Using engineered single-chain antibodies to correlate molecular binding properties and nanoparticle adhesion dynamics

Elucidation of the relationship between targeting molecule binding properties and the adhesive behavior of therapeutic or diagnostic nanocarriers would aid in the design of optimized vectors and lead to improved efficacy. We measured the adhesion of 200-nm-diameter particles under fluid flow that was mediated by a diverse array of molecular interactions, including recombinant single-chain antibodies (scFvs), full antibodies, and the avidin/biotin interaction. Within the panel of scFvs, we used a family of mutants that display a spectrum of binding kinetics, allowing us to compare nanoparticle adhesion to bond chemistry. In addition, we explored the effect of molecular size by inserting a protein linker into the scFv fusion construct and by employing scFvs that are specific for targets with vastly different sizes. Using computational models, we extracted multivalent kinetic rate constants for particle attachment and detachment from the adhesion data and correlated the results to molecular binding properties. Our results indicate that the factors that increase encounter probability, such as adhesion molecule valency and size, directly enhance the rate of nanoparticle attachment. Bond kinetics had no influence on scFv-mediated nanoparticle attachment within the kinetic range tested, however, but did appear to affect antibody/antigen and avidin/biotin mediated adhesion. We attribute this finding to a combination of multivalent binding and differences in bond mechanical strength between recombinant scFvs and the other adhesion molecules. Nanoparticle detachment probability correlated directly with adhesion molecule valency and size, as well as the logarithm of the affinity for all molecules tested. On the basis of this work, scFvs can serve as viable targeting receptors for nanoparticles, but improvements to their bond mechanical strength would likely be required to fully exploit their tunable kinetic properties and maximize the adhesion efficiency of nanoparticles that bear them.     

Targeted particulate adhesion to cellulose surfaces mediated by bifunctional fusion proteins

The adhesion of particles to surfaces is an integral element in many commercial and biological applications. In this article, we report on the direct measurements of protein-mediated deposition and binding of particles to model cellulose surfaces. This system involves a family of heterobifunctional fusion proteins that bind specifically to both a red dye and cellulose. Amine-coated particles were labeled with a red dye, and a fusion protein was attached to these particles at various number densities. The strength of adhesion of a single particle to a cellulose fiber was measured using micropipette manipulation as a function of the specificity of the protein and its surface density and contact time. The frequency and force of adhesion were seen to increase with contact time in fiber experiments. The dynamics of adhesion of the functionalized particles to cellulose-coated glass slides under controlled hydrodynamic flow was explored using a flow chamber for two scenarios: detachment of bound particles and attachment of particles in suspension as a function of the shear rate and surface density of protein. Highly specific adhesion was observed. The critical shear rate for particle detachment was an increasing function of cellulose binding domain (CBD) density on particle surface. A rapid irreversible attachment of particles to cellulose was observed under flow. Using a family of proteins that were divalent for binding either the red dye or cellulose, we found that particle detachment occurred because of the failure of the cellulose-CBD bond. A comparison of fiber binding and particle detachment results suggests that forces of adhesion of particles to cellulose of up to 2 nN can be obtained with this molecular system through multiple interactions. This study, along with the adhesion simulations currently under development, forms the basis of particulate design for specific adhesion applications.     

Adhesion of antibody-functionalized polymersomes

Polymersomes are vesicles made from synthetic block copolymers. The adhesiveness of micron-sized polymersomes, functionalized with antibodies that bind to vascular cell adhesion molecules, which could be useful for vascular targeting, was measured. Intercellular adhesion molecule-1 (ICAM-1) is an endothelial cell adhesion molecule whose expression increases during inflammatory disease, and is therefore a natural target for vascular delivery. We functionalized polymersomes with an anti-ICAM-1 antibody, using modular biotin-avidin chemistry. Micropipet aspiration was used to confirm specific adhesion and measure the adhesion strength between an anti-ICAM-1-coated polymersome and an ICAM-1-coated polystyrene microsphere at various surface densities of adhesion molecules. The adhesion is kinetically trapped, and adhesion strength is quantified by the critical tension for detachment. The adhesion strength increases in proportion to the surface density of anti-ICAM-1 molecules, in contrast to results seen previously when measuring adhesion between biotinylated vesicles and avidin-coated beads (Lin et al. Langmuir 2004, 20, 5493). The difference in dependence on the density of functional groups is likely due to the molecular presentation at the vesicle surface; in the current study, the presentation of biotinylated anti-ICAM-1 on a layer of avidin leads to the effective presentation of the anti-ICAM-1 and, thus, a monotonic increase in adhesiveness with antibody density.     

