Osteogenic Surface Modification Based on Functionalized Poly-P-Xylylene Coating

The biotechnology to immobilize biomolecules on material surfaces has been developed vigorously due to its high potentials in medical applications. In this study, a simple and effective method was designed to immobilize biomolecules via amine-N-hydroxysuccinimide (NHS) ester conjugation reaction using functionalized poly-p-xylylene coating on material surfaces. The NHS ester functionalized coating is synthesized via chemical vapor deposition, a facile and solvent-less method, creating a surface which is ready to perform a one-step conjugation reaction. Bone morphogenetic protein 2 (BMP-2) is immobilized onto material surfaces by this coating method, forming an osteogenic environment. The immobilization process is controlled at a low temperature which does not damage proteins. This modified surface induces differentiation of preosteoblast into osteoblast, manifested by alkaline phosphatase (ALP) activity assay, Alizarin Red S (ARS) staining and the expression of osteogenic gene markers, Alpl and Bglap3. With this coating technology, immobilization of growth factors onto material surface can be achieved more simply and more effectively.     

Enzymatic activity on a chip: the critical role of protein orientation

We compare the catalytic activities of enzymes immobilized on silicon surfaces with and without orientation. While oriented sulfotransferases selectively immobilized on an otherwise zero-background surface via 6xHis tags faithfully reflect activities of solution phase enzymes, those with random orientation on the surface do not. This finding demonstrates that controlling the orientation of immobilized protein molecules and designing an ideal local chemical environment on the solid surface are both essential if protein microarrays are to be used as quantitative tools in biomedical research.     

Patterning of proteins and cells on functionalized surfaces prepared by polyelectrolyte multilayers and micromolding in capillaries

A method for protein and cell patterning on polyelectrolyte-coated surfaces using simple micromolding in capillaries (MIMIC) is described. MIMIC produced two distinctive regions. One contained polyethylene glycol (PEG) microstructures fabricated using photopolymerization that provided physical, chemical, and biological barriers to the nonspecific binding of proteins, bacteria, and fibroblast cells. The second region was the polyelectrolyte (PEL) coated surface that promoted protein and cell immobilization.

The difference in surface functionality between the PEL region and background PEG microstructures resulted in simple patterning of biomolecules. Fluorescein isothiocyanate-tagged bovine serum albumin, E. coli expressing green fluorescence protein (GFP), and fibroblast cells were successfully bound to the exposed PEL surfaces at micron scale. Compared with the simple adsorption of protein, fluorescence intensity was dramatically improved (by about six-fold) on the PEL-modified surfaces. Although animal cell patterning is prerequisite for adhesive protein layer to survive on desired area, the PEL surface without adhesive proteins provides affordable microenvironment for cells.

The simple preparation of functionalized surface but universal platform can be applied to various biomolecules such as proteins, bacteria, and cells.     

Recent developments in the site-specific immobilization of proteins onto solid supports

Immobilization of proteins onto surfaces is of great importance in numerous applications, including protein analysis, drug screening, and medical diagnostics, among others. The success of all these technologies relies on the immobilization technique employed to attach a protein to the corresponding surface. Non-specific physical adsorption or chemical cross-linking with appropriate surfaces results in the immobilization of the protein in random orientations. Site-specific covalent attachment, on the other hand, leads to molecules being arranged in a definite, orderly fashion and allows the use of spacers and linkers to help minimize steric hindrances between the protein and the surface. The present work reviews the latest chemical and biochemical developments for the site-specific covalent attachment of proteins onto solid supports.     

Fabrication and selective functionalization of amine-reactive polymer multilayers on topographically patterned microwell cell culture arrays

We report an approach to the fabrication and selective functionalization of amine-reactive polymer multilayers on the surfaces of 3-D polyurethane-based microwell cell culture arrays. "Reactive" layer-by-layer assembly of multilayers using branched polyethyleneimine (BPEI) and the azlactone-functionalized polymer poly(2-vinyl-4,4'-dimethylazlactone) (PVDMA) yielded film-coated microwell arrays that could be chemically functionalized postfabrication by treatment with different amine-functionalized macromolecules or small molecule primary amines. Treatment of film-coated arrays with the small molecule amine d-glucamine resulted in microwell surfaces that resisted the adhesion and proliferation of mammalian fibroblast cells in vitro. These and other experiments demonstrated that it was possible to functionalize different structural features of these arrays in a spatially resolved manner to create dual-functionalized substrates (e.g., to create arrays having either (i) azlactone-functionalized wells, with regions between the wells functionalized with glucamine or (ii) substrates with spatially resolved regions of two different cationic polymers). In particular, spatial control over glucamine functionalization yielded 3-D substrates that could be used to confine cell attachment and growth to microwells for periods of up to 28 days and support the 3-D culture of arrays of cuboidal cell clusters. These approaches to dual functionalization could prove useful for the long-term culture and maintenance of cell types for which the presentation of specific and chemically well-defined 3-D culture environments is required for control over cell growth, differentiation, and other important behaviors. More generally, our approach provides methods for the straightforward chemical functionalization of otherwise unreactive topographically patterned substrates that could prove to be useful in a range of other fundamental and applied contexts.     

