Proteins with simplified hydrophobic cores compared to other packing mutants

Efforts to design proteins with greatly reduced sequence diversity have often resulted in proteins with so-called molten globule properties. Substitutions were made at six neighboring sites in the major hydrophobic core of staphylococcal nuclease to create variants with all leucine, all isoleucine or all valine at these sites. The mutant proteins with simplified cores constructed here are quite unstable and have poorly packed cores, attested to by interaction energies. Eight related mutants with greater sequence diversity were also constructed. Comparison to these mutants and 159 other permutations of these 3 aliphatic side chains at these same 6 sites previously constructed shows that the simplified cores are not unusual in their stabilities or interaction energies. Further, crystal structures of the two mutants with the worst packing, as measured by interaction energies, showed no unusual disorder in the core. Therefore, reduction of sequence diversity is not necessarily incompatible with a single stable native structure. Other factors must also contribute to previous protein design failures.