Figure 18.5.1   Energy spectrum for multistate protein design

Imagine that we are trying to design a pair of homodimers (target; green). The non-target competitor states (pink) that need to be considered are aggregates (Agg), the unfolded state (Unf), monomers, and heterodimers. Consider two sequences, X and Y. Sequence X has a lower energy for the target structure than sequence Y. However, its energy for the non-target heterodimer is even lower. Although its absolute energy for the target structure is higher than that for sequence X,  Sequence Y is a better design because it has a high energy for all the unwanted non-target states, including the heterodimer. The energy optimized in multistate design is ∆G_gap, the energy difference between the target state energy and the boltzmann-weighted average energy of the non-target states. Adapted from Havranek and Harbury 2003.