Protein-ligand complexes, binding mode

Raha K, Merz KM. Large-scale validation of a quantum mechanics based scoring function predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J Med Chem 2005 48 4558-75. 

In order to select a carrier solution composition which would provide an overall maximum response for MS detection, two modifiers were selected, acetonitrile and methanol, and two buffers, i.e. ammonium acetate (10 mmol pH 7.5) and ammonium formate (10 mmol L pH 7.5). Biotin and fluorescein-biotin were dissolved in various binding buffer-organic solvent mixtures ranging from 90 10 (v/v) to 50 50 (v/v) at two concentration levels (0.01 ng 1 ng pL ) and 20 pL were injected and analyzed by MS in full-scan and SIM mode. The maximum response was found with 50% methanol, which was about a factor 2x higher than for 10% methanol. Since the proteins can denaturate or protein-ligand complexes can dissociate at relatively low percentages of organic modifier in further experiments only 10% methanol is used in the carrier solution. 

Predicting Binding Modes, Binding Affinities and Hot Spots for Protein-Ligand Complexes Using a Knowledge-Based Scoring Function. 

---