Metal ion–regulated assembly of designed modular protein cages

Abstract

Coiled-coil (CC) dimers are versatile, customizable building modules for the design of diverse protein architectures unknown in nature. Incorporation of dynamic self-assembly, regulated by a selected chemical signal, represents an important challenge in the construction of functional polypeptide nanostructures. Here, we engineered metal binding sites to render an orthogonal set of CC heterodimers Zn(II)-responsive as a generally applicable principle. The designed peptides assemble into CC heterodimers only in the presence of Zn(II) ions, reversibly dissociate by metal ion sequestration, and additionally act as pH switches, with low pH triggering disassembly. The developed Zn(II)-responsive CC set is used to construct programmable folding of CC-based nanostructures, from protein triangles to a two-chain bipyramidal protein cage that closes and opens depending on the metal ion. This demonstrates that dynamic self-assembly can be designed into CC-based protein cages by incorporation of metal ion–responsive CC building modules that act as conformational switches and that could also be used in other contexts.

De Novo Design of Polyhedral Protein Assemblies: Before and After the AI Revolution

“…[35] More specifically, this approach has previously yielded sequences which break side chain conformational symmetry within the peptide dimer constituting the asymmetric subunit (ASU). Such an approach can be further applied to accurately and reversibly control the architecture of coiled-coil-based polyhedrons by regulating metal-ion binding [36] and to design dynamic, multichain complexes which can be irreversibly converted between morphologies, for example from a tetrahedral to a bipyramidal architecture. [34] In the past decade, computational methods for the de novo design of symmetric assemblies have been developed and generalised to the atomic-level accuracy production of complexes ranging from cyclic oligomers and fibres to 2D-arrays, polyhedral assemblies, and crystals.…”

“…More specifically, this approach has previously yielded sequences which break side chain conformational symmetry within the peptide dimer constituting the asymmetric subunit (ASU). Such an approach can be further applied to accurately and reversibly control the architecture of coiled‐coil‐based polyhedrons by regulating metal‐ion binding [36] and to design dynamic, multi‐chain complexes which can be irreversibly converted between morphologies, for example from a tetrahedral to a bipyramidal architecture [34] …”

Lipidation Alters the Structure and Hydration of Myristoylated Intrinsically Disordered Proteins

“…The development of new peptides/proteins has traditionally focused on engineering their amino acid sequence to regulate the structure–function for desired applications, including materials, − vaccines and biopharmaceuticals, − sensors, , and others. − In contrast, nature leverages posttranslational modifications (PTMs)the decoration of proteins with motifs such as phosphate, carbohydrates, and lipids, among othersto modulate protein structure, function, and location with exquisite spatiotemporal control . The chemical diversity of PTMs far surpasses the canonical design space of the 20–22 naturally occurring amino acids, exponentially increasing the diversity of proteinaceous molecules available to regulate the spatiotemporal flow of life-sustaining matter, energy, and information.…”

Crystal Structure of de Novo Designed Coiled-Coil Protein Origami Triangle

“…In the coiled-coil protein origami (CCPO) design strategy, CCs are used as modular building blocks to design protein nanostructures . The desired shape is defined through the topological arrangement of parallel and/or antiparallel CC dimers arranged into a precisely defined sequential order, based on the underlying mathematical rules. , Protein folds such as tetrahedron, bipyramid, as well as multichain assemblies have been assembled using CCPO, − and even the folding pathway of those assemblies has been designed . Although the CCPO has proven to be a robust strategy for the design of various protein topologies and their shape has been confirmed by electron microscopy and small-angle X-ray scattering (SAXS), no high-resolution structural information has been available for these structures.…”