Stable Structure for the Complex of Catabolite Activator Protein and Cyclic AMP: Molecular Mechanics Optimization by AMBER

Abstract

To elucidate the effect of cyclic AMP and cyclic GMP addition to the catabolite activator protein (CAP) on its complex structure, we investigated the stable structures of CAP dimer, CAP-cAMP and CAP-cGMP complexes by the molecular mechanics calculations using the AMBER Force Field. The cAMP addition is found to have rather large effect on the CAP dimer structure compared with that by the cGMP addition. This finding is qualitatively consistent with the experimental result that only cAMP has an effect on enhancing the affinity between CAP and DNA, while cGMP does not.