Positive allostery in metal ion binding by a cooperatively folded β-peptide bundle

Biomolecular Systems Engineering: Unlocking the Potential of Engineered Allostery via the Lactose Repressor Topology

Allosteric function is a critical component of many of the parts used to construct gene networks throughout synthetic biology. In this review, we discuss an emerging field of research and education, biomolecular systems engineering, that expands on the synthetic biology edifice-integrating workflows and strategies from protein engineering, chemical engineering, electrical engineering, and computer science principles. We focus on the role of engineered allosteric communication as it relates to transcriptional gene regulators-i.e., transcription factors and corresponding unit operations. In this review, we (a) explore allosteric communication in the lactose repressor LacI topology, (b) demonstrate how to leverage this understanding of allostery in the LacI system to engineer non-natural BUFFER and NOT logical operations, (c) illustrate how engineering workflows can be used to confer alternate allosteric functions in disparate systems that share the LacI topology, and (d) demonstrate how fundamental unit operations can be directed to form combinational logical operations.

Geared Toward Applications: A Perspective on Functional Sequence-Controlled Polymers

Sequence-controlled polymers are an emerging class of synthetic polymers with a regulated sequence of monomers. In the past decade, tremendous progress has been made in the synthesis of polymers with the sophisticated sequence control approaching the level manifested in biopolymers. In contrast, the exploration of novel functions that can be achieved by controlling synthetic polymer sequences represents an emerging focus in polymer science. This Viewpoint will survey recent advances in the functional applications of sequence-controlled polymers and provide a perspective on the challenges and outlook for pursuing future applications of this fascinating class of macromolecules.

Metal-Binding Foldamers

Sequence-defined oligomeric molecules with discrete folding propensities, termed foldamers, are a versatile source of agents with tailored structure and function. An inspiration for the development of the foldamer paradigm are natural biomacromolecules, the sequence-encoded folding of which is the basis of life. Metal ions and clusters are common features in proteins, where the role of metal varies from supporting structure to enabling function. The ubiquity of metals in natural systems suggests promise for metals in the context of folded artificial backbones. In this Minireview, we highlight efforts to realize this potential through a survey of published work on the design, synthesis, and characterization of metal-binding foldamers.

Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV

The Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the nonstructural proteins involved in its viral replication. One such protein, NS1, encoded as a monomer by the viral genome, plays a major role via symmetric oligomerization. We examine the homodimeric structure of the dominant β-ladder segment of NS1 with extensive all atom molecular dynamics. We find it stably bounded by two spatially separated interaction clusters (C1 and C2) with significant differences in the nature of their interactions. Four pairs of distal, intramonomeric disulfide bonds are found to be coupled to the stability, local structure, and wettability of the interfacial region. Symmetric reduction of the intramonomeric disulfides triggers marked dynamical heterogeneity, interfacial wettability, and asymmetric salt-bridging propensity. Harnessing the model-free Lipari-Szabo based formalism for estimation of conformational entropy (S_conf), we find clear signatures of heterogeneity in the monomeric conformational entropies. The observed asymmetry, very small in the unperturbed state, expands significantly in the reduced states. This allosteric effect is most noticeable in the electrostatically bound C2 cluster that underlies the greatest stability in the unperturbed state. Allosteric induction of conformational and thermodynamic asymmetry is expected to affect the pathways leading to symmetric higher-ordered oligomerization, and thereby affect crucial replication pathways.

Retarded Translocation of Nucleic Acids through α-Hemolysin Nanopore in the Presence of a Calcium Flux

Electrophysiological measurement of molecular translocation through a nanopore is the fundamental basis of nanopore sensing. Free translocation of nucleic acids however is normally so fast that the identities of the compounds are not clearly resolvable. Inspired by recent progress in fluorescence imaging based nanopore sensing, we found that during electrophysiology measurements, translocation of nucleic acids is also retarded whenever a calcium flux around the pore vicinity is established. The residence time of nucleic acids has been extended to tens of milliseconds, a result of the strong coupling between nucleic acids and free calcium ions. The methodology presented here is applicable to both DNAs and RNAs and is able to clearly discriminate between different RNA homopolymers. This offers new insights for calcium imaging based nanopore sensing and suggests a new strategy of electrophysiology-based nanopore sensing aimed at a retarded motion of nucleic acids.

