Tuning chemotactic responses with synthetic multivalent ligands

Glycopolymers Prepared by Alternating Ring-Opening Metathesis Polymerization Provide Access to Distinct, Multivalent Structures for the Probing of Biological Activity

A myriad of biological processes are facilitated by ligand-receptor interactions. The low affinities of these interactions are typically enhanced by multivalent engagements to promote binding. However, each biological interaction requires a unique display and orientation of ligands. Therefore, the availability and diversity of synthetic multivalent probes are invaluable to the investigation of ligand-receptor binding interactions. Here, we report glycopolymers prepared from bicyclo[4.2.0]oct-6-ene-7-carboxamide and 4,7-dihydro-1,3-dioxepin or cyclohexene. These glycopolymers, synthesized by alternating ring-opening metathesis polymerization, display precise ligand spacing as well as the option of a hydrophobic or acetal-functionalized polymer backbone. Small-angle X-ray scattering (SAXS) data analysis revealed that these [4.2.0] glycopolymers adopted distinct conformations in solution. In aqueous media, [4.2.0]-dioxepin glycopolymers formed swollen polymer chains with rod-like, flexible structures while [4.2.0]-cyclohexene glycopolymers assumed compact, globular structures. To illustrate how these glycopolymers could aid in the exploration of ligand-receptor interactions, we incorporated the [4.2.0] glycopolymers into a biological assay to assess their potential as activators of acrosomal exocytosis (AE) in mouse sperm. The results of the biological assay confirmed that the differing structures of the [4.2.0] glycopolymers would evoke distinct biological responses; [4.2.0]-cyclohexene glycopolymers induced AE in mouse sperm while [4.2.0]-dioxepin glycopolymers did not. Herein, we provide two options for glycopolymers with low to moderate molecular weight dispersities and low cytotoxicity that can be implemented into biological assays based on the desired hydrophobicity, rigidity, and structural conformation of the polymer probe.

Triblock Glycopolymers with Two 10-mer Blocks of Activating Sugars Enhance the Activation of Acrosomal Exocytosis in Mouse Sperm

Carbohydrate recognition is imperative for the induction of sperm acrosomal exocytosis (AE), an essential phenomenon in mammalian fertilization. In mouse sperm, polynorbornene 100-mers displaying fucose or mannose moieties were effective at inducing AE. In contrast, glycopolymers exhibiting glucose sugars resulted in no AE activation. To further elucidate the role of ligand density on the activation of AE in mouse sperm, a triple-stain flow cytometry assay was employed to determine the efficacy of polynorbornene block copolymers with barbell-like sequences as initiators of AE. Triblock (ABA or ABC) copolymers were synthesized by ring-opening metathesis polymerization (ROMP) with one or two activating sugars, mannose or fucose, and one nonactivating sugar, glucose. The active ligand fractions in the polymers varied from 10, 20, or 40%. Simultaneously, random copolymers comprising 20% activating ligands were prepared to confirm the importance of ligand positionality in AE activation in mouse sperm. Polynorbornene 100-mers possessing two 10-mer blocks of activating sugars were the most effective copolymers at inducing AE with levels of AE comparable to their homopolymer counterparts and more effective than their random analogues. Small-angle X-ray scattering (SAXS) was then performed to verify that there were no differences in the conformations of the glycopolymers contributing to their varying AE activity. SAXS data analysis confirmed that all of the glycopolymers assumed semiflexible cylindrical structures with similar radii and Kuhn lengths. These findings suggest that the overall ligand density of the sugar moieties in the polymer is less important than the positionality of short blocks of high-density ligands for AE activation in mouse sperm.

Multivalent Scaffolds to Promote B cell Tolerance

Autoimmune diseases are characterized by aberrant immune responses toward self-antigens. Current treatments lack specificity, promoting adverse effects by broadly suppressing the immune system. Therapies that specifically target the immune cells responsible for disease are a compelling strategy to mitigate adverse effects. Multivalent formats that display numerous binding epitopes off a single scaffold may enable selective immunomodulation by eliciting signals through pathways unique to the targeted immune cells. However, the architecture of multivalent immunotherapies can vary widely, and there is limited clinical data with which to evaluate their efficacy. Here, we set forth to review the architectural properties and functional mechanisms afforded by multivalent ligands and evaluate four multivalent scaffolds that address autoimmunity by altering B cell signaling pathways. First, we address both synthetic and natural polymer backbones functionalized with a variety of small molecule, peptide, and protein ligands for probing the effects of valency and costimulation. Then, we review nanoparticles composed entirely from immune signals which have been shown to be efficacious. Lastly, we outline multivalent liposomal nanoparticles capable of displaying high numbers of protein antigens. Taken together, these examples highlight the versatility and desirability of multivalent ligands for immunomodulation and illuminate strengths and weaknesses of multivalent scaffolds for treating autoimmunity.

