Polyvalent Hybrid Virus-Like Nanoparticles with Displayed Heparin Antagonist Peptides.

The potential applications for nanomaterials continue to grow as new materials are developed and environmental and safety concerns are more adequately addressed. In particular, virus-like particles (VLPs) have myriad applications in medicine and biology, exploiting both the reliable, symmetric self-assembly mechanism and the ability to take advantage of surface functionalities that may be appropriately modified through mutation or bioconjugation. Herein we describe the design and application of hybrid VLPs for use as potent heparin antagonists, providing an alternative to the toxic heparin antidote protamine. A two-plasmid system was utilized to generate VLPs that contain both the wild-type coat protein and a second coat protein with either a C- or N-terminal cationic peptide extension (4-28 amino acids). Incorporation of the modified coat proteins varied from 8 to 31%, while activated partial thromboplastin time (APTT) assays revealed a range of the heparin antagonist activity. Notably, when examined on the basis of the quantity of peptide delivered due to the varied incorporation rates, it appeared that the VLPs largely followed a similar trend, with the quantity of peptide delivered more closely correlating with heparin antagonist activity. The particle with the highest incorporation rate and best antiheparin activity displayed the C-terminal peptide ARK2A2KA, which corresponds to the Cardin-Weintraub consensus sequence for binding to glycosaminoglycans. Analysis of this particle using heparin affinity chromatography with fraction collection revealed that particles eluting at higher salt concentration had a greater proportion of peptide incorporation. Preliminary dual polarization interferometry experiments further support a strong interaction between this particle and heparin.

Heparin Binding to an Engineered Virus-like Nanoparticle Antagonist.

The anticoagulant activity of heparin administered during medical interventions must be reversed to restore normal clotting, typically by titrating with protamine. Given the acute toxicity associated with protamine, we endeavored to generate safer heparin antagonists by engineering bacteriophage Qß virus-like particles (VLPs) to display motifs that bind heparin. A particle bearing a single amino acid change from wild-type (T18R) was identified as a promising candidate for heparin antagonism. Surface potential maps generated through molecular modeling reveal that the T18R mutation adds synergistically to adjacent positive charges on the particle surface, resulting in a large solvent-accessible cationic region that is replicated 180 times over the capsid. Chromatography using a heparin-sepharose column confirmed a strong interaction between heparin and the T18R particle. Binding studies using fluorescein-labeled heparin (HepFL) resulted in a concentration-dependent change in fluorescence intensity, which could be perturbed by the addition of unlabeled heparin. Analysis of the fluorescence data yielded a dissociation constant of approximately 1 nM and a 1:1 binding stoichiometry for HepFL:VLP. Dynamic light scattering (DLS) experiments suggested that T18R forms discrete complexes with heparin when the VLP:heparin molar ratios are equivalent, and in vitro clotting assays confirmed the 1:1 binding stoichiometry as full antagonism of heparin is achieved. Biolayer interferometry and backscattering interferometry corroborated the strong interaction of T18R with heparin, yielding Kd ∼ 1-10 nM. These biophysical measurements further validated T18R, and VLPs in general, for potential clinical use as effective, nontoxic heparin antagonists.

Electrochemical and structural characterization of Azotobacter vinelandii flavodoxin II.

Azotobacter vinelandii flavodoxin II serves as a physiological reductant of nitrogenase, the enzyme system mediating biological nitrogen fixation. Wildtype A. vinelandii flavodoxin II was electrochemically and crystallographically characterized to better understand the molecular basis for this functional role. The redox properties were monitored on surfactant-modified basal plane graphite electrodes, with two distinct redox couples measured by cyclic voltammetry corresponding to reduction potentials of -483 ± 1 mV and -187 ± 9 mV (vs. NHE) in 50 mM potassium phosphate, 150 mM NaCl, pH 7.5. These redox potentials were assigned as the semiquinone/hydroquinone couple and the quinone/semiquinone couple, respectively. This study constitutes one of the first applications of surfactant-modified basal plane graphite electrodes to characterize the redox properties of a flavodoxin, thus providing a novel electrochemical method to study this class of protein. The X-ray crystal structure of the flavodoxin purified from A. vinelandii was solved at 1.17 Å resolution. With this structure, the native nitrogenase electron transfer proteins have all been structurally characterized. Docking studies indicate that a common binding site surrounding the Fe-protein [4Fe:4S] cluster mediates complex formation with the redox partners Mo-Fe protein, ferredoxin I, and flavodoxin II. This model supports a mechanistic hypothesis that electron transfer reactions between the Fe-protein and its redox partners are mutually exclusive.