Atomic force spectroscopy-based study of antibody pesticide interactions for characterization of immunosensor surface

Development of immunobiosensor detector surfaces involves the immobilization of active antibodies on the capture surface without any significant loss of antigen binding activity. An atomic force microscope (AFM) was used to directly evaluate specific interactions between pesticides and antibodies on a biosensor surface. Oriented immobilization of antibodies against two herbicide molecules 2,4-dichlorophenoxyacetic acid (2,4-D) and atrazine, on gold, was carried out to create the active immunobiosensor surfaces. The adhesive forces between immobilized antibodies and their respective antigens were measured by force spectroscopy using hapten-carrier protein functionalized AFM cantilevers. Relative functional affinity (avidity) measurements of the antibodies carried out prior to immobilization, well correlated with subsequent AFM force measurement observations. Analysis showed that immobilization had not compromised the reactivity of the surface immobilized antibody molecules for antigen nor was there any change in their relative quality with respect to each other. The utility of the immunoreactive surface was further confirmed using a Surface Plasmon Resonance (SPR) based detection system. Our study indicates that AFM can be utilized as a convenient immunobiosensing tool for confirming the presence and also assessing the strength of antibody-hapten interactions on biosensor surfaces under development.     

Protein surface representation and analysis by dimension reduction

Background

Protein structures are better conserved than protein sequences, and consequently more functional information is available in structures than in sequences. However, proteins generally interact with other proteins and molecules via their surface regions and a backbone-only analysis of protein structures may miss many of the functional and evolutionary features. Surface information can help better elucidate proteins' functions and their interactions with other proteins. Computational analysis and comparison of protein surfaces is an important challenge to overcome to enable efficient and accurate functional characterization of proteins.

Methods

In this study we present a new method for representation and comparison of protein surface features. Our method is based on mapping the 3-D protein surfaces onto 2-D maps using various dimension reduction methods. We have proposed area and neighbor based metrics in order to evaluate the accuracy of this surface representation. In order to capture functionally relevant information, we encode geometric and biochemical features of the protein, such as hydrophobicity, electrostatic potential, and curvature, into separate color channels in the 2-D map. The resulting images can then be compared using efficient 2-D image registration methods to identify surface regions and features shared by proteins.

Results

We demonstrate the utility of our method and characterize its performance using both synthetic and real data. Among the dimension reduction methods investigated, SNE, LandmarkIsomap, Isomap, and Sammon's mapping provide the best performance in preserving the area and neighborhood properties of the original 3-D surface. The enriched 2-D representation is shown to be useful in characterizing the functional site of chymotrypsin and able to detect structural similarities in heat shock proteins. A texture mapping using the 2-D representation is also proposed as an interesting application to structure visualization.

     

A strategy for the covalent functionalization of resorbable polymers with heparin and osteoinductive growth factor

The chemical strategy presented herein is the nondestructive preparation of resorbable polymer scaffolds with heparin covalently bonded to the surface and an osteoinductive growth factor, recombinant human bone morphogenetic protein-2, immobilized in the heparin layer. The coupling scheme involves functionalization of surfaces by grafting in the vapor phase with poly( l-lactide) and poly(-caprolactone) films chosen as representative substrates. The biocompatibility of functionalized surfaces was verified by a much improved attachment and proliferation of mesenchymal stem cells (MSC).     

Functionalized Amphipols: A Versatile Toolbox Suitable for Applications of Membrane Proteins in Synthetic Biology

Amphipols are amphipathic polymers that stabilize membrane proteins isolated from their native membrane. They have been functionalized with various chemical groups in the past years for protein labeling and protein immobilization. This large toolbox of functionalized amphipols combined with their interesting physico-chemical properties give opportunities to selectively add multiple functionalities to membrane proteins and to tune them according to the needs. This unique combination of properties makes them one of the most versatile strategies available today for exploiting membrane proteins onto surfaces for various applications in synthetic biology. This review summarizes the properties of functionalized amphipols suitable for synthetic biology approaches.     