Circulating IgSF Proteins Inhibit Adhesion of Antibody Targeted Microspheres to Endothelial Inflammatory Ligands

Proposed methods for detecting circulatory system disease include targeting ultrasound contrast agents to inflammatory markers on vascular endothelial cells. For antibody-based therapies, soluble forms of the targeted adhesion proteins of the immunoglobulin superfamily (IgSF) reduce adhesion yet were left unaccounted in prior reports. Microspheres labeled simply with a maximum level of antibodies can reduce the diagnostic sensitivity by adhering to proteins expressed normally at a low level, while sparsely coated particles may be rendered ineffective by circulating soluble forms of the targeted proteins. A new microdevice technique is applied to simultaneously measure the adhesion profile to a series of IgSF-protein-coated surfaces. In this investigation, we quantify the in vitro binding characteristics of 5-μm microspheres to oriented intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1) protein-coated surfaces in the presence of human serum at physiological concentrations. Defined regions of a slide were coated with recombinant chimeric Fc-human ICAM-1 and VCAM-1 in variable ratios but constant total concentration. Monoclonal human anti-ICAM-1 or anti-VCAM-1 antibodies in competition with non-binding mouse anti-rabbit antibodies coat the microsphere surface at a constant surface density with variable yet controlled surface activities. Using multiple slide surface IgSF protein and microsphere antibody concentrations, an adhesion profile was developed for the microspheres with and without IgSF proteins from human serum, which demonstrated that exposure to serum reduced microsphere binding, on average, more than 50% compared to the no-serum condition.. The serum effects were limited to antibodies on the microsphere, since binding inhibition was reversed after rinsing serum from the system and fresh antibody-coated microspheres were introduced. This analysis quantifies the binding effects of soluble IgSF proteins from human serum on antibody-based targeted ultrasound detection and drug delivery methods.     

Bridging Ligand Length Controls AT Selectivity and Enantioselectivity of Binuclear Ruthenium Threading Intercalators

The slow dissociation of DNA threading intercalators makes them interesting as model compounds in the search for new DNA targeting drugs, as there appears to be a correlation between slow dissociation and biological activity. Thus, it would be of great value to understand the mechanisms controlling threading intercalation, and for this purpose we have investigated how the length of the bridging ligand of binuclear ruthenium threading intercalators affects their DNA binding properties. We have synthesised a new binuclear ruthenium threading intercalator with slower dissociation kinetics from ct‐DNA than has ever been observed for any ruthenium complex with any type of DNA, a property that we attribute to the increased distance between the ruthenium centres of the new complex. By comparison with previously studied ruthenium complexes, we further conclude that elongation of the bridging ligand reduces the sensitivity of the threading interaction to DNA flexibility, resulting in a decreased AT selectivity for the new complex. We also find that the length of the bridging ligand affects the enantioselectivity with increasing preference for the ΔΔ enantiomer as the bridging ligand becomes longer.     

Kinetics study of the binding of multivalent ligands on size-selected gold nanoparticles

The effect of ligand multivalency and nanoparticle size on the binding kinetics of thiol ligands on gold nanoparticles is investigated by exchanging monovalently bound pyrene on gold nanoparticles against flexible mono- and multivalent thiol ligands. Variable-sized gold nanoparticles of 2.2 ± 0.4, 3.2 ± 0.7, and 4.4 ± 0.9 nm diameter are used as substrates. The particles are coated by thiol functionalized pyrene ligands and the binding kinetics of the thiol ligands is studied by time-resolved fluorescence spectroscopy. The effect of multivalency on the binding kinetics is evaluated by comparing the rate constants of ligands of different valency. This comparison reveals that the multivalent ligands are exchanging substantially more rapidly than the monovalent ones. A particle size dependence of the rate constants is also observed, which is used to derive structural information on the binding of the mono- and multivalent ligands to the nanoparticle surface.     

