Probing the non-covalent forces key to the thermodynamics of β-hairpin unfolding

Although it is well understood that the graph of the free energy of unfolding (ΔG) of a globular protein with temperature approximates to a negative parabola, there is as yet no link between this global (G) ΔG G(T) function and the individual structural elements-residue type and the non-covalent forces between groups-contributing to it. As such, there is little understanding of how each structural element contributes to the globally assessed changes of enthalpy (ΔH G), entropy (ΔS G), and heat capacity (ΔC p(G)) of unfolding calculated from the ΔG G(T) function. To address this situation, we consider here an alternative approach to examining fold stability. Specifically, we examine the local (L) reporting of the thermodynamics of unfolding provided by each residue. By using 1H NMR spectroscopy to monitor the response of the individual mainchain amide N-H groups of β-hairpin peptides with temperature, we generate local ΔG L(T) functions, using these to calculate the local enthalpy (ΔH L), entropy (ΔS L), and heat capacity (ΔC p(L)) of unfolding. Mapping the thermodynamic changes in this way, for specific point-mutations, provides new information about how specific residues, non-covalent forces, and secondary structure type, contribute to folding. This type of information provides new details of the factors contributing to the typically measured global ΔG G(T) function.

Detection and differentiation of per- and polyfluoroalkyl substances (PFAS) in water using a fluorescent imprint-and-report sensor array

Widespread industrial use of per- and polyfluoroalkyl substances (PFAS) as surfactants has led to global contamination of water sources with these persistent, highly stable chemicals. As a result, humans and wildlife are regularly exposed to PFAS, which have been shown to bioaccumulate and cause adverse health effects. Methods for detecting PFAS in water are currently limited and primarily utilize mass spectrometry (MS), which is time-consuming and requires expensive instrumentation. Thus, new methods are needed to rapidly and reliably assess the pollution level of water sources. While some fluorescent PFAS sensors exist, they typically function in high nanomolar or micromolar concentration ranges and focus on sensing only 1-2 individual PFAS. Our work aims to address this problem by developing a fluorescent sensor for both individual PFAS, as well as complex PFAS mixtures, and demonstrate its functionality in tap water samples. Here we show that dynamic combinatorial libraries (DCLs) with simple building blocks can be templated with a fluorophore and subsequently used as sensors to form an array that differentially detects each PFAS species and various mixtures thereof. Our method is a high-throughput analysis technique that allows many samples to be analyzed simultaneously with a plate reader. This is one of the first examples of a fluorescent PFAS sensor array that functions at low nanomolar concentrations, and herein we report its use for the rapid detection of PFAS contamination in water.

Combining Excellent Selectivity with Broad Target Scope: Biosensing with Arrayed Deep Cavitand Hosts

Simple macrocyclic water-soluble hosts such as cucurbiturils, cyclophanes, and calixarenes have long been used for biosensing via indicator displacement assays. Using multiple hosts and dyes in an arrayed format allows pattern recognition-based "chemical nose" sensing, which confers exquisite selectivity, even rivaling the abilities of biological recognition tools such as antibodies. However, a challenge in indicator displacement-based biosensing with macrocyclic hosts is that selectivity and scope are often inversely correlated: strong selectivity for a specific target can limit wide application, and broad scope sensing can suffer from a lack of selectivity between similar targets. This problem can be addressed by using water-soluble, self-folding deep cavitands as hosts. These flexible bowl-shaped receptors can be easily functionalized with different motifs at the upper and lower rim, and the large cavities can bind many different fluorescent dyes, causing either fluorescence enhancement or quenching upon binding.Cavity-based affinity is strongest for NMe₃⁺ groups such as trimethyl-lysine, and we have exploited this for the site-selective recognition of post-translational lysine methylations in oligopeptides. The host recognizes the NMe₃⁺ group, and by applying differently functionalized hosts in an arrayed format, discrimination between identical modifications at different positions on the oligopeptide is possible. Multiple recognition elements can be exploited for selectivity, including a defined, yet "breathable" cavity, and variable upper rim functions oriented toward the target.While the performance of the host/guest sensing system is impressive for lysine methylations, the most important advance is the use of multiple different sensing mechanisms that can target a broad range of different biorelevant species. The amphiphilic deep cavitands can both bind fluorescent dyes and interact with charged biomolecules. These non-cavity-based interactions, when paired with additives such as heavy metal ions, modulate fluorescence response in an indirect manner, and these different mechanisms allow selective recognition of serine phosphorylation, lysine acetylation, and arginine citrullination. Other targets include heavy metals, drugs of abuse, and protein isoforms. Furthermore, the hosts can be applied in supramolecular tandem assays of enzyme function: the broad scope allows analysis of such different enzymes as chromatin writers/erasers, kinases, and phosphatases, all from a single host scaffold. Finally, the indirect sensing concept allows application in sensing different oligonucleotide secondary structures, including G-quadruplexes, hairpins, triplexes, and i-motifs. Discrimination between DNA strands with highly similar structures such as G-quadruplex strands with bulges and vacancies can be achieved. Instead of relying on a single highly specific fluorescent probe, the synthetic hosts tune the fluorophore-DNA interaction, introducing multiple recognition equilibria that modulate the fluorescence signal. By applying machine learning algorithms, a classification model can be established that can accurately predict the folding state of unknown sequences. Overall, the unique recognition profile of self-folded deep cavitands provides a powerful, yet simple sensing platform, one that can be easily tuned for a wide scope of biorelevant targets, in complex biological media, without sacrificing selectivity in the recognition.

