Computational Design of Mechanically Coupled Axle-rotor Protein Assemblies

Overview of protein machine assembly and rotor component design approaches. (Left) A blueprint of a simple two-component machine consisting of an assembly of an axle and a rotor mechanically constrained by the shape of the interface between the two. (Middle) Systematic generation by computational design of a structurally diverse library of machine components and design of interfaces between axle and rotor that mechanically couple the components and direct assembly. (Right) Example of hierarchical design and assembly of a protein machine from axle and rotor components, here a D3 axle and C3 rotor, and interacting interface residues. Wheel-like cyclic DHRs are fused to the end of the axle and rotor components to increase mass and provide a modular handle and a structural signature to monitor conformational variability.
Overview of protein machine assembly and rotor component design approaches. (Left) A blueprint of a simple two-component machine consisting of an assembly of an axle and a rotor mechanically constrained by the shape of the interface between the two. (Middle) Systematic generation by computational design of a structurally diverse library of machine components and design of interfaces between axle and rotor that mechanically couple the components and direct assembly. (Right) Example of hierarchical design and assembly of a protein machine from axle and rotor components, here a D3 axle and C3 rotor, and interacting interface residues. Wheel-like cyclic DHRs are fused to the end of the axle and rotor components to increase mass and provide a modular handle and a structural signature to monitor conformational variability.

Natural molecular machines contain protein components that undergo motion relative to each other. Designing such mechanically constrained nanoscale protein architectures with internal degrees of freedom is an outstanding challenge for computational protein design. Here the de novo construction of protein machinery are explored from designed axle and rotor components with internal cyclic or dihedral symmetry. It was found that the axle-rotor systems assemble in vitro and in vivo as designed. Using cryo–electron microscopy, it was found that these systems populate conformationally variable relative orientations reflecting the symmetry of the coupled components and the computationally designed interface energy landscape. These mechanical systems with internal degrees of freedom are a step toward the design of genetically encodable nanomachines.

Designing Materials to Revolutionize and Engineer our Future (DMREF)