Tris-nitrilotriacetic acids of subnanomolar affinity toward hexahistidine tagged molecules

Overcoming Protein Orientation Mismatch Enables Efficient Nanoscale Light-Driven ATP Production

Adenosine triphosphate (ATP)-producing modules energized by light-driven proton pumps are powerful tools for the bottom-up assembly of artificial cell-like systems. However, the maximum efficiency of such modules is prohibited by the random orientation of the proton pumps during the reconstitution process into lipid-surrounded nanocontainers. Here, we overcome this limitation using a versatile approach to uniformly orient the light-driven proton pump proteorhodopsin (pR) in liposomes. pR is post-translationally either covalently or noncovalently coupled to a membrane-impermeable protein domain guiding orientation during insertion into preformed liposomes. In the second scenario, we developed a novel bifunctional linker, trisNTA-SpyTag, that allows for the reversible connection of any SpyCatcher-containing protein and a HisTag-carrying protein. The desired protein orientations are verified by monitoring vectorial proton pumping and membrane potential generation. In conjunction with ATP synthase, highly efficient ATP production is energized by the inwardly pumping population. In comparison to other light-driven ATP-producing modules, the uniform orientation allows for maximal rates at economical protein concentrations. The presented technology is highly customizable and not limited to light-driven proton pumps but applicable to many membrane proteins and offers a general approach to overcome orientation mismatch during membrane reconstitution, requiring little to no genetic modification of the protein of interest.

Tumor-specific targeting of polymer drug delivery systems with recombinant proteins bound via tris(nitrilotriacetic acid)

Antibody-mediated targeting is an efficient strategy to enhance the specificity and selectivity of polymer nanomedicines towards the target site, typically a tumor. However, direct covalent coupling of an antibody with a polymer usually results in a partial damage of the antibody binding site accompanied with a compromised biological activity. Here, an original solution based on well-defined non-covalent interactions between tris-nitrilotriacetic acid (trisNTA) and hexahistidine (His-tag) groups, purposefully introduced to the structure of each macromolecule, is described. Specifically, trisNTA groups were attached along the chains of a hydrophilic statistical copolymer based on N-(2-hydroxypropyl)methacrylamide (HPMA), and at the end or along the chains of thermo-responsive di-block copolymers based on N-isopropylmethacrylamide (NIPMAM) and HPMA; His-tag was incorporated to the structure of a recombinant single chain fragment of an anti-GD2 monoclonal antibody (scFv-GD2). Static and dynamic light scattering analyses confirmed that mixing of polymer with scFv-GD2 led to the formation of polymer/scFv-GD2 complexes; those prepared from thermo-responsive polymers formed stable micelles at 37 °C. Flow cytometry and fluorescence microscopy clearly demonstrated antigen-specific binding of the prepared complexes to GD2 positive murine T-cell lymphoma cells EL-4 and human neuroblastoma cells UKF-NB3, while no interaction with GD2 negative murine fibroblast cells NIH-3T3 was observed. These non-covalent polymer protein complexes represent a new generation of highly specific actively targeted polymer therapeutics or diagnostics.

Biosensors Based on the Binding Events of Nitrilotriacetic Acid-Metal Complexes

Molecular immobilization and recognition are two key events for the development of biosensors. The general ways for the immobilization and recognition of biomolecules include covalent coupling reactions and non-covalent interactions of antigen-antibody, aptamer-target, glycan-lectin, avidin-biotin and boronic acid-diol. Tetradentate nitrilotriacetic acid (NTA) is one of the most common commercial ligands for chelating metal ions. The NTA-metal complexes show high and specific affinity toward hexahistidine tags. Such metal complexes have been widely utilized in protein separation and immobilization for diagnostic applications since most of commercialized proteins have been integrated with hexahistidine tags by synthetic or recombinant techniques. This review focused on the development of biosensors with NTA-metal complexes as the binding units, mainly including surface plasmon resonance, electrochemistry, fluorescence, colorimetry, surface-enhanced Raman scattering spectroscopy, chemiluminescence and so on.

Analytical Method for Experimental Validation of Computer-Designed Antibody

In the computational design of antibodies, the interaction analysis between target antigen and antibody is an essential process to obtain feedback for validation and optimization of the design. Kinetic and thermodynamic parameters as well as binding affinity (K_D) allow for a more detailed evaluation and understanding of the molecular recognition. In this chapter, we summarize the conventional experimental methods which can calculate K_D value (ELISA, FP), analyze a binding activity to actual cells (FCM), and evaluate the kinetic and thermodynamic parameters (ITC, SPR, BLI), including high-throughput analysis and a recently developed experimental technique.

The Interplay of Conjugation and Metal Coordination in Tuning the Electron Transfer Abilities of NTA-Graphene Based Interfaces

An artificial leaf is a concept that not only replicates the processes taking place during natural photosynthesis but also provides a source of clean, renewable energy. One important part of such a device are molecules that stabilize the connection between the bioactive side and the electrode, as well as tune the electron transfer between them. In particular, nitrilotriacetic acid (NTA) derivatives used to form a self-assembly monolayer chemisorbed on a graphene monolayer can be seen as a prototypical interface that can be tuned to optimize the electron transfer. In the following work, interfaces with modifications of the metal nature, backbone saturation, and surface coverage density are presented by means of theoretical calculations. Effects of the type of the metal and the surface coverage density on the electronic properties are found to be key to tuning the electron transfer, while only a minor influence of backbone saturation is present. For all of the studied interfaces, the charge transfer flow goes from graphene to the SAM. We suggest that, in light of the strength of electron transfer, Co2+ should be considered as the preferred metal center for efficient charge transfer.

