Molecular Mechanism of the Drop in the p<i>K</i>_a of a Substrate Analog Bound to Medium-Chain Acyl-CoA Dehydrogenase: Implications for Substrate Activation

The p<i>K</i>_a value of a substrate analogue 3-thiaoctanoyl-CoA at αC-H is known to drop from <i>ca</i>. 16 in the free state to 5-6 upon binding to medium-chain acyl-CoA dehydrogenase (MCAD). The molecular mechanism underlying this phenomenon was investigated by taking advantage of artificial FADs, <i>i.e</i>., 8-CN-, 7, 8-Cl₂-, 8-Cl-, 8-OCH₃-, 8-NH₂-, ribityl-2'-deoxy-8-CN-, and ribityl-2'-deoxy-8-Cl-FADs, reconstituted into MCAD. The stronger the electron-withdrawing ability of the substituent, the smaller the p<i>K</i>_a value became [<i>e. g</i>., 7.4 (8-NH₂-FAD) and 4.0 (8-CN-FAD)], suggesting that the flavin ring itself affects the p<i>K</i>_a value of the ligand <i>via</i> a charge-transfer interaction with the ligand. The destruction of the hydrogen bond between the thioester C(1)=O and the ribityl-2'-OH of FAD raised the p<i>K</i>_a by <i>ca</i>. 2.5 units. These results indicate that the interaction between the ligand and the flavin ring also serves to lower the p<i>K</i>_a of the ligand, in addition to the hydrogen bonds at C(1)=O of the ligand.