even hundreds) of different molecular partners depending on the chemical-physical conditions of the microenvironment. In this case the normal biophysical methods are not useful for the study of the protein. So knowing the net charge (and a sequence analysis) is important for quickly understanding what we have for our hands (see also Pappu's papers).
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