Transfer of Noncovalent Chiral Information along an Optically Inactive Helical Peptide Chain: Allosteric Control of Asymmetry of the C-Terminal Site by External Molecule that Binds to the N-Terminal Site

Screw sense and screw sensibility: communicating information by conformational switching in helical oligomers

Biological systems have evolved a number of different strategies to communicate information on the molecular scale. Among these, the propagation of conformational change is among the most important, being the means by which G-protein coupled receptors (GPCRs) use extracellular signals to modulate intracellular processes, and the way that opsin proteins translate light signals into nerve impulses. The developing field of foldamer chemistry has allowed chemists to employ conformationally well-defined synthetic structures likewise to mediate information transfer, making use of mechanisms that are not found in biological contexts. In this review, we discuss the use of switchable screw-sense preference as a communication mechanism. We discuss the requirements for functional communication devices, and show how dynamic helical foldamers derived from the achiral monomers such as α-aminoisobutyric acid (Aib) and meso-cyclohexane-1,2-diamine fulfil them by communicating information in the form of switchable screw-sense preference. We describe the various stimuli that can be used to switch screw sense, and explore the way that propagation of the resulting conformational preference in a well-defined helical molecule allows screw sense to control chemical events remote from a source of information. We describe the operation of these conformational switches in the membrane phase, and outline the progress that has been made towards using conformational switching to communicate between the exterior and interior of a phospholipid vesicle.

Ala–Ala dipeptides with a semi-perfluoroalkyl chain: chirality driven molecular packing difference and self-assembly driven chiral transfer

The chirality of amino acids triggered the chiral molecular stacking of dipeptides and, eventually, transferred to the semi-perfluoroalkyl chain.

Selective Monofunctionalization Enabled by Reaction-History-Dependent Communication in Catalytic Rotaxanes

Selective monofunctionalization of substrates with distant, yet equally reactive functional groups is difficult to achieve, as it requires the second functional group to selectively modulate its reactivity once the first functional group has reacted. We now show that mechanically interlocked catalytic rings can effectively regulate the reactivity of stoppering groups in rotaxanes over a distance of about 2 nm. Our mechanism of communication is enabled by a unique interlocked design, which effectively removes the catalytic rings from the substrates by fast dethreading as soon as the first reaction has taken place. Our method not only led to a rare example of selective monofunctionalization, but also to a "molecular if function". Overall, the study presents a way to get distant functional groups to communicate with each other in a reaction-history-dependent manner by creating linkers that can ultimately perform logical operations at the molecular level.

Chiral information harvesting in helical poly(acetylene) derivatives using oligo(p-phenyleneethynylene)s as spacers

A chiral harvesting transmission mechanism is described in poly(acetylene)s bearing oligo(p-phenyleneethynylene)s (OPEs) used as rigid achiral spacers and derivatized with chiral pendant groups. The chiral moieties induce a positive or negative tilting degree in the stacking of OPE units along the polymer structure, which is further harvested by the polyene backbone adopting either a P or M helix.

Helicity of perfluoroalkyl chains controlled by the self-assembly of the Ala-Ala dipeptides

Four Ala-Ala dipeptides with a perfluoroalkyl chain at the N-terminal were synthesized. They were able to self-assemble into helical nanofibers and/or twisted nanobelts in a mixture of DMSO/H₂ O. The handedness of nanofibers and nanobelts was controlled by the chirality of the alanine at the N-terminal. The stacking handedness of the phenylene groups and the helicity of the perfluoroalkyl chain were studied using circular dichroism spectroscopy and vibrational circular dichroism, respectively. The chirality of the alanine at N-terminal controlled the stacking handedness of the neighboring phenylene groups. Moreover, due to the low potential barrier between M- and P-helices of the perfluorocarbon chain, the handedness of the organic self-assemblies eventually controlled the helicity of the perfluorocarbon chain. X-ray diffraction indicated that a lamellar structure was formed by the dimers of the dipeptides.

Elasticity as the Basis of Allostery in DNA

Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here, we show that trends in the interaction energy of ligands binding to DNA can be explained within an elastic birod model, which accounts for the deformation of each strand as well as the change in stacking energy due to perturbations in position and orientation of the bases caused by the binding of ligands. The strain fields produced by the ligands decay with distance from the binding site. The interaction energy of two ligands decays exponentially with the distance between them and oscillates with the periodicity of the double helix in quantitative agreement with experimental measurements. The trend in the computed interaction energy is similar to that in the perturbation of groove width produced by the binding of a single ligand, which is consistent with molecular simulations. Our analysis provides a new framework to understand allosteric interactions in DNA and can be extended to other rod-like macromolecules whose elasticity plays a role in biological functions.

