Empirical free energy analysis of the engrailed Q50K homeodomain mutant-DNA complex and its mutants

Abstract

Empirical free energy calculations were performed for the engrailed homeodomain mutant protein in complex with its consensus promoter. The program, CONGEN™, was used to generate the atomic coordinates, which were missing in the original crystal structure of the Q50K mutant protein. To generate the said atomic coordinates more accurately, the initial CONGEN-generated model was subjected to 300 ps of belly dynamics in AMBER™. Complex formation energies were calculated for the ‘wild-type’ complex as well as ten computer-generated mutants that parallel mutants/substitutions studied by Sauer's group for each of three models. The hydrophobic, electrostatic, and entropic contributions were calculated. The non-linearized finite difference Poisson–Boltzmann equation was solved for the complexes at the ionic strength under which dissociation constant measurements were taken by the aforementioned group. A good overall agreement existed between calculated and experimental ΔΔG estimates. Discrepancies between absolute experimental and calculated values for ΔΔG are hypothesized to be due to the missing conformational entropic contribution of the operator DNA molecule.