I believe this is a fairly straightforward calculation but simply something I am not yet familiar with. I have a solution of a DNA-protein complex (about 50/50 DNA/protein by weight). I need to calculate the partial specific volume of this complex in solution. I can get the full DNA and protein sequences if needed and also have a PDB of a crystalized version of the complex.
I understand that an average protein has a partial specific volume of 0.73cm^3/g. Is there a similar value for double-stranded DNA? If I have that, can I simply use the following?
v_all = (v_p * m_p + v_DNA *m_DNA) / (m_p + m_DNA)
If your protein content even a single tryptophan moiety then I have solution for you. Measure the time resolved fluorescence anisotropy of the free protein and the DNA bound protein. using the anisotropy data volume of the complex can be easily calculated. Details of formulation is available online or in books.
By the way anisotropy can be measured by other methods also.
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