Rapid and regenerable surface plasmon resonance determinations of biomarker concentration and biomolecular interaction based on tris-nitrilotriacetic acid chips

The tris-nitrilotriacetic acid (tris-NTA) chip has been used for surface plasmon resonance (SPR) kinetic studies involving histidine (His)-tagged proteins. However, its full potential, especially for analyte quantification in complex biological media, has not been realized due to a lack of systematic studies on the factors governing ligand immobilization, surface regeneration, and data analysis. We demonstrate that the tris-NTA chip not only retains His-tagged proteins more strongly than its mono-NTA counterpart, but also orients them more uniformly than protein molecules coupled to carboxymethylated dextran films. We accurately and rapidly quantified immunoglobulin (IgG) molecules in sera by using the initial association phase of their conjugation with His-tagged protein G densely immobilized onto the tris-NTA chip, and established criteria for selecting the optimal time for constructing the calibration curve. The method is highly reproducible (less than 2% RSD) and three orders of magnitude more sensitive than immunoturbidimetry. In addition, we found that the amount of His-protein immobilized is highly dependent on the protein isoelectric point (pI). Reliable kinetic data in a multi-channel SPR instrument can also be rapidly obtained by using a low density of immobilized His-tagged protein. The experimental parameters and procedures outlined in this study help expand the range of SPR applications involving His-tagged proteins.

Assessing changes in the expression levels of cell surface proteins with a turn-on fluorescent molecular probe

Tri-nitrilotriacetic acid (NTA)-based fluorescent probes were developed and used to image His-tagged-labelled outer membrane protein C (His-OmpC) in live Escherichia coli. One of these probes was designed to light up upon binding, which provided the means to assess changes in the His-OmpC expression levels by taking a simple fluorescence spectrum.

Simplified detection of polyhistidine-tagged proteins in gels and membranes using a UV-excitable dye and a multiple chelator head pair

The polyhistidine tag (His-tag) is one of the most popular protein tags used in the life sciences. Traditionally, the detection of His-tagged proteins relies on immunoblotting with anti-His antibodies. This approach is laborious for certain applications, such as protein purification, where time and simplicity are critical. The His-tag can also be directly detected by metal ion-loaded nickel-nitrilotriacetic acid-based chelator heads conjugated to fluorophores, which is a convenient alternative method to immunoblotting. Typically, such chelator heads are conjugated to either green or red fluorophores, the detection of which requires specialized excitation sources and detection systems. Here, we demonstrate that post-run staining is ideal for His-tag detection by metal ion-loaded and fluorescently labeled chelator heads in PAGE and blot membranes. Additionally, by comparing the performances of different chelator heads, we show how differences in microscopic affinity constants translate to macroscopic differences in the detection limits in environments with limited diffusion, such as PAGE. On the basis of these results, we devise a simple approach, called UVHis-PAGE, that uses metal ion-loaded and fluorescently labeled chelator heads to detect His-tagged proteins in PAGE and blot membranes. Our method uses a UV transilluminator as an excitation source, and the results can be visually inspected by the naked eye.

Tris-(Nitrilotriacetic Acid)-Decorated Polymer Conjugates as Tools for Immobilization and Visualization of His-Tagged Proteins

Recombinant proteins are commonly expressed with artificial affinity tags for purification, immobilization and characterization. The most frequently used tag, His-tag, is a sequence of consecutive histidine residues fused to the protein of interest. Specialized small molecules that bind His-tag are primarily used for purification, while antibodies are used for protein analysis. However, various issues may be encountered with the use of antibodies. Low inherent stability, the difficulty of introducing chemical modifications, and often-unreliable batch-to-batch consistency are among the limiting factors that call for better alternatives. Recently described polymer conjugates of N-(2-hydroxypropyl) methacrylamide and low-molecular-weight functional ligands, so-called iBodies, are antibody mimetics capable of replacing antibodies in biochemical applications. We tailored this system for methods utilizing His-tag by accessorizing the polymer carrier with tris-nitrilotriacetic acid targeting ligands. These anti-polyHis iBodies are additionally accessorized with fluorophores, enabling detection, and biotin ligands, enabling immobilization. Here, we characterized anti-polyHis iBodies and explored their use as antibody mimetics. We tested their stability, as well as the influence of different metal mediators and His-tag lengths on binding. With high affinity and stability, iBodies represent a new alternative for immobilization and visualization of His-tagged proteins.