Surface motifs by a computer vision technique: Searches,detection, and implications for protein–ligand recognition

We describe the application of a method geared toward structural and surface comparison of proteins. The method is based on the Geometric Hashing Paradigm adapted from Computer Vision. It allows for comparison of any two sets of 3-D coordinates, such as protein backbones, protein core or protein surface motifs, and small molecules such as drugs. Here we apply our method to 4 types of comparisons between pairs of molecules: (1) comparison of the backbones of two protein domains; (2) search for a predefined 3-D C_α motif within the full backbone of a domain; and in particular, (3) comparison of the surfaces of two receptor proteins; and (4) comparison of the surface of a receptor to the surface of a ligand. These aspects complement each other and can contribute toward a better understandingof protein structure and biomolecular recognition. Searches for 3-D surface motifs can be carried out on either receptors or on ligands. The latter may result in the detection of pharmacophoric patterns. If the surfaces of the binding sites of either the receptors or of the ligands are relatively similar, surface superpositioning may aid significantly in the docking problem. Currently, only distance invariants are used in the matching, although additional geometric surface invariants are considered. The speed of our Geometric Hashing algorithm is encouraging, with a typical surface comparison taking only seconds or minutes of CPU time on a SUN 4 SPARC workstation. The direct application of this method to the docking problem is also discussed. We demonstrate the success of this methodin its application to two members of the globin family and to two dehydrogenases. © 1993 Wiley-Liss, Inc.     

Synthesis, patterning and applications of star-shaped poly(ethylene glycol) biofunctionalized surfaces

Poly(ethylene) glycol (PEG) is an excellent material to modify surfaces to resist non-specific protein adsorption. Linear PEG has been extensively studied both theoretically and experimentally and it has been found that resistance of PEG-coated surfaces to protein adsorption depends mainly on the molecular weight of the polymer and the surface grafting density. End-functionalized star-shaped PEGs allow for interpolymer crosslinking to form a dense layer. An excellent example of such a system consists of a 6-arm PEG/PPG (4 : 1) star polymer functionalized with isocyanate using IPDI. The end functionalization may be further biofunctionalized to recognize specific biomolecules such as streptavidin, His-tagged proteins, amino-terminated oligonucleotides and cell receptors. This functionalization may be patterned into specific geometries using stamping techniques or randomly distributed by statistical reaction of the end group with the biofunctional molecule in solution. The surface preparation uses simple spin-, dip- or spray-coating and produces smooth layers with low background fluorescence. These properties, together with the advantageous chemical properties of PEG, render the surfaces ideal for immobilizing proteins on surfaces with detection limits down to the single molecule level. Proteins immobilized on such surfaces are able to maintain their folded, functional form and are able to completely refold if temporarily exposed to denaturing conditions. Immobilized enzyme molecules were able to perform their function with the same activity as the enzyme in solution. Future directions of using surfaces coated with such crosslinked star polymers in highly sensitive and robust biotechnology applications will be discussed.     

Polymerizing immobilization of acrylamide-modified nucleic acids and its application

The immobilization of nucleic acids on solid supports has been widely used in the detection of DNA and other biomolecules in sensor technology. Because three dimensional (3-D) hydrogel matrixes offer significant advantages for capturing probes over more conventional two dimensional (2-D) rigid substrates and the ability to provide a solution-mimicking environment, they are becoming increasingly attractive as desired supports for bio-analysis. Acrylamide-modified nucleic acids and acrylamide monomers being polymerized directly to immobilize nucleic acids is only one-step chemical process which is not interfered by exterior surroundings, and the 3-D polyacrylamide gel fabricated by this method is not required to be activated by some labile chemical treatments. Moreover, the attachment is extremely stable to withstand the cycling process involved in the polymerase chain reaction (PCR). In this paper, the development of polymerizing immobilization of acrylamide-modified nucleic acids is reviewed, and its applications in DNA sequence high-throughput analysis including mutation analysis and the whole genome sequencing are summarized.     