Signal transduction in oligoamide foldamers by selective non-covalent binding of chiral phosphates at a urea binding site

The transduction of biological signals depends on the spatial communication of conformational change. We report a synthetic mimic of this signal transduction process in which non-covalent binding induces a change in the position of equilibrium between two rapidly interconverting screw-sense conformers of a synthetic helical polyamide. Selectivity was achieved by incorporating at the N-terminus of the polyamide a urea-based anion recognition site capable of binding chiral phosphate anions. As a result of solvent-dependent binding, an induced conformational change propagates from the binding site through the amide chain, leading to a screw-sense preference detectable in the form of a chemical shift separation between two NMR active ¹³C labels. The remote induction of screw sense preference indicates successful communication of a signal originating solely from non-covalent binding.

A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal

Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion.

Dynamic foldamer chemistry

Foldamers can be made more than pieces of static, conformationally uniform molecular architecture by designing into their structure the conformational dynamism characteristic of functional molecular machines. We show that these dynamic foldamers display biomimetic properties reminiscent of allosteric proteins and receptor molecules. They can translate chemical signals into conformational changes, and hence into chemical outputs such as control of reactivity and selectivity. Future developments could see dynamic foldamers operating in the membrane phase providing artificial mechanisms for communication and control that integrate synthetic chemistry into synthetic biology.

Conformational Switching of a Foldamer in a Multicomponent System by pH-Filtered Selection between Competing Noncovalent Interactions

Biomolecular systems are able to respond to their chemical environment through reversible, selective, noncovalent intermolecular interactions. Typically, these interactions induce conformational changes that initiate a signaling cascade, allowing the regulation of biochemical pathways. In this work, we describe an artificial molecular system that mimics this ability to translate selective noncovalent interactions into reversible conformational changes. An achiral but helical foldamer carrying a basic binding site interacts selectively with the most acidic member of a suite of chiral ligands. As a consequence of this noncovalent interaction, a global absolute screw sense preference, detectable by (13)C NMR, is induced in the foldamer. Addition of base, or acid, to the mixture of ligands competitively modulates their interaction with the binding site, and reversibly switches the foldamer chain between its left and right-handed conformations. As a result, the foldamer-ligand mixture behaves as a biomimetic chemical system with emergent properties, functioning as a "proton-counting" molecular device capable of providing a tunable, pH-dependent conformational response to its environment.

Controlling the sign and magnitude of screw-sense preference from the C-terminus of an achiral helical foldamer

The global screw-sense preference of an achiral helical oligomer may be controlled by a single chiral monomer located at one terminus. Remarkably, maximal control is induced in oligomers of the achiral quaternary amino acid Aib by a single C-terminal alaninamide residue, probably because the Ala side chain, though small, is compatible with a 310 helical conformation. The presence or absence of a C-terminal hydrogen bond donor determines the screw sense of the entire oligomer.

Flaws in foldamers: conformational uniformity and signal decay in achiral helical peptide oligomers

Although foldamers, by definition, are extended molecular structures with a well-defined conformation, minor conformers must be populated at least to some extent in solution. We present a quantitative analysis of these minor conformers for a series of helical oligomers built from achiral but helicogenic α-amino acids. By measuring the chain length dependence or chain position dependence of NMR or CD quantities that measure screw-sense preference in a helical oligomer, we quantify values for the decay constant of a conformational signal as it passes through the molecular structure. This conformational signal is a perturbation of the racemic mixture of M and P helices that such oligomers typically adopt by the inclusion of an N or C terminal chiral inducer. We show that decay constants may be very low (<1% signal loss per residue) in non-polar solvents, and we evaluate the increase in decay constant that results in polar solvents, at higher temperatures, and with more conformationally flexible residues such as Gly. Decay constants are independent of whether the signal originates from the N or the C terminus. By interpreting the decay constant in terms of the probability with which conformations containing a screw-sense reversal are populated, we quantify the populations of these alternative minor conformers within the overall ensemble of secondary structures adopted by the foldamer. We deduce helical persistence lengths for Aib polymers that allow us to show that in a non-polar solvent a peptide helix, even in the absence of chiral residues, may continue with the same screw sense for approximately 200 residues.

Participation of non-aminoisobutyric acid (Aib) residues in the 310 helical conformation of Aib-rich foldamers: a solid state study

3₁₀ helical conformations that extend over 21 Å result when selected non-Aib terminal and central residues are incorporated into Aib-rich foldamers.

Screw sense alone can govern enantioselective extension of a helical peptide by kinetic resolution of a racemic amino acid

Helical secondary structure alone, even in the absence of local chiral residues, can direct the enantioselectivity of peptide coupling.