Heterogeneous catalysis for azide-alkyne bioconjugation in solution via spin column: Attachment of dyes and saccharides to peptides and DNA.

Copper-catalyzed azide-alkyne cycloaddition (CuAAC) "click" chemistry is widely used and has demonstrated particular utility for bio-orthogonal conjugation reactions. Here we describe a one-pot, heterogeneous bioconjugation and purification method for selectively activated CuAAC. A Cu(II) precursor, with either the neutral ligand 1,10-phenanthroline-5,6-dione or the anionic ligand 4,7-diphenyl-1,10-phenanthroline-disulfonic acid, is converted to the active Cu(I) species within an ion-exchange matrix using zinc amalgam as the reducing agent. The Cu(I) complexes are then layered on top of a size-exclusion matrix within a commercial microcentrifuge spin column; passing a mixture of an ethynyl-labeled biomolecule and an azide-bearing ligand through the column results in clean and efficient coupling. The methodology is demonstrated by glycosylating a DNA oligonucleotide as well as by labeling a membrane-penetrating peptide (octa-arginine) with a coumarin dye.

Bio-layer interferometry of a multivalent sulfated virus nanoparticle with heparin-like anticoagulant activity.

Heparin is a sulfated glycosaminoglycan that is routinely used as an anticoagulant. It is typically purified from bovine or porcine sources, leading to heterogeneity that poses several challenges when used clinically. We have found that the bacteriophage Qß can be selectively sulfated to yield virus-like nanoparticles (sulf-VLP) that elicit anticoagulant activity similar to heparin. In an effort to explore the binding interactions that heparin-like VLPs make with cationic targets, described herein are bio-layer interferometry studies utilizing the BLItz platform that evaluate the interaction of sulf-VLP with the cationic peptide CDK5 (50% Lys). Streptavidin biosensors modified with biotin-CDK5 were found to bind strongly to sulf-VLP and not to the underivatized nanoparticle. Titration of sulf-VLP yielded concentration-dependent sensorgrams, permitting calculation of rate and equilibrium constants: k(on) = (8 ± 3) × 10(6) s(-1) for the association phase, k(off )= (5 ± 2) × 10(-3) M s(-1) for the dissociation phase, yielding an overall dissociation constant K(D)~ 1 nM. Fitting was best achieved using an equation possessing both exponential and linear terms, suggesting a mechanism more complex than 1:1 binding. To mitigate multivalency and rebinding effects, experiments were conducted with protamine (~70% Arg) added during the dissociation phase, leading to more pronounced dissociation curves and k off values that yielded a near-linear relationship with protamine concentration.

Directed polyvalent display of sulfated ligands on virus nanoparticles elicits heparin-like anticoagulant activity.