Differentiation of Serratia marcescens 274 into swimmer and swarmer cells

We describe a new sensory response in the enteric bacterium Serratia marcescens. When grown in liquid media, the bacteria were short rods with one to two flagella and displayed classical swimming behavior. Upon transfer to a solid surface (0.7 to 0.8T% agar medium), the bacteria underwent a dramatic change of form. They ceased septation, elongated, and expressed numerous (10 to 100) flagella that covered the lateral sides of the cells. The bacteria now displayed a different form of locomotion--swarming--which allowed them to rapidly move over the top of the solid surface. The differentiation to either swimmer or swarmer cells could be reversed by growth on solid or liquid medium, respectively. To identify conditions that influence this differentiation, the growth environment of S. marcescens was manipulated extensively. The swarming response was monitored by visual and microscopic observation of cell movement on solid surfaces, by immunofluorescent labeling followed by microscopic observation for the presence of elongated, profusely flagellated cells, as well as by estimation of induction of flagellin protein, using Western immunoblot analysis. Conditions that imposed a physical constraint on bacterial movement, such as solid or viscous media, were the most efficient at inducing the swarming response. No chemical constituent of the medium that might contribute to the response could be identified, although the existence of such a component cannot be ruled out. Both swimmer and swarmer cells had flagellin proteins of identical molecular weight, which produced similar proteolysis patterns upon digestion with trypsin.     

A novel gene,CBP1, encoding a putative extracellular chitin-binding protein,may play an important role in the hydrophobic surface sensing of Magnaporthe grisea during appressorium differentiation

The conidial germ tube of the rice blast fungus, Magnaporthe grisea, differentiates a specialized cell, an appressorium, required for penetration into the host plant. Formation of the appressorium is also observed on artificial solid substrata such as polycarbonate. A novel emerging germ tube-specific gene, CBP1 (chitin-binding protein), was found in a cDNA subtractive differential library. CBP1 coded for a putative extracellular protein (signal peptide) with two similar chitin-binding domains at both ends of a central domain with homology to fungal chitin deacetylases and with a C-terminus domain rich in Ser/Thr related extracellular matrix protein such as agglutinin. The consensus sequence of the chitin-binding domain found in CBP1 has never been reported in fungi and is similar to the chitin-binding motif in plant lectins and plant chitinases classes I and IV. CBPI was disrupted in order to identify its function. Null mutants of CBP1 failed to differentiate appressoria normally on artificial surface but succeeded in normally differentiating appressoria on the plant leaf surface. Since the null mutant Cbp1- showed abnormal appressorium differentiation only on artificial surfaces and was sensitive to the chemical inducers, CBP1 seemed to play an important role in the recognition of physical factors on solid surfaces.     

Decorated surfaces by biofunctionalized gold beads: application to cell adhesion studies

We describe a simple but versatile method to decorate solid surfaces randomly with colloidal gold particles to which ligands of cell receptors can be coupled to generate local attraction sites for the control of cell adhesion. A self-assembled monolayer of (3-mercaptopropyl)trimethoxysilane was deposited on glass slides. Gold beads were anchored to the functionalized surface through the sulfur group. We characterized the gold bead distribution on the functionalized surface with reflection interference contrast microscopy. The gold beads were functionalized with a disulfide-coupled cyclic pentapeptide containing an arginine-glycine-aspartic acid (RGD) tripeptide sequence which is selectively recognized by integrin receptors alpha(V)beta(3) of endothelial cells. A blocking layer of bovine serum albumin was adsorbed onto the surface to prevent non-specific binding of the cells. We demonstrate that the RGD-functionalized colloidal gold beads act as local attraction centers, mediating rapid cell anchoring on a substrate impeding cell adhesion in the absence of attraction centers. Surprisingly, microinterferometry shows that after a time delay of about 1 h, the regions of the cell surface between the gold beads form close contacts with the substrate, which is attributed to strong van der Waals attraction after escape of repeller molecules from the contact surface.     

Preparation and applications of biofunctionalized,supported lipid bilayers and vesicles

Biofunctional surfaces require advanced design and preparation to match the (bio)recognition ability of biological systems [1]. This requires combined topographic, chemical and visco-elastic surface patterns to match proteins at the nm scale and cells at the micrometer scale. One example of biochemical functionalization, presented here, and which is of both fundamental and application interest, is supported biomimectic (cell)membranes. Specifically we describe preparation and applications of supported phospholipid membranes, which can be made on certain surfaces from unilamellar, 25–200 nm vesicles. On SiO2 at normal pH and with neutral lipids, the vesicles first adsorb intact, and then undergo a phase transformation to a supported bilayer. We have studied the coverage-, vesicle size-, and T-dependence of this process [2], using QCM-D [3], AFM, and SPR. When SiO2 is replaced by TiO2, vesicles adsorb intact. A surface pre-covered with intact vesicles, can be AFM patterned into areas with bilayer, vesicles, and empty surface patches [4]. The results depend critically on AFM tip interaction with vesicle and bilayer, which has been modeled by Monte Carlo simulations [5]. These biomembranes are inert towards protein adsorption [6] and cell attachement [7], which opens up for various applications. Addition of functional molecules, allows sensor functions [8]. Another application is functionalized membranes for surface-specific (stem) cell interactions [9].     