Kinetics of Histidine-Tagged Protein Association to Nickel-Decorated Liposome Surfaces

Nickel-chelating lipids offer a convenient platform for reversible immobilization of histidine-tagged proteins to liposome surfaces. This interaction recently found utility as a model system for studying membrane remodeling triggered by protein crowding. Despite its wide array of utility, the molecular details of transient protein association to the lipid surfaces decorated with such chelator lipids remains poorly understood. In this study, we explore the kinetics of protein-liposome association across a wide concentration range using stopped-flow fluorescence. The fluorescence of histidine-tagged protein containing an intrinsic fluorophore (superfolder green fluorescent protein, SfGFP) was quenched upon binding to Ni-NTA-modified liposomes containing the quencher Dabsyl-PE lipids. Stopped-flow fluorescence reveals a complex, multiexponential binding behavior with a fast (k_obs ∼ 10-20 s^-1) phase and slower (k_obs < 4 s^-1) phase. Interestingly, the observed rates for the slower phase increase initially under low concentrations but start decreasing once a critical concentration is reached. Despite differences in the binding time scales, we observe that the trend of decreasing rates is reproducible irrespective of the chelator lipid doping level, protein surface charge, or lipid composition. Consideration of the protein footprint and membrane surface area occupancy leads us to conclude that the multiphasic binding behavior is reflective of protein binding via two distinct binding conformations. We propose that preliminary steps in protein association involve binding of a sterically occlusive side-on conformation followed by reorganization that leads to an end-on conformation with increased packing density. These results are important for the improvement of histidine-tag-based immobilization strategies and offer mechanistic insight into intermediates preceding membrane bending driven by protein crowding.

Multivalent Chelators for In Vivo Protein Labeling

With the advent of single-molecule methods, chemoselective and site-specific labeling of proteins evolved to become a central aspect in chemical biology as well as cell biology. Protein labeling demands high specificity, rapid as well as efficient conjugation, while maintaining low concentration and biocompatibility under physiological conditions. Generic methods that do not interfere with the function, dynamics, subcellular localization of proteins, and crosstalk with other factors are crucial to probe and image proteins in vitro and in living cells. Alternatives to enzyme-based tags or autofluorescent proteins are short peptide-based recognition tags. These tags provide high specificity, enhanced binding rates, bioorthogonality, and versatility. Here, we report on recent applications of multivalent chelator heads, recognizing oligohistidine-tagged proteins. The striking features of this system has facilitated the analysis of protein complexes by single-molecule approaches.

The Scaffold Design of Trivalent Chelator Heads Dictates Affinity and Stability for Labeling His-tagged Proteins in vitro and in Cells

Small chemical/biological interaction pairs are at the forefront in tracing protein function and interaction at high signal-to-background ratios in cellular pathways. However, the optimal design of scaffold, linker, and chelator head still deserve systematic investigation to achieve the highest affinity and kinetic stability for in vitro and especially cellular applications. We report on a library of N-nitrilotriacetic acid (NTA)-based multivalent chelator heads (MCHs) built on linear, cyclic, and dendritic scaffolds and compare these with regard to their binding affinity and stability for the labeling of cellular His-tagged proteins. Furthermore, we describe a new approach for tracing cellular target proteins at picomolar probe concentrations in cells. Finally, we outline fundamental differences between the MCH scaffolds and define a cyclic trisNTA chelator that displays the highest affinity and kinetic stability of all reported reversible, low-molecular-weight interaction pairs.

Combined therapies with nanostructured carbon materials: there is room still available at the bottom

The progress of the chemistry of carbon nanotubes (CNT) and graphene derivatives [mainly graphene oxide (GO)] has produced a number of technologically advanced drug delivery systems (DDS) that have been used in the field of nanomedicine, mostly in studies related to oncology. However, such a demanding field of research requires continuous improvements in terms of efficiency, selectivity and versatility. The loading of two, or more, bioactive components on the same nanoparticle offers new possibilities for treating cancer, efficiently addressing issues related both to biodistribution and pharmacokinetics. Nanostructured carbon materials (NCM), with their high surface area, their efficient cellular membrane crossing and their chemical versatility are ideal candidates for easy hetero-decoration and exploitation as advanced DDS. This review describes the achievements obtained in this area focusing on those studies in which two or more active components were loaded onto the DDS.

Controlling Protein Surface Orientation by Strategic Placement of Oligo-Histidine Tags

We report oriented immobilization of proteins using the standard hexahistidine (His6)-Ni2+:NTA (nitrilotriacetic acid) methodology, which we systematically tuned to give control of surface coverage. Fluorescence microscopy and surface plasmon resonance measurements of self-assembled monolayers (SAMs) of red fluorescent proteins (TagRFP) showed that binding strength increased by 1 order of magnitude for each additional His6-tag on the TagRFP proteins. All TagRFP variants with His6-tags located on only one side of the barrel-shaped protein yielded a 1.5 times higher surface coverage compared to variants with His6-tags on opposite sides of the so-called β-barrel. Time-resolved fluorescence anisotropy measurements supported by polarized infrared spectroscopy verified that the orientation (and thus coverage and functionality) of proteins on surfaces can be controlled by strategic placement of a His6-tag on the protein. Molecular dynamics simulations show how the differently tagged proteins reside at the surface in "end-on" and "side-on" orientations with each His6-tag contributing to binding. Also, not every dihistidine subunit in a given His6-tag forms a full coordination bond with the Ni2+:NTA SAMs, which varied with the position of the His6-tag on the protein. At equal valency but different tag positions on the protein, differences in binding were caused by probing for Ni2+:NTA moieties and by additional electrostatic interactions between different fractions of the β-barrel structure and charged NTA moieties. Potential of mean force calculations indicate there is no specific single-protein interaction mode that provides a clear preferential surface orientation, suggesting that the experimentally measured preference for the end-on orientation is a supra-protein, not a single-protein, effect.

