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We have developed a computational method for the de novo design of hydrophobic cores of proteins and tested it experimentally. The method is composed of a pair of programs, (i) to optimize side-chain conformations using an updated rotamer library for potential hydrophobic residues, based on the backbone structure of the protein of interest, and (ii) to estimate changes in Gibbs free energies between the folded and unfolded structures of the optimized sequence. Using these programs, we have engineered several variants of Thermus flavus malate dehydrogenase. To quantitate the stability change in each variant, the circular dichroism spectra of the proteins were measured as a function of guanidine hydrochloride concentration and deltadeltaG(H2O) values of the proteins were determined by extrapolation of the experimental data. However, variants with double replacements showed different denaturation cooperativity from that of the wild type and therefore it was difficult to simply compare the theoretical and experimental stability of each variant using calculated deltadeltaG and experimental deltadeltaG(H2O) values. When the calculated deltadeltaG values were compared with those at 3.5 M guanidine hydrochloride, which was the transition midpoint obtained from the denaturation curve of the wild type, good correlation was observed.

Designing the hydrophobic core of Thermus flavus malate dehydrogenase based on side-chain packing