Recapitulating the Lateral Organization of Membrane Receptors at the Nanoscale

Many cell membrane functions emerge from the lateral presentation of membrane receptors. The link between the nanoscale organization of the receptors and ligand binding remains, however, mostly unclear. In this work, we applied surface molecular imprinting and utilized the phase behavior of lipid bilayers to create platforms that recapitulate the lateral organization of membrane receptors at the nanoscale. We used liposomes decorated with amphiphilic boronic acids that commonly serve as synthetic saccharide receptors and generated three lateral modes of receptor presentation─random distribution, nanoclustering, and receptor crowding─and studied their interaction with saccharides. In comparison to liposomes with randomly dispersed receptors, surface-imprinted liposomes resulted in more than a 5-fold increase in avidity. Quantifying the binding affinity and cooperativity proved that the boost was mediated by the formation of the nanoclusters rather than a local increase in the receptor concentration. In contrast, receptor crowding, despite the presence of increased local receptor concentrations, prevented multivalent oligosaccharide binding due to steric effects. The findings demonstrate the significance of nanometric aspects of receptor presentation and generation of multivalent ligands including artificial lectins for the sensitive and specific detection of glycans.

Multivalent protein-protein interactions are pivotal regulators of eukaryotic Hsp70 complexes

Heat shock protein 70 (Hsp70) is a molecular chaperone and central regulator of protein homeostasis (proteostasis). Paramount to this role is Hsp70's binding to client proteins and co-chaperones to produce distinct complexes, such that understanding the protein-protein interactions (PPIs) of Hsp70 is foundational to describing its function and dysfunction in disease. Mounting evidence suggests that these PPIs include both "canonical" interactions, which are universally conserved, and "non-canonical" (or "secondary") contacts that seem to have emerged in eukaryotes. These two categories of interactions involve discrete binding surfaces, such that some clients and co-chaperones engage Hsp70 with at least two points of contact. While the contributions of canonical interactions to chaperone function are becoming increasingly clear, it can be challenging to deconvolute the roles of secondary interactions. Here, we review what is known about non-canonical contacts and highlight examples where their contributions have been parsed, giving rise to a model in which Hsp70's secondary contacts are not simply sites of additional avidity but are necessary and sufficient to impart unique functions. From this perspective, we propose that further exploration of non-canonical contacts will generate important insights into the evolution of Hsp70 systems and inspire new approaches for developing small molecules that tune Hsp70-mediated proteostasis.

Allosteric mechanism of signal transduction in the two-component system histidine kinase PhoQ

Transmembrane signaling proteins couple extracytosolic sensors to cytosolic effectors. Here, we examine how binding of Mg²⁺ to the sensor domain of an E. coli two component histidine kinase (HK), PhoQ, modulates its cytoplasmic kinase domain. We use cysteine-crosslinking and reporter-gene assays to simultaneously and independently probe the signaling state of PhoQ’s sensor and autokinase domains in a set of over 30 mutants. Strikingly, conservative single-site mutations distant from the sensor or catalytic site strongly influence PhoQ’s ligand-sensitivity as well as the magnitude and direction of the signal. Data from 35 mutants are explained by a semi-empirical three-domain model in which the sensor, intervening HAMP, and catalytic domains can adopt kinase-promoting or inhibiting conformations that are in allosteric communication. The catalytic and sensor domains intrinsically favor a constitutively ‘kinase-on’ conformation, while the HAMP domain favors the ‘off’ state; when coupled, they create a bistable system responsive to physiological concentrations of Mg²⁺. Mutations alter signaling by locally modulating domain intrinsic equilibrium constants and interdomain couplings. Our model suggests signals transmit via interdomain allostery rather than propagation of a single concerted conformational change, explaining the diversity of signaling structural transitions observed in individual HK domains.

Amphiphilic DNA nanostructures for bottom-up synthetic biology

DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.

Synthetic linear glycopolymers and their biological applications

As typical affinities of carbohydrates with their receptors are modest, polymers of carbohydrates (glycopolymers) are exciting tools to probe the multifaceted biological activities of glycans. In this review, the linear glycopolymers and the multivalency effects are first introduced. This is followed by discussions of methods to synthesize these polymers. Subsequently, the interactions of glycopolymers with plant lectins and viral/bacterial carbohydrate binding proteins are discussed. In addition, applications of the glycopolymers in facilitating glycan microarray studies, mimicking cell surface glycans, modulation of the immune system, cryoprotection of protein, and electron-beam lithography are presented to stimulate further development of this fascinating technology.

Combining Inducible Lectin Expression and Magnetic Glyconanoparticles for the Selective Isolation of Bacteria from Mixed Populations

