Lithographic techniques and surface chemistries for the fabrication of PEG-passivated protein microarrays

This article presents a new technique to fabricate patterns of functional molecules surrounded by a coating of the inert poly(ethylene glycol) (PEG) on glass slides for applications in protein microarray technology. The chief advantages of this technique are that it is based entirely on standard lithography processes, makes use of glass slides employing surface chemistries that are standard in the microarray community, and has the potential to massively scale up the density of microarray spots. It is shown that proteins and antibodies can be made to self-assemble on the functional patterns in a microarray format, with the PEG coating acting as an effective passivating agent to prevent non-specific protein adsorption. Various standard surface chemistries such as aldehyde, epoxy and amine are explored for the functional layer, and it is conclusively demonstrated that only an amine-terminated surface satisfies all the process constraints imposed by the lithography process sequence. The effectiveness of this microarray technology is demonstrated by patterning fluorescent streptavidin and a fluorescent secondary antibody using the well-known and highly specific interaction between biotin and streptavidin.     

Controlling the reactivity of ampiphilic quantum dots in biological assays through hydrophobic assembly of custom PEG derivatives

Modifications of the quantum dot (QD) surface are routinely performed via covalent biomolecule attachment, and poly(ethylene glycol) (PEG) derivatization has previously been shown to limit nonspecific cellular interactions of QD probes. Attempts to functionalize ampiphilic QDs (AMP-QDs) with custom PEG derivatives having a hydrophobic terminus resulted in self-assembly of these PEG ligands to the AMP-QD surface in the absence of covalent coupling reagents. We demonstrate, via electrophoretic characterization techniques, that these self-assembled PEG-QDs exhibit improved passivation in biological environments and are less susceptible to unwanted protein adsorption to the QD surface. We highlight the artifactual fluorescent response protein adsorption can cause in biological assays, and discuss considerations for improved small molecule presentation to facilitate specific QD interactions.     

Poly(ethylene glycol) interfaces: an approach for enhanced performance of microfluidic systems

Microfluidic systems are extensively used platform for analytical and therapeutic applications. One of the major problems encountered in these systems is the loss of material due to non-specific surface interactions. When biological solutions are flowed through microchannels, they tend to adsorb on the surface due to the negative charge of the surface. This results in a reduced efficiency of the system which can be critical in sensitive biological analysis. Poly(ethylene glycol) (PEG) is known to form non-fouling interfaces on silicon and glass which are common materials used in microfluidic systems. The most common approach for modifying silicon/glass with PEG involves a solution phase protocol. Since the micro/nanofluidic systems have channel sizes ranging from hundreds of microns to submicron with variety of complicated network, this surface modification approach is not sufficient in forming uniform, conformal, and ultrathin films on the surface. Due to the enclosed features in these systems, the properties of liquids such as viscosity and surface tension play an important role in the clogging and eventually biofouling of these microchannels. Hence, we have developed a solvent-free vapor deposition protocol for modifying silicon/glass surfaces with PEG. Various concentrations of protein solutions were flowed through unmodified and PEG-modified glass microcapillaries of different lengths at different flow rates. PEG surfaces formed on silicon have shown 80% reduction in protein adsorption in static conditions.     

Polyethylene glycol-stabilized lipid disks as model membranes in interaction studies based on electrokinetic capillary chromatography and quartz crystal microbalance

Distearoylphosphatidylcholine (DSPC)/cholesterol/distearoylphosphatidylethanolamine (DSPE)–polyethylene glycol 5000 [PEG(5000)] lipid disks, mimicking biological membranes, were used as pseudostationary phase in partial filling electrokinetic capillary chromatography (EKC) to study interactions between pharmaceuticals and lipid disks. Capillaries were coated either noncovalently with a poly(1-vinylpyrrolidone)-based copolymer or covalently with polyacrylamide to mask the negative charges of the fused-silica capillary wall and to minimize interactions between positively charged pharmaceuticals and capillary wall. Although the noncovalent copolymer coating method was faster, better stability of the covalent polyacrylamide coating at physiological pH 7.4 made it more reliable in partial filling EKC studies. Migration times of pharmaceuticals were proportional to the amount of lipids in the pseudostationary phase, and partition coefficients were successfully determined. Because the capillary coatings almost totally suppressed the electroosmotic flow, it was not practical to use the EKC-based method for partition studies involving large molecules with low mobilities. Hence, the applicability of the biomembrane mimicking lipid disks for interactions studies with large molecules was verified by the quartz crystal microbalance technique. Biotinylated lipid disks were then immobilized on streptavidin-coated sensor chip surface, and interactions with a high-molecular-mass molecule, lysozyme, were studied. Cryo-transmission electron microscopy and asymmetrical flow field-flow fractionation were used to clarify the sizes of lipid disks used.     

