Abstract
In cases where binding ligands of proteins are not easily
available,
structural analogues are often used. For example, in the analysis
of proteins recognizing different methyl-lysine residues in histones,
methyl-lysine analogues based on methyl-amino-alkylated cysteine residues
have been introduced. Whether these are close enough to justify quantitative
interpretation of binding experiments is however questionable. To
systematically address this issue, we developed, applied, and assessed
a hybrid computational/experimental approach that extracts the binding
free energy difference between the native ligand (methyl-lysine) and
the analogue (methyl-amino-alkylated cysteine) from a thermodynamic
cycle. Our results indicate that measured and calculated binding differences
are in very good agreement and therefore allow the correction of measured
affinities of the analogues. We suggest that quantitative binding
parameters for defined ligands in general can be derived by this method
with remarkable accuracy.