In general biophysical experiments are carried out maintaining pH of around 7. For this purpose one can use various buffer systems like phosphate buffer, citrate buffer, tris buffer, bicarbonate buffer and so forth. My question is how to choose? And what is the basis? Should not be this very much system specific? What is the role of constituent ions?
The first consideration is that the pKa of the buffer ingredient should be close to the pH at which the experiment will be performed, within 0.5 pH unit, preferably, and no more that 1 pH unit away. The concentration of the buffer should be high enough to minimize any change in pH that would occur due to the treatment in the experiment. A buffer concentration of 25-100 mM is typical. If the experiment involves a change in temperature, such as differential scanning fluorescence (ThermaFluor), use a buffer that maintains pH when the temperature changes, such as HEPES, and avoid Tris. (For pH 7.0, HEPES is a very good choice in most cases.) You should also consider any effects of the buffer chemistry on the activity or stability of the protein. For example, if an enzyme is inhibited by chloride ions, then avoid using a buffer containing chloride, such as Tris-HCl (pKa = 8.1 at room temperature). You may want to avoid phosphate buffers if the protein interacts with phosphate or nucleotides.
HEPES insensitive to temperature changes? I guess thermodynamics begs to differ.
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