Proteomimetic Zinc Finger Domains with Modified Metal-binding β-Turns

The mimicry of protein tertiary folds by chains artificial in backbone chemical composition leads to proteomimetic analogues with potential utility as bioactive agents and as tools to shed light on biomacromolecule behavior. Notable successes toward such molecules have been achieved; however, as protein structural diversity is vast, design principles must be continually honed as they are applied to new prototype folding patterns. One specific structure where a gap remains in understanding how to effectively generate modified backbone analogues is the metal-binding β-turn found in zinc finger domains. Literature precedent suggests several factors that may act in concert, including the artificial moiety used to modify the turn, the sequence in which it is applied, and modifications present elsewhere in the domain. Here, we report efforts to gain insights into these issues and leverage these insights to construct a zinc finger mimetic with backbone modifications throughout its constituent secondary structures. We first conduct a systematic comparison of four turn mimetics in a common host sequence, quantifying relative efficacy for use in a metal-binding context. We go on to construct a proteomimetic zinc finger domain in which the helix, strands, and turn are simultaneously modified, resulting in a variant with 23% artificial residues, a tertiary fold indistinguishable from the prototype, and a folded stability comparable to the natural backbone on which the variant is based. Collectively, the results reported provide new insights into the effects of backbone modification on structure and stability of metal-binding domains and help inform the design of metalloprotein mimetics.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

Proteomimetics as protein-inspired scaffolds with defined tertiary folding patterns

Proteins have evolved as a variable platform that provides access to molecules with diverse shapes, sizes and functions. These features have inspired chemists for decades to seek artificial mimetics of proteins with improved or novel properties. Such work has focused primarily on small protein fragments, often isolated secondary structures; however, there has lately been a growing interest in the design of artificial molecules that mimic larger, more complex tertiary folds. In this Perspective, we define these agents as 'proteomimetics' and discuss the recent advances in the field. Proteomimetics can be divided into three categories: protein domains with side-chain functionality that alters the native linear-chain topology; protein domains in which the chemical composition of the polypeptide backbone has been partially altered; and protein-like folded architectures that are composed entirely of non-natural monomer units. We give an overview of these proteomimetic approaches and outline remaining challenges facing the field.

Zinc-dysprosium functionalized amyloid fibrils

The heterometallic Zn2Dy2 entity bearing partially saturated metal centres covalently decorates a highly ordered amyloid fibril core and the functionalised assembly exhibits catalytic Lewis acid behaviour.

Exploring the Functional Consequences of Protein Backbone Alteration in Ubiquitin through Native Chemical Ligation

Ubiquitin (Ub) plays critical roles in myriad protein degradation and signaling networks in the cell. We report herein Ub mimetics based on backbones that blend natural and artificial amino acid units. The variants were prepared by a modular route based on native chemical ligation. Biological assays show that some are enzymatically polymerized onto protein substrates, and that the resulting Ub tags are recognized for downstream pathways. These results advance the size and complexity of folded proteins mimicked by artificial backbones and expand the functional scope of such agents.

Chiral Cu(ii), Co(ii) and Ni(ii) complexes based on 2,2′-bipyridine modified peptoids

Helical peptoids bearing 2,2′-bipyridine, varied in their chiral bulky side chains and their N-terminus form chiral complexes with Cu(ii), Co(ii) and Ni(ii) via intramolecular binding.

Water soluble hydrophobic peptoids via a minor backbone modification

The incorporation of piperazine or homopiperazine within hydrophobic peptoid scaffolds leads to their water solubility while increasing their overall conformational order in water.

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.

Stereospecific control of the helical orientation of indolocarbazole–pyridine hybrid foldamers by rational modification of terminal chiral appendages

The helical handedness excess of an indolocarbazole–pyridine hybrid oligomer capable of folding into a stable helical structure was achieved up to 96% by rational modification of terminal chiral residues.

β-Peptide bundles: Design. Build. Analyze. Biosynthesize

Peptides containing β-amino acids are unique non-natural polymers known to assemble into protein-like tertiary and quaternary structures. When composed solely of β-amino acids, the structures formed, defined assemblies of 14-helices called β-peptide bundles, fold cooperatively in water solvent into unique and discrete quaternary assemblies that are highly thermostable, bind complex substrates and metal ion cofactors, and, in certain cases, catalyze chemical reactions. In this Perspective, we recount the design and elaboration of β-peptide bundles and provide an outlook on recent, unexpected discoveries that could influence research on β-peptides and β-peptide bundles (and β-amino acid-containing proteins) for decades to come.

Synthesis and Self-Assembly of Bundle-Forming α-Helical Peptide-Dendron Hybrids

Dendronized helix bundle assemblies combine the sequence diversity and folding properties of proteins with the tailored physical properties of dendrimers. Assembly of peptide-dendron hybrids into α-helical bundles encapsulates the helix bundle motif in a dendritic sheath that will allow the functional, protein-like domain to be transplanted to nonbiological environments. A bioorthogonal graft-to synthetic strategy for preparing helix bundle-forming peptide-dendron hybrids is described herein for hybrids 1a, 1b, and 2. Titration experiments monitored by circular dichroism spectroscopy support our self-assembly model for how the peptide-dendron hybrids self-assemble into α-helical bundles with the dendrons on outside of the bundle.