Specific and Differential Binding of N-Acetylgalactosamine Glycopolymers to the Human Macrophage Galactose Lectin and Asialoglycoprotein Receptor

A range of glycopolymers composed of N-acetylgalactosamine were prepared via sequential Cu(I)-mediated polymerization and alkyne-azide click (CuAAC). The resulting polymers were shown, via multichannel surface plasmon resonance, to interact specifically with human macrophage galactose lectin (MGL; CD301) with high affinity (K_D = 1.11 μM), but they did not bind to the mannose/fucose-selective human lectin dendritic-cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN; CD209). The effect of sugar ligand valency on the binding (so-called "glycoside cluster effect") of poly(N-acetylgalactosamine) to MGL was investigated by varying first the polymer chain length (DP: 100, 64, 40, 23, 12) and then the architecture (4- and 8-arm star glycopolymers). The chain length did not have a significant effect on the binding to MGL (K_D = 0.17-0.52 μM); however, when compared to a hepatic C-type lectin of a similar monosaccharide specificity, the asialoglycoprotein receptor (ASGPR), the binding affinity was more noticeably affected (K_D = 0.37- 6.65 μM). These data suggest that known differences in the specific configuration/orientation of the carbohydrate recognition domains of MGL and ASGPR are responsible for the differences in binding observed between the different polymers of varied chain length and architecture. In the future, this model has the potential to be employed for the development of tissue-selective delivery systems.

Affinity Capturing and Surface Enrichment of a Membrane Protein Embedded in a Continuous Supported Lipid Bilayer

Investigations of ligand-binding kinetics to membrane proteins are hampered by their poor stability and low expression levels, which often translates into sensitivity-related limitations impaired by low signal-to-noise ratios. Inspired by affinity capturing of water-soluble proteins, which utilizes water as the mobile phase, we demonstrate affinity capturing and local enrichment of membrane proteins by using a fluid lipid bilayer as the mobile phase. Specific membrane-protein capturing and enrichment in a microfluidic channel was accomplished by immobilizing a synthesized trivalent nitrilotriacetic acid (tris-NTA)-biotin conjugate. A polymer-supported lipid bilayer containing His6-tagged β-secretase (BACE) was subsequently laterally moved over the capture region by using a hydrodynamic flow. Specific enrichment of His6-BACE in the Ni2+-NTA-modified region of the substrate resulted in a stationary three-fold increase in surface coverage, and an accompanied increase in ligand-binding response.

iBodies: Modular Synthetic Antibody Mimetics Based on Hydrophilic Polymers Decorated with Functional Moieties

Antibodies are indispensable tools for biomedicine and anticancer therapy. Nevertheless, their use is compromised by high production costs, limited stability, and difficulty of chemical modification. The design and preparation of synthetic polymer conjugates capable of replacing antibodies in biomedical applications such as ELISA, flow cytometry, immunocytochemistry, and immunoprecipitation is reported. The conjugates, named “iBodies”, consist of an HPMA copolymer decorated with low‐molecular‐weight compounds that function as targeting ligands, affinity anchors, and imaging probes. We prepared specific conjugates targeting several proteins with known ligands and used these iBodies for enzyme inhibition, protein isolation, immobilization, quantification, and live‐cell imaging. Our data indicate that this highly modular and versatile polymer system can be used to produce inexpensive and stable antibody substitutes directed toward virtually any protein of interest with a known ligand.

Constructing 3D microtubule networks using holographic optical trapping

Developing abilities to assemble nanoscale structures is a major scientific and engineering challenge. We report a technique which allows precise positioning and manipulation of individual rigid filaments, enabling construction of custom-designed 3D filament networks. This approach uses holographic optical trapping (HOT) for nano-positioning and microtubules (MTs) as network building blocks. MTs are desirable engineering components due to their high aspect ratio, rigidity, and their ability to serve as substrate for directed nano-transport, reflecting their roles in the eukaryotic cytoskeleton. The 3D architecture of MT cytoskeleton is a significant component of its function, however experimental tools to study the roles of this geometric complexity in a controlled environment have been lacking. We demonstrate the broad capabilities of our system by building a self-supporting 3D MT-based nanostructure and by conducting a MT-based transport experiment on a dynamically adjustable 3D MT intersection. Our methodology not only will advance studies of cytoskeletal networks (and associated processes such as MT-based transport) but will also likely find use in engineering nanostructures and devices.

pH-Triggered Reversible Multiple Protein-Polymer Conjugation Based on Molecular Recognition

Polymer conjugation for protein-based therapeutics has been developed extensively, but it still suffers from conjugation leading to decrease in protein activity and generates complexes with limited diversity due to general classical systems only incorporating one protein per each complex. Here we introduce a site-specific noncovalent protein-polymer conjugation, which can reduce the heterogeneity of the conjugates without disrupting protein function, while allowing for the modulation of binding affinity and stability, affecting the pH dependent binding of the number of proteins per polymer. We compared classical one protein-polymer conjugates with multiple protein-polymer conjugates using His-tagged enhanced yellow fluorescence protein (His6-eYFP) and metal-coordinated tris-nitrilotriacetic acid (trisNTA-Me(n+)) in a site-specific way. trisNTA-Me(n+)-His6 acts as a reversible linker with pH-triggered release of functional protein from the trisNTA-functionalized copolymers. The nature of the selected Me(n+) and number of available trisNTA-Me(n+) on poly(N-isopropylacrylamide-co-tris-nitrilotriacetic acid acrylamide) (PNTn) copolymers enables predictable modulation of the conjugates binding affinity (0.09-1.35 μM), stability, cell toxicity, and pH responsiveness. This represents a promising platform that allows direct control over the properties of multiple protein-polymer conjugates compared to the classical single protein-polymer conjugates.