Protein microarrays on hybrid polymeric thin films prepared by self-assembly of polyelectrolytes for multiple-protein immunoassays

We report here the development and characterization of protein microarrays fabricated on nanoengineered 3-D polyelectrolyte thin films (PET) deposited on glass slide by consecutive adsorption of polyelectrolytes via self-assembly technique. Antibodies or antigens were immobilized in the PET-coated glass slides by electrostatic adsorption and entrapment of porous structure of the 3-D polymer film and thus establishing a platform for parallel analysis. Both antigen and antibody microarrays were fabricated on the PET-coated slides, and direct and indirect immunoassays on protein microarrays for multiple-analyte detection were demonstrated. Microarrays produced on these PET-coated slides have consistent spot morphology and provide performance features needed for proteomic analysis. The protein microarrays on the PET films provide LOD as low as 6 pg/mL and dynamic ranges up to three orders of magnitude, which are wider than the protein microarrays fabricated on aldehyde and poly-L-lysine functionalized slides. The PET films constructed by self-assembly technique in aqueous solution is green chemistry based, cost-effective method to generate 3-D thin film coatings on glass surface, and the coated slide is well suited for immobilizing many types of biological molecules so that a wide variety of microarray formats can be developed on this type of slide.     

Salicylhydroxamic Acid Functionalized Affinity Membranes for Specific Immobilization of Proteins and Oligonucleotides

Immobilization of proteins and other biological macromolecules on solid supports is a method suitable for purification or screening applications in life science research. Prolinx, Inc. has developed a novel chemical affinity system that can be used for specific immobilization of proteins and other macromolecules via interaction of two small synthetic molecules, phenyldiboronic acid (PDBA) and salicylhydroxamic acid (SHA). This report describes immobilization applications of activated microporous membranes that have been functionalized with SHA derivatives. These SHA-membranes exhibit high capacity and specificity for binding of PDBA-labeled nucleic acids and proteins. Conjugation of active protein with PDBA is performed in solution independent of the immobilization step on SHA membranes. The resulting PDBA–protein conjugate is immobilized directly without purification and retains biological activity. PDBA conjugates may also be released from these SHA-affinity membranes in a controlled manner. Capture and release of PBA-modified oligonucleotides is also demonstrated. SHA-membranes can be used as surfaces for microarrays, and are therefore compatible with high-throughput analyses. These properties make them useful for development of numerous preparative or screening applications.     

Insulin adsorption on functionalized silica surfaces: an accelerated molecular dynamics study

We study the influence of surface functionalization of a silica surface on insulin adsorption using accelerated molecular dynamics simulation. Three different functional groups are studied, CH₃, OH, and COOH. Due to the partial charges of these groups, the surface polarity of silica is strongly altered. We find that the adsorption energies of insulin change in agreement with the decreasing surface polarity. Conformational changes in the adsorbed protein and the magnitude of the molecular dipole moment in the adsorbed state are consistent with this result. We conclude that protein adsorption on functionalized polar surfaces is governed by the induced changes in surface polarity.     

Effects of three-dimensional culturing in a fibrous matrix on cell cycle, apoptosis, and MAb production by hybridoma cells

The effects of culturing hybridoma cells in a three-dimensional (3-D) poly(ethylene terephthalate) (PET) fibrous matrix on cell cycle, apoptosis, metabolism, and monoclonal antibody (MAb) production were evaluated by comparing with two-dimensional (2-D) culturing on microcarrier and multiwell plate surfaces. The percentage of cells in the G1/G0 phase increased during the long-term culturing period of approximately 4 weeks. Compared to the 2-D culture systems, cells grown in 3-D matrices had higher MAb productivity for long-term culture. Decreasing serum content in the culture medium increased both MAb productivity and apoptosis. However, the 3-D culture had a greater increase in MAb productivity and a much lower apoptotic rate than the 2-D culture, especially at 0% serum. Most cells in the 3-D fibrous matrix formed large aggregates and were smaller than cells grown on a 2-D surface or in suspension. The smaller cell size allowed cells to survive better in the high-cell-density environment. The fibrous matrix also selectively retained healthy, nonapoptotic cells. These results suggested that the 3-D fibrous matrix contributed to growth arrest, protected cells to better resist low-serum environments, and reduced apoptosis, all of which contributed to the high viable cell density and volumetric MAb productivity in the long-term 3-D culture.