When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water

Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.

Mimicking Biological Recognition: Lessons in Binding Hydrophilic Guests in Water

Selective molecular recognition of hydrophilic guests in water plays a fundamental role in a vast number of biological processes, but synthetic mimicry of biomolecular recognition in water still proves challenging both in terms of achieving comparable affinities and selectivities. This Review highlights strategies that have been developed in the field of supramolecular chemistry to selectively and non-covalently bind three classes of biologically relevant molecules: nucleotides, carbohydrates, and amino acids. As several groups have systematically modified receptors for a specific guest, an evolutionary perspective is also provided in some cases. Trends in the most effective binding forces for each class are described, providing insight into selectivity and potential directions for future work.

An easily accessible, lower rim substituted calix[4]arene selectively binds N,N-dimethyllysine

Post-translational modifications (PTMs) are critical controllers of protein functions. One set of important PTMs are N-methylated side chains of lysine and arginine, which exist in several functionally distinct forms. Multiple groups have demonstrated the selective binding of the most hydrophobic family member, trimethyllysine (Kme3), using various macrocyclic hosts, but the selective binding of lower methylation states remains challenging. Herein we report that the installation of a sulfonate ester on the lower rim phenol of p-sulfonatocalix[4]arene efficiently generates a potent, N,N-dimethyllysine (Kme2)-selective host in one step from commercially available starting materials. We characterize its binding behaviors in solution, and examine the relationship between its unusual conformational dynamics and its guest-binding properties.

Dynamic Covalent Formation of Concave Disulfide Macrocycles Mechanically Interlocked with Single-Walled Carbon Nanotubes

The formation of discrete macrocycles wrapped around single-walled carbon nanotubes (SWCNTs) has recently emerged as an appealing strategy to functionalize these carbon nanomaterials and modify their properties. Here, we demonstrate that the reversible disulfide exchange reaction, which proceeds under mild conditions, can install relatively large amounts of mechanically interlocked disulfide macrocycles on the one-dimensional nanotubes. Size-selective functionalization of a mixture of SWCNTs of different diameters were observed, presumably arising from error correction and the presence of relatively rigid, curved π-systems in the key building blocks. A combination of UV/Vis/NIR, Raman, photoluminescence excitation, and transient absorption spectroscopy indicated that the small (6,4)-SWCNTs were predominantly functionalized by the small macrocycles 1₂ , whereas the larger (6,5)-SWCNTs were an ideal match for the larger macrocycles 2₂ . This size selectivity, which was rationalized computationally, could prove useful for the purification of nanotube mixtures, since the disulfide macrocycles can be removed quantitatively under mild reductive conditions.

The dark side of disulfide-based dynamic combinatorial chemistry

During the last two decades, disulfide-based dynamic combinatorial chemistry has been extensively used in the field of molecular recognition to deliver artificial receptors for molecules of biological interest. Commonly, the nature of library members and their relative amounts are provided from HPLC-MS analysis of the libraries, allowing the identification of potential binders for a target (bio)molecule. By re-investigating dynamic combinatorial libraries generated from a simple 2,5-dicarboxy-1,4-dithiophenol building block in water, we herein demonstrated that multiple analytical tools were actually necessary in order to comprehensively describe the libraries in terms of size, stereochemistry, affinity, selectivity, and finally to get a true grasp on the different phenomena at work within dynamic combinatorial systems.