The selective isolation of bacteria from mixed populations has been investigated in varied applications ranging from differential pathogen identification in medical diagnostics and food safety to the monitoring of microbial stress dynamics in industrial bioreactors. Selective isolation techniques are generally limited to the confinement of small populations in defined locations, may be unable to target specific bacteria, or rely on immunomagnetic separation, which is not universally applicable. In this proof-of-concept work, we describe a novel strategy combining inducible bacterial lectin expression with magnetic glyconanoparticles (MGNPs) as a platform technology to enable selective bacterial isolation from cocultures. An inducible mutant of the type 1 fimbriae, displaying the mannose-specific lectin FimH, was constructed in Escherichia coli allowing for "on-demand" glycan-binding protein presentation following external chemical stimulation. Binding to glycopolymers was only observed upon fimbrial induction and was specific for mannosylated materials. A library of MGNPs was produced via the grafting of well-defined catechol-terminal glycopolymers prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization to magnetic nanoparticles. Thermal analysis revealed high functionalization (≥85% polymer by weight). Delivery of MGNPs to cocultures of fluorescently labeled bacteria followed by magnetic extraction resulted in efficient depletion of type 1 fimbriated target cells from wild-type or afimbriate E. coli. Extraction efficiency was found to be dependent on the molecular weight of the glycopolymers utilized to engineer the nanoparticles, with MGNPs decorated with shorter Dopa-(ManAA)₅₀ mannosylated glycopolymers found to perform better than those assembled from a longer Dopa-(ManAA)₂₀₀ analogue. The extraction efficiency of fimbriated E. coli was also improved when the counterpart strain did not harbor the genetic apparatus for the expression of the type 1 fimbriae. Overall, this work suggests that the modulation of the genetic apparatus encoding bacterial surface-associated lectins coupled with capture through MGNPs could be a versatile tool for the extraction of bacteria from mixed populations.

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

The synthesis of a sulfate-modified dendritic peptide amphiphile and its self-assembly into one-dimensional rod-like architectures in aqueous medium is reported. The influence of the ionic strength on the supramolecular polymerization was probed via circular dichroism spectroscopy and cryogenic transmission electron microscopy. Physiological salt concentrations efficiently screen the charges of the dendritic building block equipped with eight sulfate groups and trigger the formation of rigid supramolecular polymers. Since multivalent sulfated supramolecular structures mimic naturally occurring L-selectin ligands, the corresponding affinity was evaluated using a competitive SPR binding assay and benchmarked to an ethylene glycol-decorated supramolecular polymer.

Microwave-assisted synthesis of glycopolymers by ring-opening metathesis polymerization (ROMP) in an emulsion system

Well-defined glycopolymers fabricated by microwave-accelerated emulsion polymerization offer promising prospects for deciphering glycan-dependent interactions.

Antigen-Specific Binding of Multivalent Soluble Antigen Arrays Induces Receptor Clustering and Impedes B Cell Receptor Mediated Signaling

A pressing need exists for autoimmune disease therapies that act in an antigen-specific manner while avoiding global immunosuppression. Multivalent soluble antigen arrays (SAgAPLP:LABL), designed to induce tolerance to a specific multiple sclerosis autoantigen, consist of a flexible hyaluronic acid (HA) polymer backbone cografted with multiple copies of autoantigen peptide (PLP) and cell adhesion inhibitor peptide (LABL). Previous in vivo studies revealed copresentation of both signals on HA was necessary for therapeutic efficacy. To elucidate therapeutic cellular mechanisms, in vitro studies were performed in a model B cell system to evaluate binding and specificity. Compared to HA and HA arrays containing only grafted PLP or LABL, SAgAPLP:LABL displaying both PLP and LABL exhibited greatly enhanced B cell binding. Furthermore, the binding avidity of SAgAPLP:LABL was primarily driven by the PLP antigen, determined via flow cytometry competitive dissociation studies. Fluorescence microscopy showed SAgAPLP:LABL induced mature receptor clustering that was faster than other HA arrays with only one type of grafted peptide. SAgAPLP:LABL molecules also reduced and inhibited IgM-stimulated signaling as discerned by a calcium flux assay. The molecular mechanisms of enhanced antigen-specific binding, mature receptor clustering, and dampened signaling observed in B cells may contribute to SAgAPLP:LABL therapeutic efficacy.

Molecular Dynamics of Multivalent Soluble Antigen Arrays Support a Two-Signal Co-delivery Mechanism in the Treatment of Experimental Autoimmune Encephalomyelitis

Many current therapies for autoimmune diseases such as multiple sclerosis (MS) result in global immunosuppression, rendering insufficient efficacy with increased risk of adverse side effects. Multivalent soluble antigen arrays, nanomaterials presenting both autoantigen and secondary inhibitory signals on a flexible polymer backbone, are hypothesized to shift the immune response toward selective autoantigenic tolerance to repress autoimmune disease. Two-signal co-delivery of both autoantigen and secondary signal were deemed necessary for therapeutic efficacy against experimental autoimmune encephalomyelitis, a murine model of MS. Dynamic light scattering and in silico molecular dynamics simulations complemented these studies to illuminate the role of two-signal co-delivery in determining therapeutic potential. Physicochemical characteristics such as particle size and molecular affinity for intermolecular interactions and chain entanglement likely facilitated cotransport of two signals to produce efficacy. These findings elucidate potential mechanisms whereby soluble antigen arrays enact their therapeutic effect and help to guide the development of future multivalent antigen-specific immunotherapies.

