Computational design of affinity and specificity at protein-protein interfaces

Abstract

The computer-based design of protein-protein interactions is a rigorous test of our understanding of molecular recognition and an attractive approach for creating novel tools for cell and molecular research. Considerable attention has been placed on redesigning the affinity and specificity of naturally occurring interactions. Several studies have shown that reducing the desolvation costs for binding while preserving shape complimentarity and hydrogen bonding is an effective strategy for improving binding affinities. In favorable cases specificity has been designed by focusing only on interactions with the target protein, while in cases with closely related off-target proteins it has been necessary to explicitly disfavor unwanted binding partners. The rational design of protein-protein interactions from scratch is still an unsolved problem, but recent developments in flexible backbone design and energy functions hold promise for the future.

Figure 1. Reducing desolvation costs is an effective way to increase protein binding affinities

Mutations are shown from four separate studies [9,13,14,16]. In each case, a polar residue buried at the interface (shown in space filling) was mutated to a hydrophobic residue. Between 6-fold and 12-fold increases in binding affinity were observed.

Figure 2. The use of single vs. multiple templates in studies of specificity/promiscuity

(TOP LEFT) Calmodulin (light orange/light blue) bound to two different peptides (orange/blue). Because the conformation of calmodulin and the peptide orientation are signficantly different, mutations designed in the context of one interface are essentially random in the context of the other interface. These can therefore be assumed to generally be destabilizing to the “competing” interface, allowing specificity to be achieved through consideration of only a single template [27] (implicit negative design). (TOP RIGHT) By contrast, structures of bZIP coiled-coil structures are in general very similar to each other (shown are the c-Jun homodimer and the c-Fos/c-Jun heterodimer, with c-Jun in light orange/light blue/orange and c-Fos in blue). For this reason, consideration of multiple competing templates is critical for achieving specificity [21] (explicit negative design). (BOTTOM LEFT) Taking cues from Nature, promiscuous proteins that recognize similar proteins often reuse specific residue contacts (gp130 (light orange/light blue) is shown bound to IL-6 (orange) and a viral analog of IL-6 (blue)) [36]. Design problems falling into this category may not require explicit consideration of each template, since mutations to the promiscuous protein can be expected to have a similar effect on all binding partners. (BOTTOM RIGHT) By constrast, designing a promiscuous protein that recognizes vastly different partners (ubiquitin (light orange/light blue) is shown with Hrs (orange) and UBC1 (blue)) will require extensive compromise in selecting the identities of surface residues [36]. In such cases, it is therefore anticipated that multiple design templates must be considered explicitly.