HaloTag is an effective expression and solubilisation fusion partner for a range of fibroblast growth factors

The production of recombinant proteins such as the fibroblast growth factors (FGFs) is the key to establishing their function in cell communication. The production of recombinant FGFs in E. coli is limited, however, due to expression and solubility problems. HaloTag has been used as a fusion protein to introduce a genetically-encoded means for chemical conjugation of probes. We have expressed 11 FGF proteins with an N-terminal HaloTag, followed by a tobacco etch virus (TEV) protease cleavage site to allow release of the FGF protein. These were purified by heparin-affinity chromatography, and in some instances by further ion-exchange chromatography. It was found that HaloTag did not adversely affect the expression of FGF1 and FGF10, both of which expressed well as soluble proteins. The N-terminal HaloTag fusion was found to enhance the expression and yield of FGF2, FGF3 and FGF7. Moreover, whereas FGF6, FGF8, FGF16, FGF17, FGF20 and FGF22 were only expressed as insoluble proteins, their N-terminal HaloTag fusion counterparts (Halo-FGFs) were soluble, and could be successfully purified. However, cleavage of Halo-FGF6, -FGF8 and -FGF22 with TEV resulted in aggregation of the FGF protein. Measurement of phosphorylation of p42/44 mitogen-activated protein kinase and of cell growth demonstrated that the HaloTag fusion proteins were biologically active. Thus, HaloTag provides a means to enhance the expression of soluble recombinant proteins, in addition to providing a chemical genetics route for covalent tagging of proteins.

Site-specific protein labeling in the pharmaceutical industry: experiences from novartis drug discovery

Chemically modified proteins play an important role in several fields of pharmaceutical R&D, starting from various activities in drug discovery all the way down to biopharmaceuticals with improved properties such as antibody-drug conjugates. In the first part of the present chapter the significance and use of labeled proteins in biophysical methods, biochemical and cellular assays, in vivo imaging, and biopharmaceuticals is reviewed in general. In this context, the most relevant methods for site-specific modification of proteins and their application are also described. In the second part of the chapter, in-house (Novartis) results and experience with different techniques for selective protein labeling are discussed, with a focus on chemical or enzymatic (Avi-tag) biotinylation of proteins and their application in biophysical and biochemical assays. It can be concluded that while modern methods of site-specific protein labeling offer new possibilities for pharmaceutical R&D, classical methods are still the mainstay mainly due to being well established. However, site-specific protein labeling is expected to increase in importance, in particular for antibody-drug conjugates and other chemically modified biopharmaceuticals.

Designer lipids for drug delivery: from heads to tails

For four decades, liposomes composed of both naturally occurring and synthetic lipids have been investigated as delivery vehicles for low molecular weight and macromolecular drugs. These studies paved the way for the clinical and commercial success of a number of liposomal drugs, each of which required a tailored formulation; one liposome size does not fit all drugs! Instead, the physicochemical properties of the liposome must be matched to the pharmacology of the drug. An extensive biophysical literature demonstrates that varying lipid composition can influence the size, membrane stability, in vivo interactions, and drug release properties of a liposome. In this review we focus on recently described synthetic lipid headgroups, linkers and hydrophobic domains that can provide control over the intermolecular forces, phase preference, and macroscopic behavior of liposomes. These synthetic lipids further our understanding of lipid biophysics, promote targeted drug delivery and improve liposome stability. We further highlight the immune reactivity of novel synthetic headgroups as a key design consideration. For instance it was originally thought that synthetic PEGylated lipids were immunologically inert; however, it's been observed that under certain conditions PEGylated lipids induce humoral immunity. Such immune activation may be a limitation to the use of other engineered lipid headgroups for drug delivery. In addition to the potential immunogenicity of engineered lipids, future investigations on liposome drugs in vivo should pay particular attention to the location and dynamics of payload release.