Glycopolymers Prepared by Ring-Opening Metathesis Polymerization Followed by Glycoconjugation Using a Triazole-Forming "Click" Reaction

We describe a protocol for the preparation of glycopolymers derived from the ring-opening polymerization of a norbornene carboxylic acid derivative. Polymerization is followed by attachment of a linker and subsequent glycoconjugation via a triazole-forming azide-alkyne click reaction. The use of a protected amine-terminating agent allows for the attachment of a probe molecule such as a fluorescein dye. The syntheses of a neutral galactopolymer as well a polyanionic poly-3-O-sulfo-galactopolymer are described.

Bacterial chemoreceptors and chemoeffectors

Bacteria use chemotaxis signaling pathways to sense environmental changes. Escherichia coli chemotaxis system represents an ideal model that illustrates fundamental principles of biological signaling processes. Chemoreceptors are crucial signaling proteins that mediate taxis toward a wide range of chemoeffectors. Recently, in deep study of the biochemical and structural features of chemoreceptors, the organization of higher-order clusters in native cells, and the signal transduction mechanisms related to the on-off signal output provides us with general insights to understand how chemotaxis performs high sensitivity, precise adaptation, signal amplification, and wide dynamic range. Along with the increasing knowledge, bacterial chemoreceptors can be engineered to sense novel chemoeffectors, which has extensive applications in therapeutics and industry. Here we mainly review recent advances in the E. coli chemotaxis system involving structure and organization of chemoreceptors, discovery, design, and characterization of chemoeffectors, and signal recognition and transduction mechanisms. Possible strategies for changing the specificity of bacterial chemoreceptors to sense novel chemoeffectors are also discussed.

Photoactivatable glycopolymers for the proteome-wide identification of fucose-α(1-2)-galactose binding proteins

Although fucose-α(1-2)-galactose (Fucα(1-2)Gal)-containing glycans have been implicated in cognitive processes such as learning and memory, their precise molecular mechanisms are poorly understood. Here we employed the use of multivalent glycopolymers to enable the first proteome-wide identification of weak affinity, low abundance Fucα(1-2)Gal glycan-binding proteins (GBPs). Biotin-terminated glycopolymers containing photoactivatable cross-linking groups were designed to capture and enrich GBPs from rat brain lysates. Candidate proteins were tested for their ability to bind Fucα(1-2)Gal, and the functional significance of the interaction was investigated for the synaptic vesicle protein SV2a using a knockout mouse system. The results suggest a role for SV2a-Fucα(1-2)Gal interactions in SV2a trafficking and synaptic vesicle recycling. More broadly, our studies outline a general chemical approach for the systems-level discovery of novel GBPs.

Glycopolymer probes of signal transduction

Glycans are key participants in biological processes ranging from reproduction to cellular communication to infection. Revealing glycan roles and the underlying molecular mechanisms by which glycans manifest their function requires access to glycan derivatives that vary systematically. To this end, glycopolymers (polymers bearing pendant carbohydrates) have emerged as valuable glycan analogs. Because glycopolymers can readily be synthesized, their overall shape can be varied, and they can be altered systematically to dissect the structural features that underpin their activities. This review provides examples in which glycopolymers have been used to effect carbohydrate-mediated signal transduction. Our objective is to illustrate how these powerful tools can reveal the molecular mechanisms that underlie carbohydrate-mediated signal transduction.

End-labeled amino terminated monotelechelic glycopolymers generated by ROMP and Cu(I)-catalyzed azide-alkyne cycloaddition

Functionalizable monotelechelic polymers are useful materials for chemical biology and materials science. We report here the synthesis of a capping agent that can be used to terminate polymers prepared by ring-opening metathesis polymerization of norbornenes bearing an activated ester. The terminating agent is a cis-butene derivative bearing a Teoc (2-trimethylsilylethyl carbamate) protected primary amine. Post-polymerization modification of the polymer was accomplished by amidation with an azido-amine linker followed by Cu(I)-catalyzed azide–alkyne cycloaddition with propargyl sugars. Subsequent Teoc deprotection and conjugation with pyrenyl isothiocyanates afforded well-defined end-labeled glycopolymers.

Biophysical regulation of stem cell behavior within the niche

Stem cells reside within most tissues throughout the lifetimes of mammalian organisms. To maintain their capacities for division and differentiation and thereby build, maintain, and regenerate organ structure and function, these cells require extensive and precise regulation, and a critical facet of this control is the local environment or niche surrounding the cell. It is well known that soluble biochemical signals play important roles within such niches, and a number of biophysical aspects of the microenvironment, including mechanical cues and spatiotemporally varying biochemical signals, have also been increasingly recognized to contribute to the repertoire of stimuli that regulate various stem cells in various tissues of both vertebrates and invertebrates. For example, biochemical factors immobilized to the extracellular matrix or the surface of neighboring cells can be spatially organized in their placement. Furthermore, the extracellular matrix provides mechanical support and regulatory information, such as its elastic modulus and interfacial topography, which modulate key aspects of stem cell behavior. Numerous examples of each of these modes of regulation indicate that biophysical aspects of the niche must be appreciated and studied in conjunction with its biochemical properties.