We show that multiple analytical tools are necessary in order to describe the different phenomena within disulfide-based dynamic combinatorial libraries in terms of size, stereochemistry, affinity and selectivity.

Louis LE, Waters ML. Using changes in speciation in a dynamic combinatorial library as a fingerprint to differentiate the methylation states of arginine

A dynamic combinatorial library was shown to provide a direct method of sensing methylated arginine and lysine due to differences in speciation. This provides the first sensor array for all the methylation states of arginine.

Sensing of citrulline modifications in histone peptides by deep cavitand hosts

Arrayed cavitand:fluorophore sensor complexes can selectively sense small citrulline modifications at arginine residues on post-translationally modified peptides. The sensor can differentiate between different numbers of citrulline modifications, and a simple two-fluorophore, 6-component array can effect cross-reactive discrimination between single modifications in aqueous solution.

Diastereoselective Synthesis of a Dyn[3]arene with Distinct Binding Behaviors toward Linear Biogenic Polyamines

The extension of the family of dyn[ n]arenes toward a three-membered macrocycle is reported. Through a templated approach, a single diastereoisomer of a dyn[3]arene that bears six carboxyl groups could be isolated by precipitation in 59-63% yield and excellent purity (≥95%). A combination of experimental and computational experiments in water at physiological pH revealed that the macrocycle could bind parent biogenic polyamines with a unique diversity of surface-binding modes. Whereas no binding event could be accurately measured with 1,3-diaminopropane, spermidine formed a classical stoichiometric complex with the dyn[3]arene in the millimolar concentration range. On the other hand, the data obtained for spermine could only be attributed to a more complex binding event with the formation of a 2:1 complex at high [host]/[guest] ratios and redistribution toward a 1:1 complex upon further addition of guest.

Separation of Methylated Histone Peptides via Host-Assisted Capillary Electrophoresis

Lysine methylation in protein is one important epigenetic mechanism that regulates diverse biological processes but is challenging to study due to the large variability in methylation levels and sites. Here, we show that supramolecular hosts such as calixarenes and cucurbiturils can be applied in the background electrolyte (BGE) of capillary electrophoresis (CE) for highly effective separation of post-translationally methylated histone peptides. The molecular recognition event causes a shift in the electrophoretic mobility of the peptide, allowing affinity measurement for binding between the synthetic receptor and various methylated lysine species. Successful separation of the H3 peptides carrying different methylation levels at the K9 position can be achieved using CX4 and CX6 as the BGE additives in CE, enabling monitoring of the activity of the histone lysine demethylase JMJD2E. This reveals the power of combining high resolution CE with synthetic hosts for study of protein methylation, and the method should be capable of analyzing complex biological samples for better understanding of the functions of histone methylation.

Site selective reading of epigenetic markers by a dual-mode synthetic receptor array

Variably functionalized self-folding deep cavitands form an arrayed, fluorescent indicator displacement assay system for the detection of post-translationally modified (PTM) histone peptides. The hosts bind trimethyllysine (KMe3) groups, and use secondary upper rim interactions to provide more sensitive discrimination between targets with identical KMe3 binding handles. The sensor array uses multiple different recognition modes to distinguish between miniscule differences in target, such as identical lysine modifications at different sites of histone peptides. In addition, the sensor is affected by global changes in structure, so it is capable of discriminating between identical PTMs, at identical positions on amino acid fragments that vary only in peptide backbone length, and can be applied to detect non-methylation modifications such as acetylation and phosphorylations located multiple residues away from the targeted binding site. The synergistic application of multiple variables allows dual-mode deep cavitands to approach levels of recognition selectivity usually only seen with antibodies.

Selective recognition of the di/trimethylammonium motif by an artificial carboxycalixarene receptor

Chemical tools that recognise post-translational modifications have promising applications in biochemistry and in therapy. We report a simple carboxycalixarene that selectively binds molecules containing di/trimethylammonium moieties in isolation, in cell lysates and when incorporated in histone peptides. Our findings reveal the potential of using carboxycalixarene-based receptors to study epigenetic regulation.

