On Jun 16, 2011, at 8:30 PM, Dima Klenchin wrote: You recommended "determining extinction coefficients experimentally". How is plugging number of specific residues into a formula constitute experimental determination?
That is a deeply philosophical question! Eventually, you'll be plugging in numbers into a formula in any method. At least, the Edelhoch method requires you to do an experiment, whereas Gill & von Hippel and Pace et al. don't. Ultimately, though, all these methods are based on experiments that someone somewhere executed. Nothing beats quantitative amino acid determination but it's one technique that requires specialized lab and good standartization. By now, it's almost a lost art. The distinction that I am trying to make, and that I am apparently having trouble conveying, is that the "theoretical" methods presented by Gill & von Hippel and Pace et al. are based on statistical averages and thus may or may not be valid for a given protein, whereas the Edelhoch method is specific to a given protein and has been shown by Pace at al. to be the most accurate method (more accurate than quantitative amino acid determination, even when using a specialized lab and good standardization. Three times the charm.