Multivalent ligand: design principle for targeted therapeutic delivery approach

Multivalent interactions of biological molecules play an important role in many biochemical events. A multivalent ligand comprises of multiple copies of ligands conjugated to scaffolds, allowing the simultaneous binding of multivalent ligands to multiple binding sites or receptors. Many research groups have successfully designed and synthesized multivalent ligands to increase the binding affinity, avidity and specificity of the ligand to the receptor. A multimeric ligand is a promising option for the specific treatment of diseases. In this review, the factors affecting multivalent interactions, including the size and shape of the ligand, geometry and an arrangement of ligands on the scaffold, linker length, thermodynamic, and kinetics of the interactions are discussed. Examples of the multivalent ligand applications for therapeutic delivery are also summarized.

Polyvalent nucleic acid aptamers and modulation of their activity: a focus on the thrombin binding aptamer

Nucleic acid-based aptamers can be selected from combinatorial libraries of synthetic oligonucleotides to bind, with affinity and specificity similar to antibodies, a wide range of biomedically relevant targets. Compared to protein therapeutics, aptamers exhibit significant advantages in terms of size, non-immunogenicity and wide synthetic accessibility. Various chemical modifications have been introduced in the natural oligonucleotide backbone of aptamers in order to increase their half-life, as well as their pharmacological properties. Very effective alternative approaches, devised in order to improve both the aptamer activity and stability, were based on the design of polyvalent aptamers, able to establish multivalent interactions with the target: thus, multiple copies of an aptamer can be assembled on the same molecular- or nanomaterial-based scaffold. In the present review, the thrombin binding aptamers (TBAs) are analyzed as a model system to study multiple-aptamer constructs aimed at improving their anticoagulation activity in terms of binding to the target and stability to enzymatic degradation. Indeed - even if the large number of chemically modified TBAs investigated in the last 20 years has led to encouraging results - a significant progress has been obtained only recently with bivalent or engineered dendritic TBA aptamers, or assemblies of TBAs on nanoparticles and DNA nanostructures. Furthermore, the modulation of the aptamers activity by means of tailored drug-active reversal agents, especially in the field of anticoagulant aptamers, as well as the reversibility of the TBA activity through the use of antidotes, such as porphyrins, complementary oligonucleotides or of external stimuli, are discussed.

Architecture effects on L-selectin shedding induced by polypeptide-based multivalent ligands

Multivalent interactions between selectins and their ligands play key roles in mediating the rolling and tethering of leukocytes in the early steps of the inflammatory response, as well as in lymphocyte circulation. L-selectin shedding, which is the proteolytic cleavage of L-selectin, can be induced by L-selectin clustering through the binding of multivalent ligands to multiple L-selectin molecules, and it has been shown to regulate leukocyte rolling and subsequent integrin activation for firm adhesion. In this paper, we report the production of homogenous glycopolypeptides modified with a 3,6-disulfo-galactopyranoside equipped with a caproyl linker. The saccharide residue was chemically attached to various polypeptide backbones of differing architectures; the composition and purity of the sulfated glycopolypeptides was confirmed via¹H-NMR spectroscopy, amino acid analysis (AAA), and electrophoretic analysis. The retention of the conformation of the polypeptide backbone was confirmed via circular dichroic spectroscopy. The shedding of l-selectin from the surface of Jurkat cells induced by these sulfated glycopolypeptides, determined via ELISA-based methods, varied based on differences in the architectures of the polypeptide scaffolds, suggesting opportunities for these strategies in probing cell-surface receptor arrays and directing cell signaling events.

Phototactic and chemotactic signal transduction by transmembrane receptors and transducers in microorganisms

Microorganisms show attractant and repellent responses to survive in the various environments in which they live. Those phototaxic (to light) and chemotaxic (to chemicals) responses are regulated by membrane-embedded receptors and transducers. This article reviews the following: (1) the signal relay mechanisms by two photoreceptors, Sensory Rhodopsin I (SRI) and Sensory Rhodopsin II (SRII) and their transducers (HtrI and HtrII) responsible for phototaxis in microorganisms; and (2) the signal relay mechanism of a chemoreceptor/transducer protein, Tar, responsible for chemotaxis in E. coli. Based on results mainly obtained by our group together with other findings, the possible molecular mechanisms for phototaxis and chemotaxis are discussed.

Manipulation of electrostatic and saccharide linker interactions in the design of efficient glycopolypeptide-based cholera toxin inhibitors

Multivalent, glycopolymer inhibitors designed for the treatment of disease and pathogen infection have shown improvements in binding correlated with general changes in glycopolymer architecture and composition. We have previously demonstrated that control of glycopolypeptide backbone extension and ligand spacing significantly impacts the inhibition of the cholera toxin B subunit pentamer (CT B(5)) by these polymers. In the studies reported here, we elucidate the role of backbone charge and linker length in modulating the inhibition event. Peptides of the sequence AXPXG (where X is a positive, neutral or negative amino acid), equipped with the alkyne functionality of propargyl glycine, were designed and synthesized via solid-phase peptide synthetic methods and glycosylated via Cu(I)-catalyzed alkyne-azide cycloaddition reactions. The capacity of the glycopeptides to inhibit the binding of the B(5) subunit of cholera toxin was evaluated. These studies indicated that glycopeptides with a negatively charged backbone show improved inhibition of the binding event relative to the other glycopeptides. In addition, variations in the length of the linker between the peptide and the saccharide ligand also affected the inhibition of CT by the glycopeptides. Our findings suggest that, apart from appropriate saccharide spacing and polypeptide chain extension, saccharide linker conformation and the systematic placement of charges on the polypeptide backbone are also significant variables that can be tuned to improve the inhibitory potencies of glycopolypeptide-based multivalent inhibitors.