Heparin is a sulfated glycosaminoglycan that is widely used as an anticoagulant. It is typically extracted from porcine or bovine sources to yield a heterogeneous mixture that varies both in molecular weight and in degree of sulfation. This heterogeneity, coupled with concern for contamination, has led to widespread interest in developing safer alternatives. Described herein are sulfated bacteriophage Qß virus-like particles (VLPs) that elicit heparin-like anticoagulant activity. Sulfate groups were appended to the VLP by synthesis of single- and triple-sulfated ligands that also contained azide groups. Following conversion of VLP surface lysine groups to alkynes, the sulfated ligands were attached to the VLP via copper-catalyzed azide-alkyne cycloaddition (CuAAC). MALDI-MS analysis of the intermediate alkyne VLP indicated that the majority of the coat proteins contained 5-7 of the alkyne linkers; similar analysis of the intermediate alkyne particles conjugated to a fluorescein azide suggest that nearly the same number of attachment points (3-6) are modified via CuAAC. Analysis by SDS-PAGE with fluorescent staining indicated altered migration patterns for the various constructs: compared to the wild-type nanoparticle, the modified coat proteins appeared to migrate farther toward the positive pole in the gel, with coat proteins displaying the triple-sulfated ligand migrating significantly farther. Clotting activity analyzed by activated partial thrombin time (APTT) assay showed that the sulfated particles were able to perturb coagulation, with VLPs displaying the triple-sulfated ligand approximately as effective as heparin on a per mole basis; this activity could be partially reversed by protamine. ELISA experiments to assess the response of the complement system to the VLPs indicate that sulfating the particles may reduce complement activation.

Engineered virus-like nanoparticle heparin antagonists.

Virus nanoparticles provide a self-assembling, reproducible multivalent platform that can be chemically and genetically manipulated for the presentation of a wide array of epitopes. Presented herein are engineered bacteriophage Qß nanoparticles that function as potent heparin antagonists. Three successful approaches have been used: 1) chemically appending poly-Arg peptides; 2) point mutations to Arg on the virus capsid; 3) incorporation of heparin-binding peptides displayed externally on the virus surface. Each approach generates particles with good heparin antagonist activity with none of the toxic side effects of protamine, the only drug currently FDA-approved for clinical use as a heparin antagonist.

Electrochemistry of mammalian cytochrome P450 2B4 indicates tunable thermodynamic parameters in surfactant films.

Electrochemical methods continue to present an attractive means for achieving in vitro biocatalysis with cytochromes P450; however understanding fully the nature of electrode-bound P450 remains elusive. Herein we report thermodynamic parameters using electrochemical analysis of full-length mammalian microsomal cytochrome P450 2B4 (CYP 2B4) in didodecyldimethylammonium bromide (DDAB) surfactant films. Electronic absorption spectra of CYP 2B4-DDAB films on silica slides reveal an absorption maximum at 418nm, characteristic of low-spin, six-coordinate, water-ligated Fe(III) heme in P450. The Fe(III/II) and Fe(II/I) redox couples (E1/2) of substrate-free CYP 2B4 measured by cyclic voltammetry are -0.23V and -1.02V (vs. SCE, or 14mV and -776mV vs. NHE) at 21°C. The standard heterogeneous rate constant for electron transfer from the electrode to the heme for the Fe(III/II) couple was estimated at 170s(-1). Experiments indicate that the system is capable of catalytic reduction of dioxygen, however substrate oxidation was not observed. From the variation of E1/2 with temperature (18-40°C), we have measured entropy and enthalpy changes that accompany heme reduction, -151Jmol(-1)K(-1) and -46kJmol(-1), respectfully. The corresponding entropy and enthalpy values are less for the six-coordinate low-spin, imidazole-ligated enzyme (-59Jmol(-1)K(-1) and -18kJmol(-1)), consistent with limited conformational changes upon reduction. These thermodynamic parameters are comparable to those measured for bacterial P450 from Bacillus megaterium (CYP BM3), confirming our prior reports that the surfactant environment exerts a strong influence on the redox properties of the heme.

Electron-transfer rates govern product distribution in electrochemically-driven P450-catalyzed dioxygen reduction.

Developing electrode-driven biocatalytic systems utilizing the P450 cytochromes for selective oxidations depends not only on achieving electron transfer (ET) but also doing so at rates that favor native-like turnover. Herein we report studies that correlate rates of heme reduction with ET pathways and resulting product distributions. We utilized single-surface cysteine mutants of the heme domain of P450 from Bacillus megaterium and modified the thiols with N-(1-pyrene)-iodoacetamide, affording proteins that could bond to basal-plane graphite. Of the proteins examined, Cys mutants at position 62, 383, and 387 were able to form electroactive monolayers with similar E(1/2) values (-335 to -340mV vs AgCl/Ag). Respective ET rates (k(s)(o)) and heme-cysteine distances for 62, 383, and 387 are 50 s(-1) and 16Ǻ, 0.8 s(-1) and 25Ǻ, and 650 s(-1) and 19Ǻ. Experiments utilizing rotated-disk electrodes were conducted to determine the products of P450-catalyzed dioxygen reduction. We found good agreement between ET rates and product distributions for the various mutants, with larger k(s)(o) values correlating with more electrons transferred per dioxygen during catalysis.