Metal speciation dynamics in colloidal ligand dispersions

In this work we propose a dynamic metal speciation theory for colloidal systems in which the complexing ligands are localized on the surface of the particles; i.e., there is spatial heterogeneity of binding sites within the sample volume. The differences between the complex formation and dissociation rate constants of complexes in colloidal dispersions and those in homogeneous solutions originate from the differences in kinetic and mass transport conditions. In colloidal systems, when the effective rate of dissociation of the surface complexes becomes fully diffusion controlled, its value is defined via the geometrical parameters of the particle. We assess the extent to which the conventional approach of assuming a homogeneously smeared-out ligand distribution overestimates the lability of surface complexes in colloidal ligand dispersions. The validity of the theory is illustrated by application to binding of lead and cadmium by carboxyl modified latex particles: our approach correctly predicts the formation/dissociation rate constants, which differ by several orders of magnitude from their homogeneous solution counterparts.     

Dissociation Rate Kinetics in a Solid-Phase Flow Immunoassay

Abstract

Solid-phase displacement assays allow extremely fast analyses when performed under continuous flow conditions. Continuous dissociation of labeled antigen from the immobilized saturated antibodies occurs even in the absence of competing unlabeled antigen. This spontaneous dissociation creates more unoccupied antibody binding sites which affect the magnitude of the signal generated. In order to evaluate the impact of this phenomenon in more detail, we extended the law of mass action to solid-phase binding assays and analyzed the dissociation kinetics of labeled antigen under continuous flow conditions. The effect of the flow on the dissociation kinetics was determined by calculation of the apparent dissociation rate constants (k_d) which increase with an increase in the flow rate. These dissociation rate constants are approximately 20- to 30-fold lower than those obtained from displacement studies (i.e., in the presence of competing unlabeled antigen). The difference in the dissociation rate constants obtained in the two studies is most likely a function of the degree of reassociation. The results of this study provide a basis for better understanding antibody kinetics at solid-liquid interfaces under flow conditions.     

Improving immunobinding using oriented immobilization of an oxidized antibody

Recent technical advances in biorecognition engineering and microparticle fabrication enabled us to develop a single-step purification process using magnetic particles (MPs). The process is simple, efficacious, easy to automate, and economical. The method immobilizes the ligand molecule in a particular orientation on commercial MPs that have surface carboxyl groups. Mouse IgG and anti-mouse IgG antibody were the model capture and ligand molecules for this study. The immunobinding efficacy of anti-mouse IgG antibody using "oriented immobilization" was compared with the efficacy of a conventional amine-coupling system that results in random orientation and of another standard method, the biotin-streptavidin system. The oriented immobilization was accomplished by oxidizing the sugar moiety in the CH(2) domain of the antibody's Fc and covalently conjugating the moiety to the hydrazine-coated MP. The specific binding affinity of the oriented immobilization process was about 2.5 times that of the amine-coupling system, and selectivity from a binary mixture was about 2 times greater for the oriented immobilization method. Results were nearly identical for the biotin-streptavidin system and the oriented immobilization system, matching the calculated binding stoichiometry between mouse IgG and anti-mouse IgG antibody. The binding improvement over the amine-coupling system shown by assay was confirmed by a separate surface plasmon resonance experiment. In summary, the oriented immobilization method was as effective as the streptavidin-biotin system, yet simpler and cost-effective.     

Label-free, microfluidic separation and enrichment of human breast cancer cells by adhesion difference

A label-free microfluidic method for separation and enrichment of human breast cancer cells is presented using cell adhesion as a physical marker. To maximize the adhesion difference between normal epithelial and cancer cells, flat or nanostructured polymer surfaces (400 nm pillars, 400 nm perpendicular, or 400 nm parallel lines) were constructed on the bottom of polydimethylsiloxane (PDMS) microfluidic channels in a parallel fashion using a UV-assisted capillary moulding technique. The adhesion of human breast epithelial cells (MCF10A) and cancer cells (MCF7) on each channel was independently measured based on detachment assays where the adherent cells were counted with increasing flow rate after a pre-culture for a period of time (e.g., one, two, and four hours). It was found that MCF10A cells showed higher adhesion than MCF7 cells regardless of culture time and surface nanotopography at all flow rates, resulting in label-free separation and enrichment of cancer cells. For the cell types used in our study, an optimum separation was found for 2 hours pre-culture on the 400 nm perpendicular line pattern followed by flow-induced detachment at a flow rate of 200 microl min(-1). The fraction of MCF7 cells was increased from 0.36 +/- 0.04 to 0.83 +/- 0.04 under these optimized conditions.     