An AFM determination of the effects on surface roughness caused by cleaning of fused silica and glass substrates in the process of optical biosensor preparation

The covalent attachment of organic films and of biological molecules to fused silica and glass substrates is important for many applications. For applications such as biosensor development, it is desired that the immobilised molecules be assembled in a uniform layer on the surface so as to provide for reproducibility and speed of surface interactions. For optimal derivatisation the surface must be appropriately cleaned to remove contamination, to create surface attachment sites such as hydroxyl groups, and to control surface roughness. The irregularity of the surface can be significant in defining the integrity and density of immobilised films. Numerous cleaning methods exist for fused silica and glass substrates and these include gas plasmas, and combinations of acids, bases and organic solvents that are allowed to react at varying temperatures. For many years, we have used a well established method based on a combination of washing with basic peroxide followed by acidic peroxide to clean and hydroxylate the surface of fused silica and glass substrates before oligonucleotide immobilisation. Atomic force microscopy (AFM) has been used to evaluate the effect of cleaning on surface roughness for various fused silica and glass samples. The results indicate that surface roughness remains substantial after use of this common cleaning routine, and can provide a surface area that is more than 10% but less than 30% larger than anticipated from geometric considerations of a planar surface.     

A water-stable protected isocyanate glass array substrate

We describe the performance of a new glass attachment chemistry for arrays that is particularly well suited to attachment of small molecules, such as peptides. The attachment chemistry is a protected isocyanate (PI) group. Isocyanate groups are well suited to serving as a glass coating for arrays, in that they are highly reactive with many different types of biological compounds. However, they are generally so reactive as to be unstable. The new feature of the PI slide coating is its stability. It can withstand immersion in water without loss of reactivity and has at least a 1-year shelf life. The high reactivity of the PI group results in a rapid coupling reaction (< 15min) and is particularly useful for attaching small molecules, such as peptides. Since isocyanates bind to both amines (forming a urea linkage) and hydroxyl groups (forming a carbamate bond), we tested the ability of the PI coating to bind to a wide variety of compounds. We found that the PI slide coating can directly attach to peptides, proteins, carbohydrates, lipooligosaccharides, and DNA. The sensitivity of detection for these compounds is comparable to that of other previously published array substrates.     

Isolation of cell surface proteins for mass spectrometry-based proteomics

Defining the cell surface proteome has profound importance for understanding cell differentiation and cell–cell interactions, as well as numerous pathogenic abnormalities. Owing to their hydrophobic nature, plasma membrane proteins that reside on the cell surface pose analytical challenges and, despite efforts to overcome difficulties, remain under-represented in proteomic studies. Limitations in the classically employed ultracentrifugation-based approaches have led to the invention of more elaborate techniques for the purification of cell surface proteins. Three of these methods – cell surface coating with cationic colloidal silica beads, biotinylation and chemical capture of surface glycoproteins – allow for marked enrichment of this subcellular proteome, with each approach offering unique advantages and characteristics for different experiments. In this article, we introduce the principles of each purification method and discuss applications from the recent literature.     

A crumpled surface having transverse attractive interactions as a simplified model with biological significance

Using extensive analogical simulations with square sheets of paper we investigate the influence of short-range transverse attractive interactions on the packing properties of a crumpled surface. These interactions are due to transverse connections or local bridges associated with a given number of binding sites localized on the two-dimensional surface and distributed in several patterns in the three-dimensional physical space. Geometrical relations and critical exponents describing the statistical properties of the crumpled surface are obtained as a function of the strength of the attractive interactions. Our model suggests how the presence of short-range interactions as, e.g. van der Waals forces can be important for the geometric plasticity of biological molecules, which in turn is important for biological function. The relevance of our results to the study of molecular conformation of proteins and membranes is discussed, and a comparison is also made between the behavior of the crumpled surface studied here and other important non-equilibrium fractal structures.     

