Because the burial of hydrophobic surface area is a major driving force for the folding of proteins, many early protein design efforts have been based on a "minimalist approach" where one seeks the simplest sequence compatible with a given fold. The inherent question being asked in minimalist design is whether a loosely chosen set of hydrophobic amino acids is sufficient for directing a peptide sequence to fold? To date, the unanimous answer appears to be "no" since all designed proteins have had non-native characteristics in the sense that the final folded structures are more dynamic and less precisely structured than most naturally occurring proteins. An evolving hypothesis is that nonspecific hydrophobic interactions are sufficient to drive polypeptide folding to a reasonably stable and compact state, but dense complementary side chain packing is necessary for proteins to adopt unique and well-defined structures. These conclusions are reinforced from mutational studies which demonstrate a significant energy penalty for the introduction of cavity creating mutations in the core of natural proteins.
In the present work, we focus on redesigning the cores of proteins because of the dominant role of core interactions in protein folding. To this end, we have developed and experimentally tested a novel computational approach that globally optimizes for a low energy core sequence and structure. This approach differs from total de novo design in that much of the native sequence is preserved, but it allows us to focus on one of the most important features of the protein structure with greater scrutiny because the complexity of the problem is reduced. Furthermore, in contrast to most other design strategies which are dependent on rules for secondary structure formation and therefore specific to a particular folding motif (e.g. four-helix bundle, b-barrel, coiled coil), the current strategy is meant to be completely general for any single domain protein architecture. The success of our experimental results suggest that de novo design of hydrophobic cores is feasible, and reinforces the importance of specific packing interactions for the stability and precise structural features of proteins. A surprising result is that the non-core residues of a protein also play a significant role in determining the uniqueness of the folded structure. Thus future efforts will be aimed at developing strategies to redesign the surface residues of the protein, with the ultimate goal of complete computationally driven protein design.