Calculation of the reduction potential of Flavin Adenine dinucleotide in medium
chain acyl-CoA dehydrogenase using combined DFTB/MM simulations

Sudeep Bhattacharyay, sudeep@chemsun.chem.umn.edu1, Marian T. Stankovich,
stankovi@chem.umn.edu2, and Jiali Gao2. (1) Chemistry, University of Minnesota,
207 Pleasant Street SE, Minneapolis, MN, MN 55455, (2) Department of Chemistry,
University of Minnesota, 207Pleasant St. SE, Minneapolis, MN 55455

The enzyme active site can have significant effects on the redox properties of
cofactors. In acyl-CoA dehydrogenase, which is involved in the first step of
metabolic oxidation of fatty acids, the midpoint potential was found to have
shifted by 110 mV when the substrate is bound to form the Michaelis complex
(1). The change of the redox potential has been proposed to be a key regulatory
factor in the reaction. To understand the roles of specific active site residues
on the change in the reduction potential, we have carried out molecular dynamics
simulations and free energy calculations of the FAD-bound enzyme. The
experimentally observed reduction of Flavin Adenine Dinucleotide (FAD) in medium
chain acyl-CoA dehydrogenase occurs with the transfer of two electrons and one
proton:

FAD + 2e + H+ -> FADH- ; E0 = -0.145 V

Using a similar approach described previously (2), we have carried out a free
energy simulations, by treating the FAD cofactor quantum-mechanically using the
self-consistent charge tight-binding density functional theory (SCC-DFTB)
embedded in the classically treated protein environment. We present the
strengths and shortcomings of this computational approach for computing redox
potentials of organic cofactors in an enzyme, and discuss the findings in the
active site of acyl-CoA dehydrogenase.

1. Mancini-Samuelson, G. J., Kieweg, V., Sabaj, K. M., Ghisla, S., and
   Stankovich, M. T. (1998) Redox properties of human medium-chain acyl-CoA
   dehydrogenase, modulation by charged active-site amino acid residues,
   Biochemistry 37, 14605-14612. 2. Formaneck, M. S., Li, G., Zhang, X., and
   Cui, Q. (2003) Calculating Accurate Redox Ppotentials in Enzymes with a
   Combined QM/MM Free Energy Perturbation Aproach, J Theor Comp Chem 1, 53-67.