Analysis of monoPEGylated human galectin-2 by small-angle X-ray and neutron scattering: concentration dependence of PEG conformation in the conjugate

Protein conjugation with polyethylene glycol (PEG) is a valuable means for improving stability, solubility, and bioavailability of pharmaceutical proteins. Using human galectin-2 (hGal-2) and 5 kDa PEG as a model system we first produced a PEG-hGal-2 conjugate exclusively at the Cys75 residue, resulting in two monosubstituted subunits per hGal-2 homodimer. Small angle X-ray and neutron scattering (SAXS and SANS) were combined to provide complementary structural information about the PEG-hGal-2 conjugate, wherein signal generation in SAXS depends mainly on the protein while SANS data presents signals from both the protein and PEG moieties. SAXS data gave a constant radius of gyration (R(g) = 21.5 ?) for the conjugate at different concentrations and provided no evidence for an alteration of homodimeric structure or hGal-2 ellipsoidal shape upon PEGylation. In contrast, SANS data revealed a concentration dependence of R(g) for the conjugate, with the value decreasing from 31.5 ? at 2 mg/mL to 26 ? at 14 mg/mL (based on hGal-2 concentration). Scattering data have been successfully described by the model of the ellipsoidal homogeneous core (hGal-2) attached with polymer chains (PEG) at the surface. Evidently, the PEG conformation of the conjugate strongly depends on conjugate concentration and PEG's radius of gyration decreases from 24.5 to 15 ?. An excluded volume effect, arising from steric clashes between PEG molecules at high concentration, was quantified by estimating the second virial coefficient, A(2), of PEGylated hGal-2 from the SANS data. A positive value of A(2) (6.0 ± 0.4 × 10(-4) cm(3) mol g(-2)) indicates repulsive interactions between molecules, which are expected to protect the PEGylated protein against aggregation.     

A proteomics approach to the cell-surface interactome using the enzyme-mediated activation of radical sources reaction

We previously reported a simple method to analyze the interaction of cell-surface molecules in living cells. This method termed enzyme-mediated activation of radical sources (EMARS) is featured by radical formation of the labeling reagent by horseradish peroxidase (HRP). Herein, we propose an approach to the cell-surface molecular interactome by using combination of this EMARS reaction and MS-based proteomics techniques. In the current study, we employed a novel labeling reagent, fluorescein-conjugated arylazide. The fluorescein-tagged proteins resulting from the EMARS reaction were directly detected in the electrophoresis gels with a fluorescence image analyzer. These products were also purified and concentrated by immunoaffinity chromatography with anti-fluorescein antibody-immobilized resins. The purified fluorescein-tagged proteins were subsequently subjected to an MS-based proteomics analysis. Analysis using HRP-conjugated cholera toxin subunit B, which recognizes a lipid raft marker, ganglioside GM1, revealed 30 membrane and secreted proteins that were candidates for the cell-surface molecules coclustering with GM1. The proposed approach will provide a clue to study functional molecular interactions in a variety of biological events on the cell surface.     

Excluded volume effects on the partition of single- and double-stranded oligodeoxynucleotides between two liquid phases.

The distribution coefficients of single- and double-stranded oligodeoxynucleotides in a PEG 8000/phosphate two-phase system are a function of their chain length. Values of the distribution coefficients are in general agreement with a simple extension of a model for excluded volume effects (the "available volume model") which was applied previously to the distribution of proteins in this system. The current results therefore provide a second set of examples for molecules of very different geometry where the distribution added molecules is controlled by excluded volume interactions between those molecules and the PEG 8000 of the two-phase system.     

Patterned biofunctional poly(acrylic acid) brushes on silicon surfaces

Protein patterning was carried out using a simple procedure based on photolithography wherein the protein was not subjected to UV irradiation and high temperatures or contacted with denaturing solvents or strongly acidic or basic solutions. Self-assembled monolayers of poly(ethylene glycol) (PEG) on silicon surfaces were exposed to oxygen plasma through a patterned photoresist. The etched regions were back-filled with an initiator for surface-initiated atom transfer radical polymerization (ATRP). ATRP of sodium acrylate was readily achieved at room temperature in an aqueous medium. Protonation of the polymer resulted in patterned poly(acrylic acid) (PAA) brushes. A variety of biomolecules containing amino groups could be covalently tethered to the dense carboxyl groups of the brush, under relatively mild conditions. The PEG regions surrounding the PAA brush greatly reduced nonspecific adsorption. Avidin was covalently attached to PAA brushes, and biotin-tagged proteins could be immobilized through avidin-biotin interaction. Such an immobilization method, which is based on specific interactions, is expected to better retain protein functionality than direct covalent binding. Using biotin-tagged bovine serum albumin (BSA) as a model, a simple strategy was developed for immobilization of small biological molecules using BSA as linkages, while BSA can simultaneously block nonspecific interactions.     

