A Tetrameric Model of the Dihydrolipoamide Dehydrogenase Component of the Pyruvate Dehydrogenase Complex: Construction and Evaluation by Molecular Modeling Techniques

Abstract

On the basis of the homodimeric X-ray structure of dihydrolipoamide dehydrogenase from Azotobacter vinelandii we demonstrate by protein modeling techniques that two dimeric units of this enzyme can associate to a tetrameric structure with intense contacts between the building blocks. Complementary structures of the respective other unit in the tetramer contribute to the active sites. The coenzyme FAD becomes shielded from the environment, thus its binding is stabilized. By energy minimization techniques binding energies and RMS-values were computed and the contact areas between the building blocks were determined to quantify the interaction. In the cell tetramerization of dihydrolipoamide dehydrogenase will be realized upon its incorporation as an enzyme component into the pyruvate dehydrogenase multienzyme complex and will have consequences for the structure and subunit stoichiometry of the complex. Especially, the multiplicity of the three enzyme components, i.e. pyruvate dehydrogenase, dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase in the enzyme complex must be 24:24:24 instead of 24:24:12 assumed so far.