Engineered virus-like nanoparticles reverse heparin anticoagulation more consistently than protamine in plasma from heparin-treated patients.

Heparin is widely used for anticoagulation, often requiring the subsequent administration of a reversal agent. The only approved reversal agent for heparin is protamine sulfate, which induces well described adverse reactions in patients. Previously we reported a novel class of heparin antagonists based on the bacteriophage Qß platform, displaying polyvalent cationic motifs which bind with high affinity to heparin. Here we report heparin reversal by the most effective of these virus-like particles (VLP) in samples from patients who were administered heparin during cardiac procedures or therapeutically for treatment of various thrombotic conditions. The VLP consistently reversed heparin in these samples, including those from patients that received high doses of heparin, with greater efficiency than a negative control VLP and with significantly less variability than protamine sulfate. These results provide the first step towards validation of heparin antagonist VLPs as viable alternatives to protamine.

Defining criteria for oligomannose immunogens for HIV using icosahedral virus capsid scaffolds.

The broadly neutralizing antibody 2G12 recognizes a conserved cluster of high-mannose glycans on the surface envelope spike of HIV, suggesting that the "glycan shield" defense of the virus can be breached and may, under the right circumstances, serve as a vaccine target. In an attempt to recreate features of the glycan shield semisynthetically, oligomannosides were coupled to surface lysines on the icosahedral capsids of bacteriophage Q beta and cowpea mosaic virus (CPMV). The Q beta glycoconjugates, but not CPMV, presented oligomannose clusters that bind the antibody 2G12 with high affinity. However, antibodies against these 2G12 epitopes were not detected in immunized rabbits. Rather, alternative oligomannose epitopes on the conjugates were immunodominant and elicited high titers of anti-mannose antibodies that do not crossreact with the HIV envelope. The results presented reveal important design considerations for a carbohydrate-based vaccine component for HIV.

Metal- and metallocycle-binding sites engineered into polyvalent virus-like scaffolds.

Metal-binding motifs appear on protein scaffolds throughout nature and are critical for a vast array of functions that span structure, electron transfer, and catalysis. In an effort to reproduce and exploit this activity in vitro, described herein are versatile bacteriophage Qbeta particles bearing metal-binding motifs polyvalently. The three motifs, His(6), His(6)-His(6), and Cys-His(6), were incorporated into the capsid via a coexpression methodology at ratios of 1.1:1, 1.1:1, and 2.3:1 for wild-type to modified coat protein. Size-exclusion chromatography yielded elution profiles identical to wild-type particles, while Ni-NTA affinity chromatography resulted in retention times that increase according to Qbeta-His(6) < Qbeta-Cys-His(6) < Qbeta-His(6)-His(6). In addition to interacting with metal-derivatized surfaces, Qbeta-Cys-His(6) and Qbeta-His(6)-His(6) bind heme as evidenced by the appearance of new absorbances at 416 and 418 nm, respectively, upon addition of hemin-Cl. The heme-bearing particles were also found to be electrochemically active as a surface-confined system. While both constructs yield similar E(1/2) values anaerobically and with carbon monoxide present, and both display similar pH dependences, a standard rate constant k degrees could only be measured for Qbeta-Cys-His(6) (83 s(-1)), as electron transfer for Qbeta-His(6)-His(6) was too rapid to estimate. Experiments with rotated-disk electrodes yielded significant activity of the constructs toward dioxygen reduction. The versatility of the particles is further underscored by their multivalent nature, permitting simultaneously a range of activities for applications demanding polyfunctionality.

Heparin antagonism by polyvalent display of cationic motifs on virus-like particles.

