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Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the transition can be tuned by modulating buried histidine-containing hydrogen bond networks. Computational protein design thus provides a route to creating unbound nanomaterials that rapidly respond to small pH changes.

 

Abstract Hierarchical nucleation pathways are ubiquitous in the synthesis of minerals and materials. In the case of zeolites and metal–organic frameworks, pre‐organized multi‐ion “secondary building units” (SBUs) have been proposed as fundamental building blocks. However, detailing the progress of multi‐step reaction mechanisms from monomeric species to stable crystals and defining the structures of the SBUs remains an unmet challenge. Combining in situ nuclear magnetic resonance, small‐angle X‐ray scattering, and atomic force microscopy, we show that crystallization of the framework silicate, cyclosilicate hydrate, occurs through an assembly of cubic octameric Q 3 8 polyanions formed through cross‐linking and polymerization of smaller silicate monomers and other oligomers. These Q 3 8 are stabilized by hydrogen bonds with surrounding H 2 O and tetramethylammonium ions (TMA + ). When Q 3 8 levels reach a threshold of ≈32 % of the total silicate species, nucleation occurs. Further growth proceeds through the incorporation of [(TMA) x (Q 3 8 )⋅ n  H 2 O] ( x −8) clathrate complexes into step edges on the crystals. 

Hierarchical nucleation pathways are ubiquitous in the synthesis of minerals and materials. In the case of zeolites and metal–organic frameworks, pre-organized multi-ion “secondary building units” (SBUs) have been proposed as fundamental building blocks. However, detailing the progress of multi-step reaction mechanisms from monomeric species to stable crystals and defining the structures of the SBUs remains an unmet challenge. Combining in situ nuclear magnetic resonance, small-angle X-ray scattering, and atomic force microscopy, we show that crystallization of the framework silicate, cyclosilicate hydrate, occurs through an assembly of cubic octameric Q38 polyanions formed through cross-linking and polymerization of smaller silicate monomers and other oligomers. These Q38 are stabilized by hydrogen bonds with surrounding H2O and tetramethylammonium ions (TMA+). When Q38 levels reach a threshold of ≈32 % of the total silicate species, nucleation occurs. Further growth proceeds through the incorporation of [(TMA)x(Q38)⋅n H2O](x−8) clathrate complexes into step edges on the crystals. 

Protein scaffolds direct the organization of amorphous precursors that transform into mineralized tissues, but the templating mechanism remains elusive. Motivated by models for the biomineralization of tooth enamel, wherein amyloid-like amelogenin nanoribbons guide the mineralization of apatite filaments, we investigated the impact of nanoribbon structure, sequence, and chemistry on amorphous calcium phosphate (ACP) nucleation. Using full-length human amelogenin and peptide analogs with an amyloid-like domain, films of β-sheet nanoribbons were self-assembled on graphite and characterized by in situ atomic force microscopy and molecular dynamics simulations. All sequences substantially reduce nucleation barriers for ACP by creating low-energy interfaces, while phosphoserines along the length of the nanoribbons dramatically enhance kinetic factors associated with ion binding. Furthermore, the distribution of negatively charged residues along the nanoribbons presents a potential match to the Ca–Ca distances of the multi-ion complexes that constitute ACP. These findings show that amyloid-like amelogenin nanoribbons provide potent scaffolds for ACP mineralization by presenting energetically and stereochemically favorable templates of calcium phosphate ion binding and suggest enhanced surface wetting toward calcium phosphates in general.