Optimization of a synthetic receptor for dimethyllysine using a biphenyl-2,6-dicarboxylic acid scaffold: insights into selective recognition of hydrophilic guests in water

Introduction of an endo-carboxylate in a building block for dynamic combinatorial chemistry resulted in amplification of a new host with a K_d of 200 nM for dimethyllysine, a biologically important post-translational modification.

From supramolecular chemistry to the nucleosome: studies in biomolecular recognition

This review highlights the author’s indirect path to research at the interface of supramolecular chemistry and chemical biology.

Fluorogenic sensor platform for the histone code using receptors from dynamic combinatorial libraries

A sensor array has been developed that can differentiate multiple post-translational modifications in the same peptide and their relative positions in the sequence, including multiple methylations, providing a promising new tool for deciphering the histone code.

Post-translational modifications (PTMs) on histone tails act in diverse combinations in the ‘histone code’ to control gene expression, with dysregulation observed in a variety of diseases. However, detection and sensing methods are limited, expensive, and/or low-throughput, including MS and antibody based detection. We found that by combining four synthetic receptors developed by dynamic combinatorial chemistry (DCC) in an indicator displacement system, we are able to create a pattern-based sensor platform that can discriminate single PTMs such as methylation and acetylation on a representative histone peptide with 100% accuracy as well as peptides bearing both dimethyl and trimethyl lysine in the presence of arginine methylation, which has not previously been demonstrated, and can even correctly distinguish the position of lysine methylation individually or in the presence of other PTMs. To extend this approach, a full panel of thirteen analytes containing different combinations of PTMs were classified with 96 ± 1% overall accuracy in a 50% left-out analysis, demonstrating the robustness and versatility of the sensor array. Finally, the sensor platform was also used to demonstrate proof of concept for enzymatic assays by analysing the mock reaction of a threonine kinase, successfully identifying analytes representative of substrate conversion both with and without neighboring PTMs. This work provides a rapid platform for the analysis of peptides bearing complex modifications and highlights the utility of receptors discovered though DCC that display variations in binding affinity and selectivity.

Molecular Recognition of Lys and Arg Methylation

A network of reader proteins and enzymes precisely controls gene transcription through the dynamic addition, removal, and recognition of post-translational modifications (PTMs) of histone tails. Histone PTMs work in concert with this network to regulate gene transcription through the histone code, and the dysregulation of PTM maintenance is linked to a large number of diseases, including many types of cancer. A wealth of research aims to elucidate the functions of this code, but our understanding of the effects of PTMs, specifically the methylation of lysine (Lys) and arginine (Arg), is lacking. The development of new tools to study PTMs relies on a sophisticated understanding of the mechanisms that drive protein and small molecule recognition in water. In this review, we outline the physical organic concepts that drive the molecular recognition of Lys and Arg methylation by reader proteins and draw comparisons to the binding mechanisms of small molecule receptors for methylated Lys and Arg that have been developed recently.

Discoveries from a phenanthroline-based dynamic combinatorial library: catenane from a copper(i) or copper(ii) template?

We report here a DCL study of a phenanthroline-based building block focusing on catenane formation with copper templates.

Host–guest chemistry that directly targets lysine methylation: synthetic host molecules as alternatives to bio-reagents

Post-translational methylation regulates the function of hundreds of proteins in profound ways, and is the target of many efforts to use host–guest chemistry to solve biochemical and biological problems.

Late stage modification of receptors identified from dynamic combinatorial libraries

Small molecule receptors are attractive potential sensors of post-translational modifications, including methylated lysine and methylated arginine. Using dynamic combinatorial chemistry (DCC), our lab previously identified a suite of receptors that bind to Kme3 with a range of affinities ranging from low micromolar to high nanomolar, each with a unique selectivity for Kme3 over the lower methylation states. To enable these receptors to have broad application as Kme3 sensors, we have developed a method for their late-stage modification, which we used to synthesize biotinylated derivatives of A2B, A2D, and A2G in a single step. For our most attractive receptor for applications, A2N, we needed to develop an alternative method for its selective functionalization, which we achieved by "activating" the carboxylic acids on the constituent monomer A or N by pre-functionalizing them with glycine (Gly). Using the resulting Gly-A and Gly-N monomers, we synthesized the novel A2N variants A2Gly-N, Gly-A2N, and Gly-A2Gly-N, which enabled the late stage biotinylation of A2N wherever Gly was incorporated. Finally, we performed ITC and NMR binding experiments to study the effect that carboxylate spacing has on the affinity and selectivity of A2Gly-N and Gly-A2N for KmeX guests compared to A2N. These studies revealed the proximity of the carboxylates to play a complex role in the molecular recognition event, despite their positioning on the outside of the receptor.

