Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β‑Sheets by α/β-Peptides

The sophistication of folding patterns and functions displayed by unnatural-backbone oligomers has increased tremendously in recent years. Design strategies for the mimicry of tertiary structures seem within reach; however, a general method for the mimicry of sheet segments in the context of a folded protein is an unmet need preventing realization of this goal. Previous work has shown that 1→1 α→β-residue substitutions at cross-strand positions in a hairpin-forming α-peptide sequence can generate an α/β-peptide analogue that folds in aqueous conditions but with a change in side-chain display relative to the natural sequence; this change would prevent application of single β-residue substitutions in a larger protein. Here, we evaluate four different substitution strategies based on replacement of αα dipeptide segments for the ability to retain both sheet folding encoded by a parent α-peptide sequence as well as nativelike side-chain display in the vicinity of the β-residue insertion point. High-resolution structure determination and thermodynamic analysis of folding by multidimensional NMR suggest that three of the four designs examined are applicable to larger proteins

Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β‑Sheets by α/β-Peptides

The sophistication of folding patterns and functions displayed by unnatural-backbone oligomers has increased tremendously in recent years. Design strategies for the mimicry of tertiary structures seem within reach; however, a general method for the mimicry of sheet segments in the context of a folded protein is an unmet need preventing realization of this goal. Previous work has shown that 1→1 α→β-residue substitutions at cross-strand positions in a hairpin-forming α-peptide sequence can generate an α/β-peptide analogue that folds in aqueous conditions but with a change in side-chain display relative to the natural sequence; this change would prevent application of single β-residue substitutions in a larger protein. Here, we evaluate four different substitution strategies based on replacement of αα dipeptide segments for the ability to retain both sheet folding encoded by a parent α-peptide sequence as well as nativelike side-chain display in the vicinity of the β-residue insertion point. High-resolution structure determination and thermodynamic analysis of folding by multidimensional NMR suggest that three of the four designs examined are applicable to larger proteins

Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β‑Sheets by α/β-Peptides

The sophistication of folding patterns and functions displayed by unnatural-backbone oligomers has increased tremendously in recent years. Design strategies for the mimicry of tertiary structures seem within reach; however, a general method for the mimicry of sheet segments in the context of a folded protein is an unmet need preventing realization of this goal. Previous work has shown that 1→1 α→β-residue substitutions at cross-strand positions in a hairpin-forming α-peptide sequence can generate an α/β-peptide analogue that folds in aqueous conditions but with a change in side-chain display relative to the natural sequence; this change would prevent application of single β-residue substitutions in a larger protein. Here, we evaluate four different substitution strategies based on replacement of αα dipeptide segments for the ability to retain both sheet folding encoded by a parent α-peptide sequence as well as nativelike side-chain display in the vicinity of the β-residue insertion point. High-resolution structure determination and thermodynamic analysis of folding by multidimensional NMR suggest that three of the four designs examined are applicable to larger proteins

Tuning Assembly Size in Peptide-Based Supramolecular Polymers by Modulation of Subunit Association Affinity

Nature uses proteins and nucleic acids to form a wide array of functional architectures, and scientists have found inspiration from these structures in the rational design of synthetic biomaterials. We have recently shown that a modular subunit consisting of two α-helical coiled coil peptides attached at their midpoints by an organic linking group can spontaneously self-assemble in aqueous solution to form a soluble supramolecular polymer. Here we explore the use of coiled-coil association affinity, readily tuned by amino acid sequence, as a means to predictably alter properties of these supramolecular assemblies. A series of dimeric coiled-coil peptide sequences with identical quaternary folded structures but systematically altered folded stability were designed and biophysically characterized. The sequences were cross-linked to generate a series of branched, self-assembling biomacromolecular subunits. A clear relationship is observed between coiled-coil association affinity and apparent hydrodynamic diameter of the supramolecular polymers formed by these subunits. Our results provide a family of soluble supramolecular polymers of tunable size and well-characterized coiled-coil sequences that add to the library of building blocks available for use in the rational design of protein-based supramolecular biomaterials

Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β‑Sheets by α/β-Peptides

The sophistication of folding patterns and functions displayed by unnatural-backbone oligomers has increased tremendously in recent years. Design strategies for the mimicry of tertiary structures seem within reach; however, a general method for the mimicry of sheet segments in the context of a folded protein is an unmet need preventing realization of this goal. Previous work has shown that 1→1 α→β-residue substitutions at cross-strand positions in a hairpin-forming α-peptide sequence can generate an α/β-peptide analogue that folds in aqueous conditions but with a change in side-chain display relative to the natural sequence; this change would prevent application of single β-residue substitutions in a larger protein. Here, we evaluate four different substitution strategies based on replacement of αα dipeptide segments for the ability to retain both sheet folding encoded by a parent α-peptide sequence as well as nativelike side-chain display in the vicinity of the β-residue insertion point. High-resolution structure determination and thermodynamic analysis of folding by multidimensional NMR suggest that three of the four designs examined are applicable to larger proteins

Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β‑Sheets by α/β-Peptides

The sophistication of folding patterns and functions displayed by unnatural-backbone oligomers has increased tremendously in recent years. Design strategies for the mimicry of tertiary structures seem within reach; however, a general method for the mimicry of sheet segments in the context of a folded protein is an unmet need preventing realization of this goal. Previous work has shown that 1→1 α→β-residue substitutions at cross-strand positions in a hairpin-forming α-peptide sequence can generate an α/β-peptide analogue that folds in aqueous conditions but with a change in side-chain display relative to the natural sequence; this change would prevent application of single β-residue substitutions in a larger protein. Here, we evaluate four different substitution strategies based on replacement of αα dipeptide segments for the ability to retain both sheet folding encoded by a parent α-peptide sequence as well as nativelike side-chain display in the vicinity of the β-residue insertion point. High-resolution structure determination and thermodynamic analysis of folding by multidimensional NMR suggest that three of the four designs examined are applicable to larger proteins

Heterogeneous-Backbone Foldamer Mimics of Zinc Finger Tertiary Structure

A variety of oligomeric backbones with compositions deviating from biomacromolecules can fold in defined ways. Termed “foldamers,” these agents have diverse potential applications. A number of protein-inspired secondary structures (e.g., helices, sheets) have been produced from unnatural backbones, yet examples of tertiary folds combining several secondary structural elements in a single entity are rare. One promising strategy to address this challenge is the systematic backbone alteration of natural protein sequences, through which a subset of the native side chains is displayed on an unnatural building block to generate a heterogeneous backbone. A drawback to this approach is that substitution at more than one or two sites often comes at a significant energetic cost to fold stability. Here we report heterogeneous-backbone foldamers that mimic the zinc finger domain, a ubiquitous and biologically important metal-binding tertiary motif, and do so with a folded stability that is superior to the natural protein on which their design is based. A combination of UV–vis spectroscopy, isothermal titration calorimetry, and multidimensional NMR reveals that suitably designed oligomers with >20% modified backbones can form native-like tertiary folds with metal-binding environments identical to the prototype sequence (the third finger of specificity factor 1) and enhanced thermodynamic stability. These results expand the scope of heterogeneous-backbone foldamer design to a new tertiary structure class and show that judiciously applied backbone modification can be accompanied by improvement to fold stability

Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β‑Sheets by α/β-Peptides

The sophistication of folding patterns and functions displayed by unnatural-backbone oligomers has increased tremendously in recent years. Design strategies for the mimicry of tertiary structures seem within reach; however, a general method for the mimicry of sheet segments in the context of a folded protein is an unmet need preventing realization of this goal. Previous work has shown that 1→1 α→β-residue substitutions at cross-strand positions in a hairpin-forming α-peptide sequence can generate an α/β-peptide analogue that folds in aqueous conditions but with a change in side-chain display relative to the natural sequence; this change would prevent application of single β-residue substitutions in a larger protein. Here, we evaluate four different substitution strategies based on replacement of αα dipeptide segments for the ability to retain both sheet folding encoded by a parent α-peptide sequence as well as nativelike side-chain display in the vicinity of the β-residue insertion point. High-resolution structure determination and thermodynamic analysis of folding by multidimensional NMR suggest that three of the four designs examined are applicable to larger proteins

Protein-like Tertiary Folding Behavior from Heterogeneous Backbones

Because proteins play vital roles in life, much effort has been invested in their mimicry by synthetic agents. One approach is to design unnatural backbone oligomers (“foldamers”) that fold like natural peptides. Despite success in secondary structure mimicry by such species, protein-like tertiary folds remain elusive. A fundamental challenge underlying this task is the design of a sequence of side chains that will specify a complex tertiary folding pattern on an unnatural backbone. We report here a sequence-based approach to convert a natural protein with a compact tertiary fold to an analogue with a backbone composed of ∼20% unnatural building blocks but folding behavior similar to that of the parent protein

Introduction of Cyclically Constrained γ‑Residues Stabilizes an α‑Peptide Hairpin in Aqueous Solution

The synthesis and structural characterization of hybrid α/γ-peptides resulting from a 1:1 α→γ residue substitution at cross-strand positions in a hairpin-forming α-peptide sequence are described. Cyclically constrained γ-residues based on 1,3-substituted cyclohexane or benzene scaffolds support a native-like hairpin fold in aqueous solution, and the unnatural residues stabilize the folded state by ∼0.2 kcal/mol per α→γ substitution