Flow cytometry reveals that multivalent chemoattractants effect swarmer cell dedifferentiation

Bacterial cells can differentiate into states that allow them to respond efficiently to their environment. An example of such a transformation is the differentiation of planktonic bacteria into highly motile swarmer cells. The hyperflagellated, filamentous swarmer cells can use coordinated movement to seek out and colonize new sites for pathogenic infection. Because the chemotaxis proteins are essential for swarmer differentiation, we sought to probe the relationship between differentiation and chemoattractants. To this end, we developed a method to screen large populations of swarmer cells using flow cytometry. Using this approach, we found that highly potent multivalent chemoattractants can induce the dedifferentiation of swarmer cells. Our results indicate that chemotactic signaling functions as a target for agents that interfere with bacterial swarming. In addition, the identification of ligands that promote the dedifferentiation of swarmer cells offers new strategies for modulating this multicellular behavior.

Supramolecular assemblies of amphiphilic homopolymers

Amphiphilic molecules self-assemble in solvents because of the differential solvation of the hydrophilic and lipophilic functionalities. Small-molecule surfactants have long been known to form micelles in water that can solubilize lipophilic guest molecules in their water-excluded interior. Polymeric surfactants based on block copolymers are also known to form several types of aggregates in water owing either to the mutual incompatibility of the blocks or better solvation of one of the blocks by the solvent. Incorporating amphiphilicity at smaller length scales in polymers would provide an avenue to capture the interesting properties of macromolecules and fine tune their supramolecular assemblies. To address this issue, we designed and synthesized amphiphilic homopolymers containing hydrophilic and lipophilic functionalities in the monomer. Such a polymer can be imagined to be a string of small-molecule surfactants tethered together such that the hydrophilic and lipophilic functionalities are located on opposite faces, rendering the assemblies facially amphiphilic. This feature article describes the self-assembly of our amphiphilic homopolymers in polar and apolar solvents. These homopolymers not only form micelles in water but also form inverse micelles in organic solvents. Subtle changes to the molecular structure have been demonstrated to yield vesicles in water and inverted micelles in organic solvents. The characterization of these assemblies and their applications in separations, catalysis, and sensing are described here.

Structure-based design of a periplasmic binding protein antagonist that prevents domain closure

Many receptors undergo ligand-induced conformational changes to initiate signal transduction. Periplasmic binding proteins (PBPs) are bacterial receptors that exhibit dramatic conformational changes upon ligand binding. These proteins mediate a wide variety of fundamental processes including transport, chemotaxis, and quorum sensing. Despite the importance of these receptors, no PBP antagonists have been identified and characterized. In this study, we identify 3-O-methyl-d-glucose as an antagonist of glucose/galactose-binding protein and demonstrate that it inhibits glucose chemotaxis in E. coli. Using small-angle X-ray scattering and X-ray crystallography, we show that this antagonist acts as a wedge. It prevents the large-scale domain closure that gives rise to the active signaling state. Guided by these results and the structures of open and closed glucose/galactose-binding protein, we designed and synthesized an antagonist composed of two linked glucose residues. These findings provide a blueprint for the design of new bacterial PBP inhibitors. Given the key role of PBPs in microbial physiology, we anticipate that PBP antagonists will have widespread uses as probes and antimicrobial agents.

Engineered single- and multi-cell chemotaxis pathways in E. coli

We have engineered the chemotaxis system of Escherichia coli to respond to molecules that are not attractants for wild-type cells. The system depends on an artificially introduced enzymatic activity that converts the target molecule into a ligand for an E. coli chemoreceptor, thereby enabling the cells to respond to the new attractant. Two systems were designed, and both showed robust chemotactic responses in semisolid and liquid media. The first incorporates an asparaginase enzyme and the native E. coli aspartate receptor to produce a response to asparagine; the second uses penicillin acylase and an engineered chemoreceptor for phenylacetic acid to produce a response to phenylacetyl glycine. In addition, by taking advantage of a ‘hitchhiker' effect in which cells producing the ligand can induce chemotaxis of neighboring cells lacking enzymatic activity, we were able to design a more complex system that functions as a simple microbial consortium. The result effectively introduces a logical ‘AND' into the system so that the population only swims towards the combined gradients of two attractants.

