Biochemistry and enzymology texts are a good place to start. In general, stronger bases are better nucleophiles (it doesn't correspond exactly) but you also have to consider the population of the deprotonated species at the relevant pH, and the role of neighboring residues in altering 'native' pKa values of ionizable residues and the local dielectric constant.
Is your Asp hypothetically acting as a nucleophile, or as a general base? The latter is a more common role for Asp. His, Cys, or metal-hydroxide are more common nucleophilic catalysts: these residues are both good nucleophiles and can act as decent leaving groups. Roger Rowlett On Jul 21, 2012 1:05 AM, "Peter Hsu" <[email protected]> wrote: > I too am also studying the reaction mechanism of an enzyme, but my > chemistry/enzymatic biochemistry is rather weak after many years of non-use > and no review. Does anyone know just as a general rule which residues are > the best to worst nucleophiles? > > Sorry if this seems rather presumptuous, just not sure where to look in > literature for a summary of these things. >