Particles to the rescue! The construction of cationic amino acid motifs on the surface of bacteriophage Qbeta by genetic engineering or chemical conjugation gives particles that are potent inhibitors of the anticoagulant action of heparin, which is a common anticlotting agent subject to clinical overdose.Polyvalent interactions allow biological structures to exploit low-affinity ligand-receptor binding events to affect physiological responses. We describe here the use of bacteriophage Qbeta as a multivalent platform for the display of polycationic motifs that act as heparin antagonists. Point mutations to the coat protein allowed us to generate capsids bearing the K16M, T18R, N10R, or D14R mutations; because 180 coat proteins form the capsid, the mutants provide a spectrum of particles differing in surface charge by as much as +540 units (K16M vs. D14R). Whereas larger poly-Arg insertions (for example, C-terminal Arg(8)) did not yield intact virions, it was possible to append chemically synthesized oligo-Arg peptides to stable wild-type (WT) and K16M platforms. Heparin antagonism by the particles was evaluated by using the activated partial thrombin time (aPTT) clotting assay; this revealed that T18R, D14R, and WT-(R(8)G(2))(95) were the most effective at disrupting heparin-mediated anticoagulation (>95 % inhibition). This activity agreed with measurements of zeta potential (ZP) and retention time on cation exchange chromatography for the genetic constructs, which distribute their added positive charge over the capsid surface (+180 and +360 for T18R and D14R relative to WT). The potent activity of WT-(R(8)G(2))(95), despite its relatively diminished overall surface charge is likely a consequence of the particle's presentation of locally concentrated regions with high positive charge density that interact with heparin's extensively sulfated domains. The engineered cationic capsids retained their ability to inhibit heparin at high concentrations and showed no anticlotting activity of the kind that limits the utility of antiheparin polycationic agents that are currently in clinical use.

Immobilization of bacteriophage Qbeta on metal-derivatized surfaces via polyvalent display of hexahistidine tags.

Metal-binding peptide motifs are widely used for protein purification, catalysis, and metal-mediated self assembly in the construction of novel materials and multivalent light harvesting complexes. Herein we describe hexahistidine sequences incorporated into the virus-like particle derived from bacteriophage Qbeta via co-expression of the wild-type (WT) and hexahistidine-modified coat proteins in Escherichia coli. The resulting polyvalent display of approximately 37 hexahistidine moieties per virion gave rise to altered properties of Zeta potential and hydrodynamic radius, but no observed change in stability compared to WT. While the resulting display density did not permit hexahistidine chains to cooperate in the coordination of heme, the multiple tags did impart a strong affinity for immobilized metal ions. A dissociation constant for binding to Ni-NTA of approximately 10nM was measured by SPR under non-competitive, physiological conditions. Affinity chromatography over immobilized metal columns was used to purify the particles from both crude cell lysates and after chemical derivatization. These results illustrate the potential of metal-NTA surfaces for the self-assembled presentation of multi-functionalized particles to interrogate systems ranging from small molecule binding to whole cell interactions.

Electrochemically protected copper(I)-catalyzed azide-alkyne cycloaddition.

The copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction has found broad application in myriad fields. For the most demanding applications that require high yields at low substrate concentrations, highly active but air-sensitive copper complexes must be used. We describe here the use of an electrochemical potential to maintain catalysts in the active Cu(I) oxidation state in the presence of air. This simple procedure efficiently achieves excellent yields of CuAAC products from both small-molecule and protein substrates without the use of potentially damaging chemical reducing agents. A new water-soluble carboxylated version of the popular tris(benzyltriazolylmethyl)amine (TBTA) ligand is also described. Cyclic voltammetry revealed reversible or quasi-reversible electrochemical redox behavior of copper complexes of the TBTA derivative (2; E(1/2)=60 mV vs. Ag/AgCl), sulfonated bathophenanthroline (3; E(1/2)=-60 mV), and sulfonated tris(benzimidazoylmethyl)amine (4; E(1/2) approximately -70 mV), and showed catalytic turnover to be rapid relative to the voltammetry time scale. Under the influence of a -200 mV potential that was established by using a reticulated vitreous carbon working electrode, CuSO4 and 3 formed a superior catalyst. Electrochemically protected bioconjugations in air were performed by using bacteriophage Qbeta that was derivatized with azide moieties at surface lysine residues. Complete derivatization of more than 600 reactive sites per particle was demonstrated within 12 h of electrolysis with substoichiometric quantities of Cu3.