Contributions of pocket depth and electrostatic interactions to affinity and selectivity of receptors for methylated lysine in water

Dynamic combinatorial chemistry was used to generate a set of receptors for peptides containing methylated lysine (KMen, n = 0-3) and study the contribution of electrostatic effects and pocket depth to binding affinity and selectivity. We found that changing the location of a carboxylate resulted in an increase in preference for KMe2, presumably based on ability to form a salt bridge with KMe2. The number of charged groups on either the receptor or peptide guest systematically varied the binding affinities to all guests by approximately 1-1.5 kcal mol(-1), with little influence on selectivity. Lastly, formation of a deeper pocket led to both increased affinity and selectivity for KMe3 over the lower methylation states. From these studies, we identified that the tightest binder was a receptor with greater net charge, with a Kd of 0.2 μM, and the receptor with the highest selectivity was the one with the deepest pocket, providing 14-fold selectivity between KMe3 and KMe2 and a Kd for KMe3 of 0.3 μM. This work provides key insights into approaches to improve binding affinity and selectivity in water, while also demonstrating the versatility of dynamic combinatorial chemistry for rapidly exploring the impact of subtle changes in receptor functionality on molecular recognition in water.

Template-Triggered Emergence of a Self-Replicator from a Dynamic Combinatorial Library

Self-assembly of a specific member of a dynamic combinatorial library (DCL) may lead to self-replication of this molecule. However, if the concentration of the potential replicator in the DCL fails to exceed its critical aggregation concentration (CAC), then self-replication will not occur. We now show how addition of a template can raise the concentration of a library member-template complex beyond its CAC, leading to the onset of self-replication. Once in existence, the replicator aggregates promote further replication also in the absence of the template that induced the initial emergence of the replicator.

Molecular Insights into Inhibition of the Methylated Histone-Plant Homeodomain Complexes by Calixarenes

Plant homeodomain (PHD) finger-containing proteins are implicated in fundamental biological processes, including transcriptional activation and repression, DNA damage repair, cell differentiation, and survival. The PHD finger functions as an epigenetic reader that binds to posttranslationally modified or unmodified histone H3 tails, recruiting catalytic writers and erasers and other components of the epigenetic machinery to chromatin. Despite the critical role of the histone-PHD interaction in normal and pathological processes, selective inhibitors of this association have not been well developed. Here we demonstrate that macrocyclic calixarenes can disrupt binding of PHD fingers to methylated lysine 4 of histone H3 in vitro and in vivo. The inhibitory activity relies on differences in binding affinities of the PHD fingers for H3K4me and the methylation state of the histone ligand, whereas the composition of the aromatic H3K4me-binding site of the PHD fingers appears to have no effect. Our approach provides a novel tool for studying the biological roles of methyllysine readers in epigenetic signaling.

Structural study of a small molecule receptor bound to dimethyllysine in lysozyme

Lysine is a ubiquitous residue on protein surfaces. Post translational modifications of lysine, including methylation to the mono-, di- or trimethylated amine result in chemical and structural alterations that have major consequences for protein interactions and signalling pathways. Small molecules that bind to methylated lysines are potential tools to modify such pathways. To make progress in this direction, detailed structural data of ligands in complex with methylated lysine is required. Here, we report a crystal structure of p-sulfonatocalix[4]arene (sclx₄) bound to methylated lysozyme in which the lysine residues were chemically modified from Lys-NH₃⁺ to Lys-NH(Me₂)⁺. Of the six possible dimethyllysine sites, sclx₄ selected Lys116-Me₂ and the dimethylamino substituent was deeply buried in the calixarene cavity. This complex confirms the tendency for Lys-Me₂ residues to form cation-π interactions, which have been shown to be important in protein recognition of histone tails bearing methylated lysines. Supporting data from NMR spectroscopy and MD simulations confirm the selectivity for Lys116-Me₂ in solution. The structure presented here may serve as a stepping stone to the development of new biochemical reagents that target methylated lysines.