Chemically functionalized carbon films for single molecule imaging

Many biological complexes are naturally low in abundance and pose a significant challenge to their structural and functional studies. Here we describe a new method that utilizes strong oxidation and chemical linkage to introduce a high density of bioactive ligands onto nanometer-thick carbon films and enable selective enrichment of individual macromolecular complexes at subnanogram levels. The introduced ligands are physically separated. Ni-NTA, Protein G and DNA/RNA oligonucleotides were covalently linked to the carbon surface. They embody negligible mass and their stability makes the functionalized films able to survive long-term storage and tolerate variations in pH, temperature, salts, detergents, and solvents. We demonstrated the application of the new method to the electron microscopic imaging of the substrate-bound C3PO, an RNA-processing enzyme important for the RNA interference pathway. On the ssRNA-linked carbon surface, the formation of C3PO oligomers at subnanomolar concentrations likely mimics their assembly onto ssRNA substrates presented by their native partners. Interestingly, the 3D reconstructions by negative stain EM reveal a side port in the C3PO/ssRNA complex, and the 15Å cryoEM map showed extra density right above the side port, which probably represents the ssRNA. These results suggest a new way for ssRNAs to interact with the active sites of the complex. Together our data demonstrate that the surface-engineered carbon films are suitable for selectively enriching low-abundance biological complexes at nanomolar level and for developing novel applications on a large number of surface-presented molecules.

Quantitation of affinity, avidity, and binding kinetics of protein analytes with a dynamically switchable biosurface

A label-free method for the analysis of interactions of proteins with surface-tethered ligands is introduced. Short DNA levers are electrically actuated on microelectrodes by ac potentials, and their switching dynamics are measured in real-time by fluorescence energy transfer. Binding of proteins to ligands attached to the top of the DNA levers is detected by time-resolved measurements of the levers' dynamic motion. We demonstrate the quantitation of binding kinetics (k(on), k(off) rate constants), dissociation constants (K(D) in the pM regime), and the influence of competitive binders (EC(50) values). Moreover, the "switchSENSE" method reveals avidity effects and allows discriminating between analytes with one or more binding sites. In a comparative study, interactions of six hexa-histidine-tagged proteins with tris-nitrilotriacetic acid (NTA(3)) ligands are quantitated. Their binding kinetics and affinities are found to vary over up to 2 orders of magnitude, evidencing that the proteins' individual chemical environments significantly influence the His(6)-NTA(3) interaction.

Mass spectrometric screening of ligands with lower off-rate from a clicked-based pooled library

This paper describes a convenient screening method using ion trap electrospray ionization mass spectrometry to classify ligands to a target molecule in terms of kinetic parameters. We demonstrate this method in the screening of ligands to a hexahistidine tag from a pooled library synthesized by click chemistry. The ion trap mass spectrometry analysis revealed that higher stabilities of ligand-target complexes in the gas phase were related to lower dissociation rate constants, i.e., off-rates in solution. Finally, we prepared a fluorescent probe utilizing the ligand with lowest off-rate and succeeded in performing single molecule observations of hexahistidine-tagged myosin V walking on actin filaments.

Importance of nanoparticle size in colorimetric and SERS-based multimodal trace detection of Ni(II) ions with functional gold nanoparticles

Colorimetric detection of analytes using gold nanoparticles along with surface-enhanced Raman spectroscopy (SERS) are areas of intense research activity since they both offer sensing of very low concentrations of target species. Multimodal detection promotes the simultaneous detection of a sample by a combination of different techniques; consequently, surface chemistry design in the development of multimodal nanosensors is important for rapid and sensitive evaluation of the analytes by diverse analytical methods. Herein it is shown that nanoparticle size plays an important role in the design of functional nanoparticles for colorimetric and SERS-based sensing applications, allowing controlled nanoparticle assembly and tunable sensor response. The design and preparation of robust nanoparticle systems and their assembly is reported for trace detection of Ni(II) ions as a model system in an aqueous solution. The combination of covalently attached nitrilotriacetic acid moieties along with the L-carnosine dipeptide on the nanoparticle surface represents a highly sensitive platform for rapid and selective detection of Ni(II) ions. This systematic study demonstrates that significantly lower detection limits can be achieved by finely tuning the assembly of gold nanoparticles of different core sizes. The results clearly demonstrate the feasibility and usefulness of a multimodal approach.

Building and characterizing antibody-targeted lipidic nanotherapeutics

Immunoliposomes provide a complementary, and in many instances advantageous, drug delivery strategy to antibody-drug conjugates. Their high carrying capacity of 20,000-150,000 drug molecules/liposome, allows for the use of a significantly broader range of moderate-to-high potency small molecule drugs when compared to the comparably few subnanomolar potency maytansinoid- and auristatin-based immunoconjugates. The multivalent display of 5-100 antibody fragments/liposome results in an avidity effect that can make use of even moderate affinity antibodies, as well as a cross-linking of cell surface receptors to induce the internalization required for intracellular drug release and subsequent activity. The underlying liposomal drug must be effectively engineered for long circulating pharmacokinetics and stable in vivo drug retention in order to allow for the drug to be efficiently delivered to the target tissue and take advantage of the site-specific bioavailability provided for by the targeting arm. In this chapter, we describe the rationale for engineering stable immunoliposome-based therapeutics, methods required for preparation of immunoliposomes, as well as for their physicochemical and in vivo characterization.