Phosphorylcholine Group-immobilized Surface Prepared on Polydimethylsiloxane Membrane by In Situ Reaction for Its Reduced Biofouling

To reduce interactions between biological molecules and the surface of microchip devices including the microchip, which should be conducted to improve sensitivity, reactivity, and the typical phospholipid polar group, the phosphorylcholine group-immobilized surfaces were prepared. The surface modification of polydimethylsiloxane (PDMS) was performed by in situ reaction during curing by cross-linking the PDMS prepolymers. Since it is known that 2-methacryloyloxyethyl phosphorylcholine (MPC) facilitates the preparation of biomedical polymers with excellent biocompatibility and antithrombogenicity, it was used as the reactant for surface modification. The MPC was coated on the glass substrate, and two-liquid-type PDMS prepolymers were then applied. During the curing process of the vinyl groups of poly(dimetylsiloxane-co-methylsiloxane) and poly(dimethylsiloxane-co-methylvinylsiloxane), the methacrylate group in MPC was attached onto the PDMS surface via a hydrosilyl group. Analysis of the surface characteristics by X-ray photoelectron spectroscopy and measurement of the surface contact angle revealed that the introduction of the phosphorylcholine group in the MPC unit on the surface induced hydrophilicity at the surface. Further, protein adsorption on the surface decreased with an increase in the number of phosphorylcholine groups. Based on these results, we concluded that the construction of the phosphorylcholine group-enriched surface on the PDMS substrate could be achieved by immobilization of MPC, and it may facilitate fabrication of biomedical devices, particularly microfluidic devices.     

Ultrathin functional star PEG coatings for DNA microarrays

In this study, star PEG coatings on glass substrates have been used as support material for oligonucleotide microarrays. These coatings are prepared from solutions of six armed star shaped prepolymers that carry reactive isocyanate endgroups. As described earlier, such films prevent the adsorption of proteins and the adhesion of cells but can easily be functionalized for specific biological recognition. Here we used the high functionality of these coatings for the covalent immobilization of amino terminated 20mer oligonucleotides, both by microcontact printing and spotting techniques. The permanent immobilization of fluorescently labeled DNA as well as hybridization of 20mer oligonucleotides have been monitored by fluorescence microscopy. The hybridization efficiency as determined by fluorescence intensity varied from 30% to 80% depending on the way of layer preparation. The direct spotting without additional activation and blocking steps of the surface demonstrates the potential of star PEG coatings as ultrathin surface modification for microarrays.     

Amphiphilic triblock copolymers with PEGylated hydrocarbon structures as environmentally friendly marine antifouling and fouling-release coatings

The ideal marine antifouling (AF)/fouling-release (FR) coating should be non-toxic, while effectively either resisting the attachment of marine organisms (AF) or significantly reducing their strength of attachment (FR). Many recent studies have shown that amphiphilic polymeric materials provide a promising solution to producing such coatings due to their surface dual functionality. In this work, poly(ethylene glycol) (PEG) of different molecular weights (M_w?=?350, 550) was coupled to a saturated difunctional alkyl alcohol to generate amphiphilic surfactants (PEG-hydrocarbon-OH). The resulting macromolecules were then used as side chains to covalently modify a pre-synthesized PS₈?_K-b-P(E/B)₂₅?_K-b-PI₁₀?_K (SEBI or K3) triblock copolymer, and the final polymers were applied to glass substrata through an established multilayer surface coating technique to prepare fouling resistant coatings. The coated surfaces were characterized with AFM, XPS and NEXAFS, and evaluated in laboratory assays with two important fouling algae, Ulva linza (a green macroalga) and Navicula incerta, a biofilm-forming diatom. The results suggest that these polymer-coated surfaces undergo surface reconstruction upon changing the contact medium (polymer/air vs polymer/water), due to the preferential interfacial aggregation of the PEG segment on the surface in water. The amphiphilic polymer-coated surfaces showed promising results as both AF and FR coatings. The sample with longer PEG chain lengths (M_w?=?550?g?mol^?1) exhibited excellent properties against both algae, highlighting the importance of the chemical structures on ultimate biological performance. Besides reporting synthesis and characterization of this new type of amphiphilic surface material, this work also provides insight into the nature of PEG/hydrocarbon amphiphilic coatings, and this understanding may help in the design of future generations of fluorine-free, environmentally friendly AF/FR polymeric coatings.     