Synthesis and helical structures of poly(ω-alkynamide)s having chiral side chains: effect of solvent on their screw-sense inversion

New ω-alkynamides, (S)-HC≡CCH2CONHCH2CH(CH3)CH2CH3 (1) and (S)-HC≡CCH2CH2CONHCH(CH3)CH2CH2CH2CH2CH3 (2) were synthesized and polymerized with a rhodium catalyst in CHCl3 to obtain cis-stereoregular poly(ω-alkynamide)s (poly(1) and poly(2)). Polarimetric, CD, and IR spectroscopic studies revealed that in solution the polymers adopted predominantly one-handed helical structures stabilized by intramolecular hydrogen bonds between the pendent amide groups. This behavior was similar to that of the corresponding poly(N-alkynylamide) counterparts (poly(3) and poly(4)) reported previously, whereas the helical senses were opposite to each other. The helical structures of the poly(ω-alkynamide)s were stable upon heating similar to those of the poly(N-alkynylamide)s, but the solvent response was completely different. An increase in MeOH content in CHCl3/MeOH resulted in inversion of the predominant screw-sense for poly(1) and poly(2). Conversely, poly(3) was transformed into a random coil, and poly(4) maintained the predominant screw-sense irrespective of MeOH content. The solvent dependence of predominant screw-sense for poly(1) and poly(2) was reasonably explained by molecular orbital studies using the conductor-like screening model (COSMO).

Designing foldamer-foldamer interactions in solution: the roles of helix length and terminus functionality in promoting the self-association of aminoisobutyric acid oligomers

The biological activity of antibiotic peptaibols has been linked to their ability to aggregate, but the structure-activity relationship for aggregation is not well understood. Herein, we report a systematic study of a class of synthetic helical oligomer (foldamer) composed of aminoisobutyric acid (Aib) residues, which mimic the folding behavior of peptaibols. NMR spectroscopic analysis was used to quantify the dimerization constants in solution, which showed hydrogen-bond donors at the N terminus promoted aggregation more effectively than similar modifications at the C terminus. Elongation of the peptide chain also favored aggregation. The geometry of aggregation in solution was investigated by means of titrations with [D6]DMSO and 2D NOE NMR spectroscopy, which allowed the NH protons most involved in intermolecular hydrogen bonds in solution to be identified. X-ray crystallography studies of two oligomers allowed a comparison of the inter- and intramolecular hydrogen-bonding interactions in the solid state and in solution and gave further insight into the geometry of foldamer-foldamer interactions. These solution-based and solid-state studies indicated that the preferred geometry for aggregation is through head-to-tail interactions between the N and C termini of adjacent Aib oligomers.

End-to-end conformational communication through a synthetic purinergic receptor by ligand-induced helicity switching

The long-range communication of information, exemplified by signal transduction through membrane-bound receptors, is a central biochemical function. Reversible binding of a messenger ligand induces a local conformational change that is relayed through the receptor, inducing a chemical effect typically several nanometres from the binding site. We report a synthetic receptor mimic that transmits structural information from a boron-based ligand binding site to a spectroscopic reporter located more than 2 nm away. Reversible binding of a diol ligand to the N-terminal binding site induces a screw-sense preference in a helical oligo(aminoisobutyric acid) foldamer, which is relayed to a reporter group at the remote C-terminus, communicating information about the structure and stereochemistry of the ligand. The reversible nature of boronate esterification was exploited to switch the receptor sequentially between left- and right-handed helices, while the exquisite conformational sensitivity of the helical relay allowed the reporter to differentiate even between purine and pyrimidine nucleosides as ligands.

Efficient long-range stereochemical communication and cooperative effects in self-assembled Fe4L6 cages

A series of large, optically active Fe(4)L(6) cages was prepared from linear 5,5'-bis(2-formylpyridines) incorporating varying numbers (n = 0-3) of oligo-p-xylene spacers, chiral amines, and Fe(II). When a cage was constructed from the ligand bridged by one p-xylene spacer (n = 1) and a bulky chiral amine, both a homochiral Fe(2)L(3) helicate and Fe(4)L(6) cage were observed to coexist in solution due to a delicate balance between steric factors. In contrast, when a less bulky chiral amine was used, only the Fe(4)L(6) cage was observed. In the case of larger cages (n = 2, 3), long-range (>2 nm) stereochemical coupling between metal centers was observed, which was minimally diminished as the ligands were lengthened. This communication was mediated by the ligands' geometries and rigidity, as opposed to gearing effects between xylene methyl groups: the metal-centered stereochemistry was not observed to affect the axial stereochemistry of the ligands.

Chemical communication: conductors and insulators of screw-sense preference between helical oligo(aminoisobutyric acid) domains

(1)H NMR studies quantify the abilities of achiral amino acids to communicate a left-handed screw-sense preference from one helical Aib(4) domain to another: certain quaternary amino acids (e.g. Ac(6)c) act as effective conductors of conformational preference while others (e.g. diphenylglycine) acts as insulators.