Design of hydrophobic core of E. coli malate dehydrogenase based on the side-chain packing

We have developed computational programs for the de novo design of hydrophobic cores of proteins. The first program optimizes side-chain conformations using an updated rotamer library for potential hydrophobic residues, based on the backbone structure of the protein of interest. The second program selects candidates to be engineered among the sequences by estimating changes in Gibbs free energy between the folded and unfolded structure of the proteins with new sequence. Using these programs, we constructed several variants of E. coli malate dehydrogenase (eMDH) which could have increased stability at 25 degrees C, compared to the wild type enzyme. To quantitate stability change between variants and the wild type, circular dichroism spectra were measured as a function of guanidine hydrochloride concentration at 25 degrees C, pH 7.0. This analysis showed that three variants constructed in this study were stabilized more than or equal to the wild type. This demonstrated that our programs may be powerful tools to design new proteins with high stability.