Phenotypic and functional heterogeneity of human bone marrow- and amnion-derived MSC subsets

Bone marrow-derived mesenchymal stromal/stem cells (MSCs) are nonhematopoietic cells that are able to differentiate into osteoblasts, adipocytes, and chondrocytes. In addition, they are known to participate in niche formation for hematopoietic stem cells and to display immunomodulatory properties. Conventionally, these cells are functionally isolated from tissue based on their capacity to adhere to the surface of culture flasks. This isolation procedure is hampered by the unpredictable influence of secreted molecules, the interactions between cocultured hematopoietic and other unrelated cells, and by the arbitrarily selected removal time of nonadherent cells before the expansion of MSCs. Finally, functionally isolated cells do not provide biological information about the starting population. To circumvent these limitations, several strategies have been developed to facilitate the prospective isolation of MSCs based on the selective expression, or absence, of surface markers. In this report, we summarize the most frequently used markers and introduce new targets for antibody-based isolation procedures of primary bone marrow- and amnion-derived MSCs.     

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.     

Steric exclusion is the principal source of the preferential hydration of proteins in the presence of polyethylene glycols.

The preferential interactions of bovine serum albumin, lysozyme, chymotrypsinogen, ribonuclease A, and beta-lactoglobulin with polyethylene glycols (PEGs) of molecular weight 200-6,000 have been measured by dialysis equilibrium coupled with high precision densimetry. All the proteins were found to be preferentially hydrated in all the PEGs, and the magnitude of the preferential hydration increased with increasing PEG size for each protein. The change in the chemical potentials of the proteins with the addition of the PEGs had highly positive values, indicating a strong thermodynamic destabilization of the system by the PEGs. A viscosity study of the PEGs showed them to be randomly coiled polymers, as their radii of gyration were related to the molecular weight by Rg = aM0.55. The thickness of the effective shell impenetrable to PEG around protein molecules, calculated from the preferential hydration, was found to vary with PEG molecular weight in similar fashion as the PEG radius of gyration, supporting the proposal (Arakawa, T. & Timasheff, S.N., 1985a, Biochemistry 24, 6756-6762) that the preferential exclusion of PEGs from proteins is due principally to the steric exclusion of PEG from the protein domain, although favorable interactions with protein surface residues, in particular nonpolar ones, may compete with the exclusion. These thermodynamically unfavorable preferential exclusion interactions lead to the action of PEGs as precipitants, although they may destabilize protein structure at higher temperatures.     

Hidden partners: Using cross‐docking calculations to predict binding sites for proteins with multiple interactions

Protein‐protein interactions control a large range of biological processes and their identification is essential to understand the underlying biological mechanisms. To complement experimental approaches, in silico methods are available to investigate protein‐protein interactions. Cross‐docking methods, in particular, can be used to predict protein binding sites. However, proteins can interact with numerous partners and can present multiple binding sites on their surface, which may alter the binding site prediction quality. We evaluate the binding site predictions obtained using complete cross‐docking simulations of 358 proteins with 2 different scoring schemes accounting for multiple binding sites. Despite overall good binding site prediction performances, 68 cases were still associated with very low prediction quality, presenting individual area under the specificity‐sensitivity ROC curve (AUC) values below the random AUC threshold of 0.5, since cross‐docking calculations can lead to the identification of alternate protein binding sites (that are different from the reference experimental sites). For the large majority of these proteins, we show that the predicted alternate binding sites correspond to interaction sites with hidden partners, that is, partners not included in the original cross‐docking dataset. Among those new partners, we find proteins, but also nucleic acid molecules. Finally, for proteins with multiple binding sites on their surface, we investigated the structural determinants associated with the binding sites the most targeted by the docking partners.