A rationally designed metal-binding helical peptoid for selective recognition processes

A helical peptoid bearing two distinct metal binding ligands at positions i and i+3 (Helix HQT i+3) enables the selective recognition of one or two metal ions depending on its environment, thus mimicking the unique recognition abilities of natural biopolymers.

Metal-binding biopolymers play a significant role in processes, such as regulation, recognition and catalysis, due to their high affinity towards specific metal ions, which they bind selectively from the cellular pool. Many enzymes can bind two or more metal ions, each at a specific binding site, to enable efficient cooperative function. Imitating these recognition abilities might lead to the production of biomimetic materials such as unique chelators and catalysts. Herein, we report a rationally designed helical peptoid bearing two distinct metal binding ligands at positions i and i + 3 (Helix HQT i + 3), which enables the selective recognition of one or two metal ions depending on its environment. Using various spectroscopic techniques, we describe (1) the selective intramolecular binding of Cu²⁺ and its extraction from a mixture of neighboring metal ions in high concentrations, and (2) the selective intermolecular binding of two different metal ions, including the pair Cu²⁺ and Zn²⁺, one at each binding site, for the generation of hetero-bimetallic peptoid duplexes. Thorough analysis and comparison between the spectroscopic data and association constants of the metal complexes formed by Helix HQT i + 3 and those formed by non-helical peptoids, or helical peptoids in which the two metal binding ligands are not pre-organized, revealed that the unique recognition processes performed by Helix HQT i + 3 are controlled by both the sequence and the structure of the peptoid.

Versatile ruthenium complexes based on 2,2′-bipyridine modified peptoids

Helical peptoids bearing 2,2′-bipyridine form ruthenium complexes via intermolecular binding to linear peptoid strands or intramolecular binding to a cyclic scaffold.

From simplicity to complex systems with bioinspired pseudopeptides

This feature article highlights some of the recent advances in creating complexity from simple pseudopeptidic molecules. The bioinspired approaches discussed here allowed an increase in the structural, chemical and interactional complexity (see figure).

Self-assembled vesicles of urea-tethered foldamers as hydrophobic drug carriers

Nonamphiphilic α,β-hybrid foldamers form hollow vesicular architectures which can take up and release the anticancer hydrophobic drug curcumin.

Magnetotactic molecular architectures from self-assembly of β-peptide foldamers

The design of stimuli-responsive self-assembled molecular systems capable of undergoing mechanical work is one of the most important challenges in synthetic chemistry and materials science. Here we report that foldectures, that is, self-assembled molecular architectures of β-peptide foldamers, uniformly align with respect to an applied static magnetic field, and also show instantaneous orientational motion in a dynamic magnetic field. This response is explained by the amplified anisotropy of the diamagnetic susceptibilities as a result of the well-ordered molecular packing of the foldectures. In addition, the motions of foldectures at the microscale can be translated into magnetotactic behaviour at the macroscopic scale in a way reminiscent to that of magnetosomes in magnetotactic bacteria. This study will provide significant inspiration for designing the next generation of biocompatible peptide-based molecular machines with applications in biological systems.

A prochelator peptide designed to use heterometallic cooperativity to enhance metal ion affinity

A peptide has been designed so that its chelating affinity for one type of metal ion regulates its affinity for a second, different type of metal ion. The prochelator peptide (PCP), which is a fusion of motifs evocative of calcium loops and zinc fingers, forms a 1 : 2 Zn : peptide complex at pH 7.4 that increases its affinity for Zn²⁺ ∼3-fold in the presence of Tb³⁺ (log β₂ from 13.8 to 14.3), while the 1 : 1 luminescent complex with Tb³⁺ is brighter, longer lived, and 20-fold tighter in the presence of Zn²⁺ (log K from 6.2 to 7.5). This unique example of cooperative, heterometallic allostery in a biologically compatible construct suggests the possibility of designing conditionally active metal-binding agents that could respond to dynamic changes in cellular metal status.

Venkatesha M, Balaram P. Structural characterization of folded and extended conformations in peptides containing γ amino acids with proteinogenic side chains: crystal structures of γn, (αγ)n and γγδγ sequences

γ_n amino acid residues can be incorporated into structures in γ_n and hybrid sequences containing folded and extended α and δ residues.