Lipid nanocapsule as vaccine carriers for his-tagged proteins: evaluation of antigen-specific immune responses to HIV I His-Gag p41 and systemic inflammatory responses

The purpose of this study was to design novel nanocapsules (NCs) with surface-chelated nickel (Ni-NCs) as a vaccine delivery system for histidine (His)-tagged protein antigens. Ni-NCs were characterized for binding His-tagged model proteins through high-affinity non-covalent interactions. The mean diameter and zeta potential of the optimized Ni-NCs were 214.9 nm and -14.8 mV, respectively. The optimal binding ratio of His-tagged Green Fluorescent Protein (His-GFP) and His-tagged HIV-1 Gag p41 (His-Gag p41) to the Ni-NCs was 1:221 and 1:480 w/w, respectively. Treatment of DC2.4 cells with Ni-NCs did not result in significant loss in the cell viability up to 24h (<5%). We further evaluated the antibody response of the Ni-NCs using His-Gag p41 as a model antigen. Formulations were administered subcutaneously to BALB/c mice at day 0 (prime) and 14 (boost) followed by serum collection on day 28. Serum His-Gag p41-specific antibody levels were found to be significantly higher at 1 and 0.5 μg doses of Gag p41-His-Ni-NCs (His-Gag p41 equivalent) compared with His-Gag p41 (1 μg) adjuvanted with aluminum hydroxide (AH). The serum IgG2a levels induced by Gag p41-His-Ni-NCs (1 μg) were significantly higher than AH adjuvanted His-Gag p41. The Ni-NCs alone did not result in the elevation of systemic IL-12/p40 and CCL5/RANTES inflammatory cytokine levels upon subcutaneous administration in BALB/c mice. In conclusion, the proposed Ni-NCs can bind His-tagged proteins and have the potential to be used as antigen delivery system capable of generating strong antigen-specific antibodies at doses much lower than with aluminum-based adjuvant and causing no significant elevation of systemic pro-inflammatory IL-12/p40 and CCL5/RANTES cytokines.

In vitro and in vivo assessment of targeting lipid-based nanoparticles to the epidermal growth factor-receptor (EGFR) using a novel Heptameric ZEGFR domain

Lipid-based oil-filled nanoparticles (NPs) with a high concentration of surface-chelated nickel (Ni-NPs) were successfully prepared using a Brij 78-NTA-Ni conjugate synthesized with Brij 78 (Polyoxyethylene (20) stearyl ether) and nitrilotriacetic acid (NTA). The facile incorporation of the Brij 78-NTA-Ni conjugate into the NP formulation allowed up to 90% Ni incorporation, which was a significant improvement over the previously used standard agent DOGS-NTA-Ni which led to ~6% Ni incorporation. The Ni-NPs were targeted to the highly epidermal growth factor receptor (EGFR)-overexpressing epidermoid carcinoma cells A431. This was accomplished using a novel high affinity histidine×6-tagged EGFR-binding Z domain (heptameric Z(EGFR) domain). In vitro cell uptake studies showed enhanced internalization (up to 90%) of the targeted Ni-NPs in A431 cells with only ≤10% internalization of the untargeted Ni-NPs. ICP-MS analysis used to quantify the amount of Ni in the cells were in close agreement with flow cytometry studies, which showed a dose dependent increase in the amount of Ni with the targeted Ni-NPs. Cell uptake competition studies showed that internalization of the targeted Ni-NPs within the cells was competed off with free heptameric Z(EGFR) domain at concentrations of 8.75ng/mL or higher. In vivo studies were carried out in nude mice bearing A431 tumors to determine the biodistribution and intracellular delivery. Near Infrared (NIR) optical imaging studies using Alexa750-labeled heptameric Z(EGFR) domain showed localization of 19% of the total detected fluorescence intensity in the tumor tissue, 28% in the liver and 42% in the kidneys 16h post i.v. injection. ICP-MS analysis showed almost a two-fold increase in the amount of intracellular Ni with the targeted Ni-NPs. These new Ni-NPs could be a very useful tool for targeting and drug delivery to a wide range of EGFR positive cancers.

Reversible major histocompatibility complex I-peptide multimers containing Ni(2+)-nitrilotriacetic acid peptides and histidine tags improve analysis and sorting of CD8(+) T cells

MHC-peptide multimers containing biotinylated MHC-peptide complexes bound to phycoerythrin (PE) streptavidin (SA) are widely used for analyzing and sorting antigen-specific T cells. Here we describe alternative T cell-staining reagents that are superior to conventional reagents. They are built on reversible chelate complexes of Ni(2+)-nitrilotriacetic acid (NTA) with oligohistidines. We synthesized biotinylated linear mono-, di-, and tetra-NTA compounds using conventional solid phase peptide chemistry and studied their interaction with HLA-A*0201-peptide complexes containing a His(6), His(12), or 2×His(6) tag by surface plasmon resonance on SA-coated sensor chips and equilibrium dialysis. The binding avidity increased in the order His(6) < His(12) < 2×His(6) and NTA(1) < NTA(2) < NTA(4), respectively, depending on the configuration of the NTA moieties and increased to picomolar K(D) for the combination of a 2×His(6) tag and a 2×Ni(2+)-NTA(2). We demonstrate that HLA-A2-2×His(6)-peptide multimers containing either Ni(2+)-NTA(4)-biotin and PE-SA- or PE-NTA(4)-stained influenza and Melan A-specific CD8+ T cells equal or better than conventional multimers. Although these complexes were highly stable, they very rapidly dissociated in the presence of imidazole, which allowed sorting of bona fide antigen-specific CD8+ T cells without inducing T cell death as well as assessment of HLA-A2-peptide monomer dissociation kinetics on CD8+ T cells.