Polyvalent display of heme on hepatitis B virus capsid protein through coordination to hexahistidine tags.

The addition of a hexahistidine tag to the N terminus of the hepatitis B capsid protein gives rise to a self-assembled particle with 80 sites of high local density of histidine side chains. Iron protoporphyrin IX has been found to bind tightly at each of these sites, making a polyvalent system of well-defined spacing between metalloporphyrin complexes. The spectroscopic and redox properties of the resulting particle are consistent with the presence of 80 site-isolated bis(histidine)-bound heme centers, comprising a polyvalent b-type cytochrome mimic.

Unnatural amino acid incorporation into virus-like particles.

Virus-like particles composed of hepatitis B virus (HBV) or bacteriophage Qbeta capsid proteins have been labeled with azide- or alkyne-containing unnatural amino acids by expression in a methionine auxotrophic strain of E. coli. The substitution does not affect the ability of the particles to self-assemble into icosahedral structures indistinguishable from native forms. The azide and alkyne groups were addressed by Cu(I)-catalyzed [3 + 2] cycloaddition: HBV particles were decomposed by the formation of more than 120 triazole linkages per capsid in a location-dependent manner, whereas Qbeta suffered no such instability. The marriage of these well-known techniques of sense-codon reassignment and bioorthogonal chemical coupling provides the capability to construct polyvalent particles displaying a wide variety of functional groups with near-perfect control of spacing.

Differential ionic permeation of DNA-modified electrodes.

Ionic permselectivity of DNA films has been investigated by the analysis of the electrochemical response of methylene blue (MB) as a function of pH and ionic strength on DNA-modified electrodes in aqueous p-nitrophenol (p-NP) and phosphate buffers. We have observed a linear Pourbaix diagram in p-NP buffer indicating that the reduction of MB occurs with a two-electron plus one-proton reaction. Interestingly, in phosphate buffer the Pourbaix diagram is curved and this suggests that the thermodynamics of MB incorporated in the film depend also on the ratio of mono- versus divalent anions in the bulk. This result indicates that DNA films do not behave as pure ion-exclusion films, but instead there is a differential permselectivity that depends on the identity of the anions. Based on this consideration of the ionic distribution in the films, we provide a new method for the analysis of the DNA surface coverage based on AC impedance of an anionic species, ferricyanide. The methodology is of particular value in analyzing DNA hybridization and dehybridization. This approach presents an advantage compared to standard ruthenium hexammine assays since our methodology is insensitive to film morphology, and is highly sensitive to the amount of negative charge on the surface.

Electrochemistry of cytochrome P450 BM3 in sodium dodecyl sulfate films.

Direct electrochemistry of the cytochrome P450 BM3 heme domain (BM3) was achieved by confining the protein within sodium dodecyl sulfate (SDS) films on the surface of basal-plane graphite (BPG) electrodes. Cyclic voltammetry revealed the heme FeIII/II redox couple at -330 mV (vs Ag/AgCl, pH 7.4). Up to 10 V/s, the peak current was linear with the scan rate, allowing us to treat the system as surface-confined within this regime. The standard heterogeneous rate constant determined at 10 V/s was estimated to be 10 s-1. Voltammograms obtained for the BM3-SDS-BPG system in the presence of dioxygen exhibited catalytic waves at the onset of FeIII reduction. The altered heme reduction potential of the BM3-SDS-graphite system indicates that SDS is likely bound in the enzyme active-site region. Compared to other P450-surfactant systems, we find redox potentials and electron-transfer rates that differ by approximately 100 mV and >10-fold, respectively, indicating that the nature of the surfactant environment has a significant effect on the observed heme redox properties.