Hi Monica If protein is Homo-tetramer then one can expect the identical binding sites. I am also working on homo-dimeric protein which binds to DNA. I used PRISM to estimate the binding affinity through flourescence bindingmethod using “SATURATION and NON-LINEAR REGRESSION and ONE SITE binding Model’ considering protein concentration as dimer or monomer. Then I looked for the sensibility of the model by analyzing (comparing) best fit values (like SD, Bmax) of the parameters with reasonable certainty.
Unlike ITC binding model fitting (gives good estimate of stoichiometry, cooperativity and also binding sites (one, two or sequential binding sites)), flourescence binding models do not give very good estimate of these parameters. Thus, based on protein you should assume the model which fits to the properties of the protein. Good luck Raj On Thu, Sep 12, 2013 at 12:59 PM, MONICA MITTAL <[email protected]>wrote: > Dear All, > Firstly sorry for asking a non-crystallography > question, but i want help in understanding the data analysis for fitting a > protein-ligand binding data. > Actually i have a protein which is a tetramer in solution and i have done > its flourescence binding with a ligand. I am trying to fit the data to a > 4-site binding model in scientist. But i donot have a correct model to fit > in the data for identical or non-identical, co-operative or sequential > binding. Can anyone help me in analysing the binding data. > Any help will be highly appreciated. > Thankyou ! >