Chemical probes of bacterial signal transduction reveal that repellents stabilize and attractants destabilize the chemoreceptor array

The signal transduction cascade responsible for bacterial chemotaxis serves as a model for understanding how cells perceive and respond to their environments. Bacteria react to chemotactic signals by migrating toward attractants and away from repellents. Recent data suggest that the amplification of attractant stimuli depends on receptor collaboration: occupied and unoccupied chemoreceptors act together to relay attractant signals. Attractant signal transmission, therefore, depends on the organization of the chemoreceptors into a lattice of signaling proteins. The importance of this lattice for transducing repellent signals was unexplored. Here, we investigate the role of inter-receptor communication on repellent responses in Escherichia coli. Previously, we found that multivalent displays of attractants are more potent than their monovalent counterparts. To examine the importance of the chemoreceptor lattice in repellent signaling, we synthesized ligands displaying multiple copies of the repellent leucine. Monomeric leucine and low-valency leucine-displaying polymers were sensed as repellents. In contrast, multivalent displays of leucine capable of binding multiple chemoreceptors function not as potent repellents but as attractants. Intriguingly, chemical cross-linking studies indicate that these multivalent ligands, like monovalent attractants, disrupt the cellular chemoreceptor lattice. Thus, repellents stabilize the intrinsic chemoreceptor lattice, and attractants destabilize it. These results indicate that signals can be transmitted with high sensitivity via the disruption of protein-protein interactions. Moreover, our data demonstrate that repellents can be transformed into attractants merely by their multivalent display. These results have implications for designing agonists and antagonists for other signaling systems.

Architecture Effects on the Binding of Cholera Toxin by Helical Glycopolypeptides

A variety of binding events in biological systems are mediated by multivalent interactions between oligosaccharides and saccharide receptors present on pathogens and cell surfaces. In particular, given the important role of multivalent interaction between proteins and carbohydrates in the initial step of pathogen recognition, many glycosylated molecules and polymers have been synthesized in order to mimic the carbohydrate ligands and to inhibit the binding of the pathogen to its target. In this work, we extend our evaluation of the impact of the architecture of well-defined glycopolypeptides on the inhibition of binding of the cholera toxin B pentamer (CT B(5)) subunit. Here we report the production of two families of α-helical glycopolypeptides which were synthesized via a combination of protein engineering and chemical methods. The presentation of pendant saccharides on the polypeptide backbones, as well as their valencies, can be well controlled via these methods. Control of the backbone conformation, introduced in this report, is also possible via these strategies. The polypeptides and glycopolypeptides were characterized via SDS-PAGE analysis, (1)H NMR, and MALDI-TOF mass spectrometry. Their conformation and hydrodynamic volume were characterized by circular dichroic (CD) spectroscopy and gel permeation chromatography (GPC), respectively. The binding of CT B(5) by these glycopolypeptides was evaluated via direct enzyme-linked immunosorbent assay (DELA). The effects of spacing and conformation were elucidated by comparison of the binding exhibited by helical glycopolypeptides with that of random-coil glycopolypeptides.

Rigid multivalent scaffolds based on adamantane

We present two new synthetic strategies to rigid multivalent scaffolds of the general structure 1 based on adamantane. Both routes start from arylated adamantane derivatives and give the target compounds 12 and 18 in 5 and 7 steps, respectively. These scaffolds have been designed for the assembly of multivalent binders for cell surface epitopes. The adamantane nucleus exposes three carboxylic acid groups in a well-defined tripodal geometry for conjugation of targeting ligands. In addition, an amino group at the fourth bridgehead position provides a flexible linker for attachment of effector molecules such as contrast agents, radiotracers, or cytotoxins without interfering with the cell binding process.

Effects of Saccharide Spacing and Chain Extension on Toxin Inhibition by Glycopolypeptides of Well-Defined Architecture

Many recognition events important in biology are mediated via multivalent interactions between relevant oligosaccharides and multiple saccharide receptors present on lectins, viruses, toxins, and cell surfaces. Because of the important role played by protein-carbohydrate interactions in these pathogenic recognition events and in other human diseases, considerable effort has been devoted toward the development of multivalent polymeric ligands for carbohydrate-binding proteins. In this work, we report the synthesis of new polypeptide-based glycopolymers produced via a combination of protein engineering and chemical methods. These methodologies permit control over the number and the spacing of saccharides on the scaffold, as well as the conformation of the polymer backbone, and allow a more purposeful design of polymers for manipulation of multivalent binding events. Two families of galactose-bearing glycopolypeptides with random coil conformations, [(AG)(3)PEG](y) (y = 10 and 16) and {[(AG)(2)PSG](2)[(AG)(2)PEG][(AG)(2)PSG](2)}(y) (y = 6), have been synthesized. The carboxylic acid functionality of the glutamic acid residues allowed subsequent modification with amino-saccharides to yield the desired glycopolypeptides; selective placement of the glutamic acid group permitted investigation of the effects of multivalency and saccharide spacing on toxin inhibition. In addition, a family of galactose-functionalized PGA-based glycopolymers of varying molecular weights was also synthesized to compare the effects of backbone flexibility and hydrodynamic volume, relative to the recombinant glycopolypeptides, on toxin inhibition. Glycopolypeptides were characterized via (1)H NMR, MALDI-TOF mass spectrometry, SDS-PAGE analysis, and spectrophotometric assays. They were tested as inhibitors of the binding of the cholera toxin B subunit via direct enzyme-linked assays. The data from these experiments confirm the relevance of appropriate saccharide spacing on controlling the binding event and also indicate the influence of chain extension in improving inhibition.

Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures

D-Glucose/D-Galactose-binding protein (GGBP) mediates chemotaxis toward and active transport of glucose and galactose in a number of bacterial species. GGBP, like other periplasmic binding proteins, can exist in open (ligand-free) and closed (ligand-bound) states. We report a 0.92 angstroms resolution structure of GGBP from Escherichia coli in the glucose-bound state and the first structure of an open, unbound form of GGBP (at 1.55 angstroms resolution). These structures vary in the angle between the two structural domains; the observed difference of 31 degrees arises from torsion angle changes in a three-segment hinge. A comparison with the closely related periplasmic receptors, ribose- and allose-binding proteins, shows that the GGBP hinge residue positions that undergo the largest conformational changes are different. Furthermore, the high-quality data collected for the atomic resolution glucose-bound structure allow for the refinement of specific hydrogen atom positions, the assignment of alternate side chain conformations, the first description of CO(2) trapped after radiation-induced decarboxylation, and insight into the role of the exo-anomeric effect in sugar binding. Together, these structures provide insight into how the hinge-bending movement of GGBP facilitates ligand binding, transport, and signaling.

Synthesis of Neoglycopolymers by a Combination of “Click Chemistry” and Living Radical Polymerization

The synthesis of novel well-defined alkyne side chain functional polymers featuring narrow molecular weight distributions (PDI = 1.09-1.17) by living radical polymerization is described. Grafting of protected and unprotected carbohydrates is achieved via either a C-6 or an anomeric azide (alpha or beta) onto these polymers by Cu(I)-catalyzed "click chemistry", providing a simple and efficient route to synthetic glycopolymers. The strategy provides an extremely powerful tool for the synthesis of libraries of materials that differ only in the nature of the sugar moiety presented on a well-defined polymer scaffold. A library of multivalent ligands were then prepared following a "coclicking" synthetic protocol, and the reactivity of these glycopolymers in the presence of concanavalin A and Ricinus communis agglutinin, model lectins able to selectively bind appropriate mannose and galactose derivatives, respectively, was assessed.

Dynamic molecular recognition on the surface of vesicle membranes

The ability of a vesicle-bound receptor to associate with a water-soluble ligand increases with membrane loading level and the presence of membrane additives with cationic N-CH3 groups.

Hitting multiple targets with multimeric ligands

Multimeric ligands consist of multiple monomeric ligands attached to a single backbone molecule, creating a multimer that can bind to multiple receptors or targets simultaneously. Numerous examples of multimeric binding exist within nature. Due to the multiple and simultaneous binding events, multimeric ligands bind with an increased affinity compared to their corresponding monomers. Multimeric ligands may provide opportunities in the field of drug discovery by providing enhanced selectivity and affinity of binding interactions, thus providing molecular-based targeted therapies. However, gaps in our knowledge currently exist regarding the quantitative measures for important design characteristics, such as flexibility, length and orientation of the inter-ligand linkers, receptor density and ligand sequence. In this review, multimeric ligand binding in two separate phases is examined. The prerecruitment phase describes the binding of one ligand of a multimer to its corresponding receptor, an event similar to monomeric ligand binding. This results in transient increases in the local concentration of the other ligands, leading to apparent cooperativity. The postrecruitment phase only occurs once all receptors have been aligned and bound by their corresponding ligand. This phase is analogous to DNA-DNA interactions in that the stability of the complex is derived from physical orientation. Multiple factors influence the kinetics and thermodynamics of multimeric binding, and these are discussed.

Link between chemotactic response to Ni2+ and its adsorption onto the Escherichia coli cell surface

Bacterial chemotaxis is of medical, biological, and geological significance. Despite its importance, current chemotaxis measurements fail to account for the speciation of the chemical effector and the protonation state of the bacterial surface. We hypothesize that adsorption of Ni2+ onto the surface of Escherichia coli can influence its effective concentration and therefore influence its ability to induce a repellent response. By measuring repellent response at different pH values, the influence of Ni2+ adsorption on chemotaxis was assessed. In addition, we tested the effect of different Ni2+ chelating agents. Our data indicate that adsorption reactions influence the chemotactic response to Ni2+. We use potentiometric titration and Ni2+ adsorption experiments to develop and constrain a thermodynamic model capable of quantifying the concentration of Ni2+ at the bacteria/solution interface. Results from this model predict that the concentration of adsorbed Ni2+ is linearly proportional to the magnitude of the chemotactic response in E. coli. If adsorption is linked to chemotaxis in other cases, then chemotactic responses in realistic settings depend on a number of environmental factors such as pH, competing binding agents (e.g., aqueous organic acids, natural organic matter, mineral surfaces, etc.), and ionic strength. Our modeling approach quantifies adsorbed species on bacterial surfaces and may be used to predict the responses of different species to a variety of chemoeffectors. Our data suggest that specified changes in environmental conditions can be used to tune chemotactic responses in natural biological and geological settings.