Contact mechanics of nanoparticles

We perform molecular dynamics simulations on the detachment of nanoparticles from a substrate. The critical detachment force, f*, is obtained as a function of the nanoparticle radius, R(p), shear modulus, G, surface energy, γ(p), and work of adhesion, W. The magnitude of the detachment force is shown to increase from πWR(p) to 2.2πWR(p) with increasing nanoparticle shear modulus and nanoparticle size. This variation of the detachment force is a manifestation of neck formation upon nanoparticle detachment. Using scaling analysis, we show that the magnitude of the detachment force is controlled by the balance of the nanoparticle elastic energy, neck surface energy, and energy of nanoparticle adhesion to a substrate. It is a function of the dimensionless parameter δ ∝ γ(p)(GR(p))(-1/3)W(-2/3), which is proportional to the ratio of the surface energy of a neck and the elastic energy of a deformed nanoparticle. In the case of small values of the parameter δ ? 1, the critical detachment force approaches a critical Johnson, Kendall, and Roberts force, f* ≈ 1.5πWR(p), as is usually the case for strongly cross-linked, large nanoparticles. However, in the opposite limit, corresponding to soft small nanoparticles for which δ?1, the critical detachment force, f*, scales as f*∝ γ(p)(3/2)R(p)(1/2)G(-1/2). Simulation data are described by a scaling function f*∝ γ(p)(3/2)R(p)(1/2)G(-1/2)δ(-1.89).     

Kinetics of yeast detachment from controlled stainless steel surfaces

Using a radial flow chamber, we study Saccharomyces cerevisiae kinetics of detachment from stainless steel substrates. Samples of similar surface chemistry, but with different surface topologies are compared: mirror polished and electro-chemically etched. Different grain sizes (20, 40 and 100 microm) and different etching depths (100-650 nm) are tested. Cells are removed from the substrate according to a first-order kinetics defining two macroscopic parameters that depend on the applied stress: the detachment efficiency and the detachment rate constant. Whatever the surface topology, detachment occurs above a threshold and its rate is strongly stimulated by the applied stress. The detachment efficiency is characterized by the shear stress at which half of the cells detach and is independent of surface topology. In contrast, detachment is faster from etched than mirror polished surfaces. Finally, we also show the preferential adhesion of yeast cells to grains of < 001 > crystallographic orientation with respect to the surface.     

Oxidation of CO by NO on planar and faceted Ir(210)

Oxidation of CO by pre-adsorbed NO has been studied on planar Ir(210) and nanofaceted Ir(210) with average facet sizes of 5 nm and 14 nm by temperature programmed desorption (TPD). Both surfaces favor oxidation of CO to CO(2), which is accompanied by simultaneous reduction of NO with high selectivity to N(2). At low NO pre-coverage, the temperature (T(i)) for the onset of CO(2) desorption as well as CO(2) desorption peak temperature (T(p)) decreases with increasing CO exposure, and NO dissociation is affected by co-adsorbed CO. At high NO pre-coverage, T(i) and T(p) are independent of CO exposure, and co-adsorbed CO has no influence on dissociation of NO. Moreover, at low NO pre-coverage, planar Ir(210) is more active than faceted Ir(210) for oxidation of CO to CO(2): T(i) and T(p) are much lower on planar Ir(210) than that on faceted Ir(210). In addition, faceted Ir(210) with an average facet size of 5 nm is more active for oxidation of CO to CO(2) than faceted Ir(210) with an average facet size of 14 nm, i.e., oxidation of CO by pre-adsorbed NO on faceted Ir(210) exhibits size effects on the nanometer scale. In comparison, at low O pre-coverage planar Ir(210) is more active than faceted Ir(210) for oxidation of CO to CO(2) but no evidence has been found for size effects in oxidation of CO by pre-adsorbed oxygen on faceted Ir(210) for average facet sizes of 5 nm and 14 nm. The TPD data indicate the same reaction pathway for CO(2) formation from CO + NO and CO + O reactions on planar Ir(210). The adsorption sites of CO, NO, O, CO + O, and CO + NO on Ir are characterized by density functional theory.     