Histidine-tag-directed chromophores for tracer analyses in the analytical ultracentrifuge

Many recombinant proteins carry an oligohistidine (His(X))-tag that allows their purification by immobilized metal affinity chromatography (IMAC). This tag can be exploited for the site-specific attachment of chromophores and fluorophores, using the same metal ion-nitrilotriacetic acid (NTA) coordination chemistry that forms the basis of popular versions of IMAC. Labeling proteins in this way can allow their detection at wavelengths outside of the absorption envelopes of un-modified proteins and nucleic acids. Here we describe use of this technology in tracer sedimentation experiments that can be performed in a standard analytical ultracentrifuge equipped with absorbance or fluorescence optics. Examples include sedimentation velocity in the presence of low molecular weight chromophoric solutes, sedimentation equilibrium in the presence of high concentrations of background protein and selective labeling to simplify the assignment of species in a complex interacting mixture.

Antibody response to polyhistidine-tagged peptide and protein antigens attached to liposomes via lipid-linked nitrilotriacetic acid in mice

Particulate delivery systems enhance antibody responses to subunit antigens. However, covalent attachment of protein antigens can disrupt protein structure and mask critical epitopes, altering the antibody response to the antigen. In this report, we evaluate noncovalent metal chelation via nitrilotriacetic acid (NTA) as a nondestructive method to attach peptide and protein antigens to liposomes. Two model antigens, ovalbumin (OVA) and a peptide derived from the membrane-proximal region of HIV-1 gp41 (N-MPR), were polyhistidinylated and attached to liposomes via monovalent NTA (mono-NTA; K(D) [equilibrium dissociation constant], ∼10 μM), trivalent NTA (tris-NTA; K(D), ∼1 nM), or a covalent linkage. Attachment of N-MPR, but not OVA, to liposomes via an NTA lipid elicited stronger antibody responses in BALB/c mice than a formulation in which unassociated antigen was simply admixed with control liposomes lacking NTA. However, the tris-NTA linkage did not increase antibody responses to either N-MPR or OVA compared to the level for the mono-NTA linkage, despite the greater liposomal association of the antigen. For both antigens, covalently attaching them to a lipid elicited significantly stronger antibody responses than NTA-anchored antigens (OVA titer, 3.4 × 10(6) versus 1.4 × 10(6) to 1.6 × 10(6) [P < 0.001]; N-MPR titer, 4.4 × 10(4) versus 5.5 × 10(2) to 7.6 × 10(2) [P < 0.003]). The data indicate that NTA linkages may increase antibody titers to weak antigens such as N-MPR, but NTA-mediated attachment remains inferior to covalent conjugation. Moreover, enhancements in antigen-liposome affinity do not result in increased antibody titers. Thus, additional improvements of NTA-mediated conjugation technology are necessary to achieve an effective, nondestructive method for increasing the humoral response to antigens in particulate vaccines.

Influence of multivalent nitrilotriacetic acid lipid-ligand affinity on the circulation half-life in mice of a liposome-attached His6-protein

Metal chelation-ligand interactions, such as occur between nitrilotriacetic acid (NTA)-nickel and multihistidines, enable the noncovalent attachment of histidine-modified proteins to liposomes and other particles. We compared three lipids: a mono-NTA lipid (ca. 10 microM affinity) and two tris-NTA lipid derivatives (ca. 3 nM and 0.2 nM affinity) in their ability to retain two different his(6)-containing proteins on NTA-liposomes in the presence of serum or plasma and after intravenous injection in mice. At nanomolar affinities, the off-rate of a his(6)-ligand is sufficiently long so that his(6)-proteins attached to particle surfaces will remain with the particle for hours; thus, we hypothesized that the increased his(6) affinity of multivalent NTA-modified liposomes would retain his(6)-proteins longer both in vitro and in vivo. For each of the three lipids, we found a robust association and complete activity retention of two his(6)-modified proteins: a far red-fluorescent protein, monomeric Katushka (mKate), and a prodrug-converting enzyme, yeast cytosine deaminase (yCD). Proteins associated more tightly in vitro with tris-NTA liposomes than with mono-NTA liposomes in the presence of refiltered fetal calf serum and mouse plasma. Free yCD exchanged with previously associated mKate for tris-NTA binding sites on the liposome surface. This exchange was due to the exchange of the proteins for NTA occupancy and not due to the exchange of tris-NTA lipid out of the liposome. The amount of yCD on the surface was similar if the proteins were co-associated or if mKate was pre-associated. This exchange confirms that NTA associated proteins are in a dynamic state and can exchange with multihistidine proteins in the biological milieu. There was no difference in circulation time of the protein when it was intravenously administered by itself or attached to any of the NTA-modified liposomes because in vivo the protein was rapidly released from the NTA liposomes. Upon recovery from blood, liposomes containing tris-NTA accumulated a different plasma protein profile than control liposomes, suggesting that Ni-NTA specifically interacts with some plasma proteins. The reason for the rapid protein dissociation from the liposome in vivo is not clear; it could be due to displacement by endogenous histidine-containing proteins or to natural chelators that remove nickel from the NTA. Regardless of the cause, improvements in chelator or ligand design are needed before metal chelation will be capable of retaining histidine-modified proteins on NTA liposomes after in vivo administration.