Nature utilizes assemblies to achieve rich functionality through complex, yet highly-ordered structures made of biologically derived molecules. Engineering interactions between large conformationally flexible molecules that form such assemblies is a key technology towards the advancement of protein-based materials and therapeutics. Having a consensus tetramer scaffold which tolerates wide variation of exterior sequence is useful towards the design and study of complex protein-protein interactions. Here we report a set of designed sequences which maintain a consensus core tetramer scaffold despite displaying highly disparate exterior residues, packing interactions, and long-range structure. Specifically, atomistically resolved structures are reported for three sequences, each sharing a single <i>de novo</i> designed tetramer scaffold core. Each structure is shown to exhibit distinct exterior packing. Additionally, one of the sequences was crystalized under two sets of solution conditions. This resulted in two structures with differing exterior packing interactions and highlights the importance of design control over not only the character of the protein surface, but also the solution environment for the design of assemblies. Analysis was performed to compare the crystal structures with the designed structures. In all cases, the designed consensus tetramer core structures were found to have near sub-angstrom RMSD agreement with the resultant crystal structures having differing exterior sequence or differing solution crystallization conditions. Analysis was performed to compare sidechain conformations between each crystal structure and the designed models. Interior residues showed sub-angstrom RMSD agreement, and many exterior sidechain conformations were also found to match closely with the designed rotamer states. The resultant consensus model tetramer scaffold is a convenient structural building unit for the design and study of interactions between protein surfaces and is a step towards the capability to engineer complex protein assemblies from first principles.

Computationally <i>de novo</i> designed coiled-coil tetramer is robust with respect to variation of exterior sequences and crystallographic packing

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

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Computationally de novo designed coiled-coil tetramer is robust with respect to variation of exterior sequences and crystallographic packing