Generation and detection of single metal nanoparticles using scanning electrochemical microscopy techniques

Different pathways towards the generation and detection of a single metal nanoparticle (MNP) on a conductive carbon support for testing as an electrocatalyst are described. Various approaches were investigated including interparticle distance enhancement, electrochemical and mechanical tip-substrate MNP transfer onto macroscopic surfaces, scanning electrochemical microscopy (SECM)-controlled electrodeposition, and the use of selective binding monolayers on carbon fiber electrodes (CFEs) for solution-phase-selective adsorption. A novel SECM technique for electrodepositing MNPs on CFE tips immersed 100-200 nm below the electrolyte level was developed and used to generate single Pt and Ni nanoparticles. Following their generation, we demonstrate electrocatalytic detection of Fe3+ on individual Pt particles with the CFE in a Fe3+/H2SO4 solution. We also describe an approach of attaching MNPs to CFEs by controlling the composition of monolayers bonded to the CFE. By employing a monolayer with a low ratio of binding (e.g., 4-aminopyridine) to nonbinding molecules (e.g., aniline) and controlling the position of the CFE in a colloidal Pt solution with a SECM, we attached a single 15 nm radius Pt nanoparticle to the CFE. Such chemisorbed Pt particles exhibited a stronger adhesion on surface-modified CFEs and better mechanical stability during proton reduction than MNPs electrodeposited directly on the CFE.     

The molecular recognition of phosphorylated proteins by designed polypeptides conjugated to a small molecule that binds phosphate

The conjugation of polypeptides from a designed set to the small molecule ligand 3,5-bis[[bis(2-pyridylmethyl)amino]methyl]benzoic acid, which in the presence of Zn(2+) ions binds inorganic phosphate, has been shown to provide a polypeptide conjugate that binds α-casein, a multiply phosphorylated protein, with a dissociation constant K(D) of 17 nM. The measured affinity is more than three orders of magnitude higher than that of the small molecule ligand for phosphate and the binding of 500 nM of α-casein was not inhibited by 10 mM phosphate buffer, providing a 2000-fold excess of phosphate ion over protein. The selectivity for phosphoproteins was demonstrated by extraction of α-casein from solutions of various complexity, including milk and human serum spiked with α-casein. In addition to α-casein, β-casein was also recognized but not ovoalbumin. Conjugation of a polypeptide to the zinc chelating ligand was therefore shown to give rise to dramatically increased affinity and also increased selectivity. A set of polypeptide conjugates is expected to be able to capture a large number of phosphorylated proteins, perhaps all, and in combination with electrophoresis or mass spectrometry become a powerful tool for the monitoring of phosphorylation levels. The presented binder can easily be attached to various types of surfaces; here demonstrated for the case of polystyrene particles. The example of phosphoproteins was selected since posttranslational phosphorylation is of fundamental importance in cell biology due to its role in signaling and therefore of great interest in drug development. The reported concept for binder development is, however, quite general and high-affinity binders can conveniently be developed for a variety of proteins including those with posttranslational modifications for which small molecule recognition elements are available.     

Hydrodynamic crossover in dynamic microparticle adhesion on surfaces of controlled nanoscale heterogeneity

This note documents the crossover from a regime where shear flow hinders microparticle adhesion on collecting surfaces to that where increased flow aids particle capture. Flow generally works against adhesion and successfully hinders particle capture when the net physicochemical attractions between the particles and collector are weak compared with hydrodynamic forces on the particle. Conversely, with strong attractions between particles and collector, flow aids particle capture by increasing the mass transport of particles to the interfacial region. Here, local hydrodynamics still generally oppose adhesion but are insufficient to pull particles off of the surface. Thus, flow actually increases the particle capture rate through the increased transport to the surface. These behaviors are demonstrated using 1 mum silica spheres flowing over electrostatically heterogeneous (length scales near 10 nm) collecting surfaces at shear rates from 22 to 795 s(-1). The net surface charge on the collector is varied systematically from strongly negative (pure silica) to strongly positive (a saturated polycationic overlayer), demonstrating the interplay between physicochemical and hydrodynamic contributions. These results clearly apply to situations where heterogeneous particle-surface interactions are electrostatic in nature; however, qualitatively similar behavior was previously reported for the effect receptor density on bacterial adhesion.     

