Microcontact printing of biotin for selective immobilization of streptavidin-fused proteins and SPR analysis

Functional protein micropatterning for drug design and discovery

INTRODUCTION

The past decade has witnessed tremendous progress in surface micropatterning techniques for generating arrays of various types of biomolecules. Multiplexed protein micropatterning has tremendous potential for drug discovery providing versatile means for high throughput assays required for target and lead identification as well as diagnostics and functional screening for personalized medicine. However, ensuring the functional integrity of proteins on surfaces has remained challenging, in particular in the case of membrane proteins, the most important class of drug targets. Yet, generic strategies to control functional organization of proteins into micropatterns are emerging.

AREAS COVERED

This review includes an overview introducing the most common approaches for surface modification and functional protein immobilization. The authors present the key photo and soft lithography techniques with respect to compatibility with functional protein micropatterning and multiplexing capabilities. In the second part, the authors present the key applications of protein micropatterning techniques in drug discovery with a focus on membrane protein interactions and cellular signaling.

EXPERT OPINION

With the growing importance of target discovery as well as protein-based therapeutics and personalized medicine, the application of protein arrays can play a fundamental role in drug discovery. Yet, important technical breakthroughs are still required for broad application of these approaches, which will include in vitro "copying" of proteins from cDNA arrays into micropatterns, direct protein capturing from single cells as well as protein microarrays in living cells.

Co- and distinct existence of Tris-NTA and biotin functionalities on individual and adjacent micropatterned surfaces generated by photo-destruction

Micropatterned surfaces with Tris-NTA and biotin functionalities both in the same micropattern as well as individually in adjacent micropatterns are generated by UV light illumination through photo-masks. These surfaces are extremely useful for the immobilization of oligohistidine and biotin tagged multiple biomolecules/proteins.

A versatile toolbox for multiplexed protein micropatterning by laser lithography

Photocleavable oligohistidine peptides (POHP) allow in situ spatial organization of multiple His-tagged proteins onto surfaces functionalized with tris(nitrilotriacetic acid) (tris-NTA). Here, a second generation of POHPs is presented with improved photoresponse and site-specific covalent coupling is introduced for generating stable protein assemblies. POHPs with different numbers of histidine residues and a photocleavable linker based on the 4,5-dimethoxy-o-nitrophenyl ethyl chromophore are prepared. These peptides show better photosensitivity than the previously used o-nitrophenyl ethyl derivative. Efficient and stable caging of tris-NTA-functionalized surfaces by POHPs comprising 12 histidine residues is demonstrated by multiparameter solid-phase detection techniques. Laser lithographic uncaging by photofragmentation of the POHPs is possible with substantially reduced photodamage as compared to previous approaches. Thus, in situ micropatterning of His-tagged proteins under physiological conditions is demonstrated for the first time. In combination with a short peptide tag for a site-specific enzymatic coupling reaction, covalent immobilization of multiple proteins into target micropatterns is possible under physiological conditions.

Maleimide photolithography for single-molecule protein-protein interaction analysis in micropatterns

Spatial organization of proteins into microscopic structures has important applications in fundamental and applied research. Preserving the function of proteins in such microstructures requires generic methods for site-specific capturing through affinity handles. Here, we present a versatile bottom-up surface micropatterning approach based on surface functionalization with maleimides, which selectively react with organic thiols. Upon UV irradiation through a photomask, the functionality of illuminated maleimide groups was efficiently destroyed. Remaining maleimides in nonilluminated regions were further reacted with different thiol-functionalized groups for site-specific protein immobilization under physiological conditions. Highly selective immobilization of His-tagged proteins into tris(nitrilotriacetic acid) functionalized microstructures with very high contrast was possible even by direct capturing of proteins from crude cell lysates. Moreover, we employed phosphopantetheinyl transfer from surface-immobilized coenzyme A to ybbR-tagged proteins in order to implement site-specific, covalent protein immobilization into microstructures. The functional integrity of the immobilized protein was confirmed by monitoring protein-protein interactions in real time. Moreover, we demonstrate quantitative single-molecule analysis of protein-protein interactions with proteins selectively captured into these high-contrast micropatterns.

Enhanced microcontact printing of proteins on nanoporous silica surface

We demonstrate porous silica surface modification, combined with microcontact printing, as an effective method for enhanced protein patterning and adsorption on arbitrary surfaces. Compared to conventional chemical treatments, this approach offers scalability and long-term device stability without requiring complex chemical activation. Two chemical surface treatments using functionalization with the commonly used 3-aminopropyltriethoxysilane (APTES) and glutaraldehyde (GA) were compared with the nanoporous silica surface on the basis of protein adsorption. The deposited thickness and uniformity of porous silica films were evaluated for fluorescein isothiocyanate (FITC)-labeled rabbit immunoglobulin G (R-IgG) protein printed onto the substrates via patterned polydimethlysiloxane (PDMS) stamps. A more complete transfer of proteins was observed on porous silica substrates compared to chemically functionalized substrates. A comparison of different pore sizes (4-6 nm) and porous silica thicknesses (96-200 nm) indicates that porous silica with 4 nm diameter, 57% porosity and a thickness of 96 nm provided a suitable environment for complete transfer of R-IgG proteins. Both fluorescence microscopy and atomic force microscopy (AFM) were used for protein layer characterizations. A porous silica layer is biocompatible, providing a favorable transfer medium with minimal damage to the proteins. A patterned immunoassay microchip was developed to demonstrate the retained protein function after printing on nanoporous surfaces, which enables printable and robust immunoassay detection for point-of-care applications.

