Strategies to control the binding mode of de novo designed protein interactions

Abstract

There has been significant recent progress in the computational design of protein interactions including the creation of novel heterodimers, homodimers, nanohedra, fibril caps and a protein crystal. Essential to these successes has been the use of innovative strategies for finding binding modes that are achievable, that is, identifying binding partners and docked conformations that can be successfully stabilized via sequence optimization and backbone refinement. In many cases this has involved the use of structural motifs commonly found at naturally occurring interfaces including alpha helices inserted into hydrophobic grooves, beta-strand pairing, metal binding, established helix packing motifs, and the use of symmetry to form cooperative interactions. Future challenges include the creation of hydrogen bond networks and antibody-like interactions based on the redesign of protein surface loops.

Figure 1. Types of protein complexes designed using computational methods

Target binding [32]: a helical scaffold (red) redesigned to bind the stem region of influenza hemagglutinin (white). Two-sided design [48]: redesigned scaffolds were ankyrin repeat protein (gray) and a coenzyme A binding protein (PH1109, white), interface contacts in red. Cofactor-mediated binding [39]: A helical hairpin designed for zinc-mediated homodimerization. Histidine residues (sticks) coordinate zinc (spheres). Homodimer [38]: the γ-adaptin appendage domain – a monomer with an exposed beta strand – redesigned to allow intermolecular beta-sheet formation. Nanohedra [17]: a native trimer (red) redesigned to form an octamer of trimers, a 24-mer octahedron. P6 crystal lattice [45]: a previously designed coiled-coil homotrimer modified to form a predetermined crystal lattice in a rare space group, P6.

Figure 2. Types of interaction motifs used in de novo designed protein interactions

Known groove: influenza hemagglutinin binding (left), Gα_i1 binding (right). High-order symmetry: a trimer redesigned to form a 24-mer octahedron (left), a coiled-coil tetramer mutated to form a coiled-coil hexamer (right). Beta-strand: a monomer redesigned to form a strand-mediated homodimer (left), amyloid fibril formation inhibited with a designed binding peptide (right). Metal coordination: a monomer redesigned to form a zinc-mediated homodimer (left), a stepwise process converted a crystal-contact tetramer to a solution-phase tetramer by placing histidines at crystal contacts. Subsequently, the zinc-mediated tetramer was improved by computational design (right). Aromatic and hbond hotspot: tyrosine was used to form a hydrophobic and hydrogen bonding hotspot interaction with a preordered aspartate side chain in a hydrophobic pocket. Grafting: discontinuous side-chain and backbone interaction motifs from a known antibody-antigen pair were grafted onto an unrelated scaffold. Superhelix and glycine crossing: a previously designed and crystallized coiled-coil trimer was redesigned to form superhelix stacking interactions and helical glycine crossing interactions, generating the intended honeycomb-like P6 crystal lattice.