Energetics of a protein disorder–order transition in small molecule recognition

Many proteins recognise other proteins via mechanisms that involve the folding of intrinsically disordered regions upon complex formation. Here we investigate how the selectivity of a drug-like small molecule arises from its modulation of a protein disorder-to-order transition. Binding of the compound AM-7209 has been reported to confer order upon an intrinsically disordered ‘lid’ region of the oncoprotein MDM2. Calorimetric measurements revealed that truncation of the lid region of MDM2 increases the apparent dissociation constant of AM-7209 250-fold. By contrast, lid truncation has little effect on the binding of the ligand Nutlin-3a. Insights into these differential binding energetics were obtained via a complete thermodynamic analysis that featured adaptive absolute alchemical free energy of binding calculations with enhanced-sampling molecular dynamics simulations. The simulations reveal that in apo MDM2 the ordered lid state is energetically disfavoured. AM-7209, but not Nutlin-3a, shows a significant energetic preference for ordered lid conformations, thus shifting the balance towards ordering of the lid in the AM-7209/MDM2 complex. The methodology reported herein should facilitate broader targeting of intrinsically disordered regions in medicinal chemistry.

Molecular simulations and biophysical measurements elucidate why the ligand AM-7209 orders a disordered region of the protein MDM2 on binding. This work expands strategies available to medicinal chemists for targeting disordered proteins.     

Polyethylene Glycol Backfilling Mitigates the Negative Impact of the Protein Corona on Nanoparticle Cell Targeting

In protein‐rich environments such as the blood, the formation of a protein corona on receptor‐targeting nanoparticles prevents target recognition. As a result, the ability of targeted nanoparticles to selectively bind to diseased cells is drastically inhibited. Backfilling the surface of a targeted nanoparticle with polyethylene glycol (PEG) molecules is demonstrated to reduce the formation of the protein corona and re‐establishes specific binding. The length of the backfilled PEG molecules must be less than the length of the ligand linker; otherwise, PEG interferes with the binding of the targeting ligand to its corresponding cellular receptor.     

Ion exchange chromatography of monoclonal antibodies: Effect of resin ligand density on dynamic binding capacity

Dynamic binding capacity (DBC) of a monoclonal antibody on agarose based strong cation exchange resins is determined as a function of resin ligand density, apparent pore size of the base matrix, and protein charge. The maximum DBC is found to be unaffected by resin ligand density, apparent pore size, or protein charge within the tested range. The critical conductivity (conductivity at maximum DBC) is seen to vary with ligand density. It is hypothesized that the maximum DBC is determined by the effective size of the proteins and the proximity to which they can approach one another. Once a certain minimum resin ligand density is supplied, additional ligand is not beneficial in terms of resin capacity. Additional ligand can provide flexibility in designing ion exchange resins for a particular application as the critical conductivity could be matched to the feedstock conductivity and it may also affect the selectivity.     

Effect of nanoscale geometry on molecular conformation: vibrational sum-frequency generation of alkanethiols on gold nanoparticles

Vibrational sum frequency generation (VSFG) spectroscopy was used to study the nanoscale geometric effects on molecular conformation of dodecanethiol ligand on gold nanoparticles of varying size between 1.8 and 23 nm. By analyzing the CH3 and CH2 stretch transitions of dodecanethiol using the spectroscopic propensity rules for the SFG process, we observe the increase of the gauche defects in the alkyl chain of the ligand on the nanoparticle surface when the curvature approaches the size of the molecule ( approximately 1.6 nm). In contrast, linear infrared absorption and Raman spectra, governed by different selection rules, do not allow observation of the size-dependent conformational changes. The results are understood in terms of the geometric packing effect, where the curvature of the nanoparticle surface results in the increased conical volume available for the alkyl chain.