Lu Shin Wong

Selective Covalent Protein Immobilization: Strategies and Applications

Lu Shin Wong graduated with a Bachelor of Pharmacy from the University of Nottingham in 1997. He then practiced as a hospital pharmacist for four years while completing his postgraduate diploma in clinical pharmacy from the University of Bradford. Subsequently, he undertook his Ph.D. studies at the University of Southampton with Prof. Mark Bradley on solid-phase organic chemistry, microspectrometry, and solid-supported sensors. Upon completing this in 2005, he joined the Manchester Interdisciplinary Biocentre as a postdoctoral research associate with Prof. Jason Micklefield on the application of chemical biology to surface chemistry and biomolecular-array technologies. Lu Shin is currently an EPSRC Life Science Interface research fellow, and his interests include the combination of chemical biology, surface chemistry, and nanofabrication towards life science applications. Biography Farid Khan obtained his Ph.D. from the University of Cambridge (2004), where he studied the folding of GFP using fluorescence and NMR. Previously, he has worked for a number of years at GlaxoSmithKline in fluorescence assay development for drug discovery. He spent two years as a postdoctoral researcher at the Babraham Institute in Cambridge, where he codeveloped novel protein arrays from DNA arrays using cell free synthesis and characterized robust protein immobilization methods. He is currently employed at the University of Manchester as a Systems Biologist at the Manchester Centre of Integrative Systems Biology. His primary role is on the characterizing of enzymes in metabolic pathways, and he is a M.Sc. lecturer in Biotechnology and Enterprise. He is a founder of Lumophore Ltd., a consulting company specializing in applications of protein array technology. Biography Jason Micklefield graduated from the University of Cambridge in 1993 with a Ph.D. in Organic Chemistry, working with Prof. Sir Alan R. Battersby to complete the first total synthesis of Haem d1. He then moved to the University of Washington, U.S.A., as a NATO postdoctoral fellow with Prof. Heinz G. Floss, investigating various biosynthetic pathways and enzyme mechanisms. In 1995 he began his independent research career as a Lecturer in Chemistry at Birkbeck College, University of London, before moving to Manchester in 1998, where he is now Chair of Chemical Biology. Prof. Micklefield?s research interests are at the chemistry?biology interface and include the redesign of nucleic acids, small-molecule control of gene expression, biosynthesis and biosynthetic engineering, nonribosomal peptides, biocatalysis, and enzyme mechanism.

S-adenosyl-methionine-dependent methyltransferases: highly versatile enzymes in biocatalysis, biosynthesis and other biotechnological applications.

S‐adenosyl methionine (SAM) is a universal biological cofactor that is found in all branches of life where it plays a critical role in the transfer of methyl groups to various biomolecules, including DNA, proteins and small‐molecule secondary metabolites. The methylation process thus has important implications in various disease processes and applications in industrial chemical processing. This methyl transfer is catalysed by SAM‐dependent methyltransferases (MTases), which are by far the largest groups of SAM‐dependent enzymes. A significant amount is now known regarding the structural biology and enzymology of these enzymes, and, consequently, there is now significant scope for the development of new MTases and SAM analogues for applications from biomolecular imaging to biocatalytic industrial processes. This review will focus on current efforts in the manipulation of class I and V SAM‐dependent MTases and the use of synthetic SAM analogues, which together offer the best prospects for rational redesign towards biotechnological applications. Firstly, metabolic engineering of organisms incorporating small‐molecule MTases is discussed; this can be applied in a variety of areas from the industrial bioprocessing of flavourants and antibiotics to frontier research in biofuel production and bioremediation. Secondly, the application of MTases in combination with SAM analogues is reviewed; this allows the tagging of proteins and oligonucleotides with moieties other than the methyl group. Such tagging allows the isolation of the tagged biomolecule and aids its visualisation by a range of analytical methods. The review then summarises the potential advantages of MTase‐mediated chemistry and offers some future perspectives on downstream applications.

Direct site-selective covalent protein immobilization catalyzed by a phosphopantetheinyl transferase.

Immobilization of proteins onto solid supports is important in the preparation of functional protein microarrays and in the development of bead-based bioassays, biosensors, and industrial biocatalysts. In order to generate the stable, functional, and homogeneous materials required for these applications, attention has focused on methods that enable the efficient and site-specific covalent immobilization of recombinant proteins onto a wide range of platforms. To this end, the phosphopantetheinyl transferase Sfp was employed to catalyze the direct immobilization of recombinant proteins bearing the small, genetically encoded ybbR tag onto surfaces functionalized with CoA. Using mass spectrometry, it was shown that the Sfp catalyzes immobilization of a model acyl carrier protein (ACP) onto CoA-derivatized PEGA resin beads through specific covalent bond formation. Luciferase (Luc) and glutathione-S-transferase (GST) ybbR-fusion proteins were similarly immobilized onto PEGA resin retaining high levels of enzyme activity. This strategy was also successfully applied for the immobilization of the ACP, as well as ybbR-Luc, -GST, and -thioredoxin fusion proteins, on hydrogel microarray slides. Overall, the Sfp-catalyzed surface ligation is mild, quantitative, and rapid, occurring in a single step without prior chemical modification of the target protein. Immobilization of the target proteins directly from a cell lysate mixture was also demonstrated.