Native laser lithography of His-tagged proteins by uncaging of multivalent chelators

We report a generic approach for targeting proteins into micropatterns by in situ laser lithography. To this end, we have designed a photocleavable oligohistidine peptide for caging tris(nitrilo triacetic acid) (tris-NTA) groups on surfaces by multivalent interactions. Local photofragmentation of the peptide by UV illumination through a photomask or by a confocal laser beam uncages tris-NTA, thus generating free binding sites for rapid, site-specific capturing of His-tagged proteins into micropatterns. Iterative writing of proteins by laser lithography enabled for assembly of multiplexed functional protein microstructures on surfaces. Thus, versatile, user-defined protein micropatterns can be assembled under physiological conditions with a standard confocal laser-scanning microscope.

UV-defined flat PDMS stamps suitable for microcontact printing

We report a simple method of creating well-defined micropatterns on the surface of a flat PDMS stamp, making it suitable for microcontact printing of proteins. This method only requires a UV lamp (254 nm) and a TEM grid (as a photomask) to modify the surface of PDMS for creating desired micropatterns. By using the UV-modified stamp, a printed protein micropattern that resembles the original TEM grid can be obtained. Surprisingly, unlike the oxygen-plasma-treated PDMS, the UV-modified flat stamp is also long-lasting (>1 week). The method reported herein is very economical for microcontact printing applications because expensive silicon masters and microstructured PDMS are no longer required.

Biospecific anchoring and spatially confined germination of bacterial spores in non-biofouling microwells

In this paper, we report a simple method for spatially confining Bacillus subtilis (BS) spores into semi-three dimensional, non-biofouling microwells by using biospecific (such as biotin-streptavidin) interactions. Non-biofouling poly(ethylene glycol) (PEG)-based microwells were fabricated by employing a process of capillary molding on a glass slide. The biospecific interactions between biotinylated BS spores and streptavidin led to the selective deposition of BS spores onto the bottom of the microwells of which presented streptavidin. The viability of the patterned spores was confirmed by the induction of germination. Bacterial spores were found to maintain extreme robustness until they were exposed to favorable conditions. This work suggests that the use of bacterial spore-based sensors would increase the shelf-life (such as long-term storage and stability) of cell-based sensors.

Polyhydroxyalkanoate chip for the specific immobilization of recombinant proteins and its applications in immunodiagnostics

In this study, a novel strategy was developed for the highly selective immobilization of proteins, using the polyhydroxyalkanoate (PHA) depolymerase substrate binding domain (SBD) as an active binding domain. In order to determine the appropriacy of this method for immunodiagnostic assays, the single-chain antibody (ScFv) against the hepatitis B virus (HBV) preS2 surface protein and the severe acute respiratory syndrome coronavirus (SARS-CoV) envelope protein (SCVe) were fused to the SBD, then directly immobilized on PHA-coated slides via microspotting. The fluorescence-labeled HBV antigen and the antibody against SCVe were then utilized to examine specific interactions on the PHA-coated surfaces. Fluorescence signals were detected only at the spotted positions, thereby indicating a high degree of affinity and selectivity for their corresponding antigens/antibodies. Furthermore, we detected small amounts of ScFv-SBD (2.7 ng/mL) and SCVe-SBD fusion proteins (0.6 ng/mL). Therefore, this microarray platform technology, using PHA and SBD, appears generally appropriate for immunodiagnosis, with no special requirements with regard to synthetic or chemical modification of the biomolecules or the solid surface.

Micropatterning proteins on polyhydroxyalkanoate substrates by using the substrate binding domain as a fusion partner

A novel strategy for micropatterning proteins on the surface of polyhydroxyalkanoate (PHA) biopolymer by microcontact printing (microCP) is described. The substrate binding domain (SBD) of the Pseudomonas stutzeri PHA depolymerase was used as a fusion partner for specifically immobilizing proteins on PHA substrate. Enhanced green fluorescent protein (EGFP) and red fluorescent protein (RFP) fused to the SBD could be specifically immobilized on the micropatterns of poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyhexanoate). Laser scanning confocal microscopic studies suggested that two fusion proteins were micropatterned in their functionally active forms. Also, antibody binding assay by surface plasmon resonance suggested that protein-protein interaction studies could be carried out using this system.