Scanning probe-enabled nanocombinatorics define the relationship between fibronectin feature size and stem cell fate

We report the development of a powerful analytical method that utilizes a tilted elastomeric pyramidal pen array in the context of a scanning probe lithography experiment to rapidly prepare libraries having as many as 25 million features over large areas with a range of feature sizes from the nano- to microscale. This technique can be used to probe important chemical and biological processes, opening up the field of nanocombinatorics. In a proof-of-concept investigation of mesenchymal stem cell (MSC) differentiation, combinatorial patterns first enabled a rapid and systematic screening of MSC adhesion, as a function of feature size, while uniform patterns were used to study differentiation with statistically significant sample sizes. Without media containing osteogenic-inducing chemical cues, cells cultured on nanopatterned fibronectin substrates direct MSC differentiation towards osteogenic fates when compared to nonpatterned fibronectin substrates. This powerful and versatile approach enables studies of many systems spanning biology, chemistry, and engineering areas.

Parallel scanning near-field photolithography: The snomipede

The “Millipede”, developed by Binnig and co-workers (Bining, G. K.; et al. IBM J. Res. Devel. 2000, 44, 323.), elegantly solves the problem of the serial nature of scanning probe lithography processes, by deploying massive parallelism. Here we fuse the “Millipede” concept with scanning near-field photolithography to yield a “Snomipede” that is capable of executing parallel chemical transformations at high resolution over macroscopic areas. Our prototype has sixteen probes that are separately controllable using a methodology that is, in principle, scalable to much larger arrays. Light beams generated by a spatial modulator or a zone plate array are coupled to arrays of cantilever probes with hollow, pyramidal tips. We demonstrate selective photodeprotection of nitrophenylpropyloxycarbonyl-protected aminosiloxane monolayers on silicon dioxide and subsequent growth of nanostructured polymer brushes by atom-transfer radical polymerization, and the fabrication of 70 nm structures in photoresist by a Snomipede probe array immersed under water. Such approaches offer a powerful means of integrating the top-down and bottom-up fabrication paradigms, facilitating the reactive processing of materials at nanometer resolution over macroscopic areas.

Single-molecule protein arrays enabled by scanning probe block copolymer lithography

The ability to control the placement of individual protein molecules on surfaces could enable advances in a wide range of areas, from the development of nanoscale biomolecular devices to fundamental studies in cell biology. Such control, however, remains a challenge in nanobiotechnology due to the limitations of current lithographic techniques. Herein we report an approach that combines scanning probe block copolymer lithography with site-selective immobilization strategies to create arrays of proteins down to the single-molecule level with arbitrary pattern control. Scanning probe block copolymer lithography was used to synthesize individual sub-10-nm single crystal gold nanoparticles that can act as scaffolds for the adsorption of functionalized alkylthiol monolayers, which facilitate the immobilization of specific proteins. The number of protein molecules that adsorb onto the nanoparticles is dependent upon particle size; when the particle size approaches the dimensions of a protein molecule, each particle can support a single protein. This was demonstrated with both gold nanoparticle and quantum dot labeling coupled with transmission electron microscopy imaging experiments. The immobilized proteins remain bioactive, as evidenced by enzymatic assays and antigen-antibody binding experiments. Importantly, this approach to generate single-biomolecule arrays is, in principle, applicable to many parallelized cantilever and cantilever-free scanning probe molecular printing methods.

Protein micro- and nanopatterning using aminosilanes with protein-resistant photolabile protecting groups.

An approach to the integration of nanolithography with synthetic chemical methodology is described, in which near-field optical techniques are used to selectively deprotect films formed by the adsorption of aminosilanes protected by modified 2-nitrophenylethoxycarbonyl (NPEOC) groups. The NPEOC groups are functionalized at the m- or p-position with either a tetraethyleneglycol or a heptaethylene glycol adduct. We describe the synthesis of these bioresistant aminosilanes and the characterization of the resulting photoreactive films. Photodeprotection by exposure to UV light (λ = 325 nm) yielded the amine with high efficiency, at a similar rate for all four adsorbates, and was complete after an exposure of 2.24 J cm(-2). Following photodeprotection, derivatization by trifluoroacetic anhydride was carried out with high efficiency. Micropatterned samples, formed using a mask, were derivatized with aldehyde-functionalized polymer nanoparticles and, following derivatization with biotin, were used to form patterns of avidin-coated polymer particles. Fluorescence microscopy and atomic force microscopy data demonstrated that the intact protecting groups conferred excellent resistance to nonspecific adsorption. Nanometer-scale patterns were created using scanning near-field photolithography and were derivatized with biotin. Subsequent conjugation with avidin-functionalized polymer nanoparticles yielded clear fluorescence images that indicated dense attachment to the nanostructures and excellent protein resistance on the surrounding surface. These simple photocleavable protecting group strategies, combined with the use of near-field exposure, offer excellent prospects for the control of surface reactivity at nanometer resolution in biological systems and offer promise for integrating the top-down and bottom-up molecular fabrication paradigms.

Micrometer- and Nanometer-Scale Photopatterning Using 2-Nitrophenylpropyloxycarbonyl-Protected Aminosiloxane Monolayers

An approach to nanopatterning is reported in which a scanning near-field optical microscope coupled to a near-UV laser is used to selectively deprotect 2-nitrophenylpropyloxycarbonyl (NPPOC)-protected aminosiloxane monolayers on glass. UV deprotection was studied for unpatterned samples using X-ray photoelectron spectroscopy (XPS) and contact angle measurements. Highly efficient photodeprotection of the NPPOC moiety was observed upon irradiation at both 325 and 364 nm, and complete deprotection was found to occur within minutes. The resulting amine-terminated surfaces were then derivatized using trifluoroacetic anhydride (TFAA) and aldehyde-functionalized polymer nanoparticles. Contact angle and XPS measurements postderivatization indicated that surface functionalization was extensive, with the NPPOC-deprotected surfaces and aminopropylsiloxane control materials exhibiting essentially identical characteristics. Micrometer-scale patterns were fabricated using mask-based exposure, functionalized with polymer nanoparticles, and characterized by atomic force microscopy. Nanometer-scale patterns were fabricated using near-field exposure and characterized by friction force microscopy. The nanopatterns were derivatized with TFAA. The resulting images exhibited a clear contrast inversion that was due to an inversion of surface polarity in the patterned areas and confirmed that high spatial resolution (ca. 100 nm) was readily achievable.

An Enzyme Cascade for Selective Modification of Tyrosine Residues in Structurally Diverse Peptides and Proteins

Bioorthogonal chemistry enables a specific moiety in a complex biomolecule to be selectively modified in the presence of many reactive functional groups and other cellular entities. Such selectivity has become indispensable in biology, enabling biomolecules to be derivatized, conjugated, labeled, or immobilized for imaging, biochemical assays, or therapeutic applications. Methyltransferase enzymes (MTase) that accept analogues of the cofactor S-adenosyl methionine have been widely deployed for alkyl-diversification and bioorthogonal labeling. However, MTases typically possess tight substrate specificity. Here we introduce a more flexible methodology for selective derivatization of phenolic moieties in complex biomolecules. Our approach relies on the tandem enzymatic reaction of a fungal tyrosinase and the mammalian catechol-O-methyltransferase (COMT), which can effect the sequential hydroxylation of the phenolic group to give an intermediate catechol moiety that is subsequently O-alkylated. When used in this combination, the alkoxylation is highly selective for tyrosine residues in peptides and proteins, yet remarkably tolerant to changes in the peptide sequence. Tyrosinase-COMT are shown to provide highly versatile and regioselective modification of a diverse range of substrates including peptide antitumor agents, hormones, cyclic peptide antibiotics, and model proteins.

A High‐Throughput Assay for Arylamine Halogenation Based on a Peroxidase‐Mediated Quinone–Amine Coupling with Applications in the Screening of Enzymatic Halogenations

Arylhalides are important building blocks in many fine chemicals, pharmaceuticals and agrochemicals, and there has been increasing interest in the development of more “green” halogenation methods based on enzyme catalysis. However, the screening and development of new enzymes for biohalogenation has been hampered by a lack of high-throughput screening methods. Described herein is the development of a colorimetric assay for detecting both chemical and enzymatic arylamine halogenation reactions in an aqueous environment. The assay is based on the unique UV/Vis spectrum created by the formation of an ortho-benzoquinone-amine adduct, which is produced by the peroxidase-catalysed benzoquinone generation, followed by Michael addition of either a halogenated or non-halogenated arylamine. This assay is sensitive, rapid and amenable to high-throughput screening platforms. We have also shown this assay to be easily coupled to a flavin-dependent halogenase, which currently lacks any convenient colorimetric assay, in a “one-pot” workflow.