An Engineered Escherichia coli Strain with Synthetic Metabolism for in-Cell Production of Translationally Active Methionine Derivatives

In the last decades, it has become clear that the canonical amino acid repertoire codified by the universal genetic code is not up to the needs of emerging biotechnologies. For this reason, extensive genetic code re-engineering is essential to expand the scope of ribosomal protein translation, leading to reprogrammed microbial cells equipped with an alternative biochemical alphabet to be exploited as potential factories for biotechnological purposes. The prerequisite for this to happen is a continuous intracellular supply of noncanonical amino acids through synthetic metabolism from simple and cheap precursors. We have engineered an Escherichia coli bacterial system that fulfills these requirements through reconfiguration of the methionine biosynthetic pathway and the introduction of an exogenous direct trans-sulfuration pathway. Our metabolic scheme operates in vivo, rescuing intermediates from core cell metabolism and combining them with small bio-orthogonal compounds. Our reprogrammed E. coli strain is capable of the in-cell production of l-azidohomoalanine, which is directly incorporated into proteins in response to methionine codons. We thereby constructed a prototype suitable for economic, versatile, green sustainable chemistry, pushing towards enzyme chemistry and biotechnology-based production.

Multivalent binding of concanavalin A on variable-density mannoside microarrays

Interactions between cell surface glycans and glycan binding proteins (GBPs) have a central role in the immune response, pathogen-host recognition, cell-cell communication, and a myriad other biological processes. Because of the weak association between GBPs and glycans in solution, multivalent and cooperative interactions in the dense glycocalyx have an outsized role in directing binding affinity and selectivity. However, a major challenge in glycobiology is that few experimental approaches exist for examining and understanding quantitatively how glycan density affects avidity with GBPs, and there is a need for new tools that can fabricate glycan arrays with the ability to vary their density controllably and systematically in each feature. Here, we use thiol-ene reactions to fabricate glycan arrays using a recently developed photochemical printer that leverages a digital micromirror device and microfluidics to create multiplexed patterns of immobilized mannosides, where the density of mannosides in each feature was varied by dilution with an inert spacer allyl alcohol. The association between these immobilized glycans and FITC-labeled concanavalin A (ConA) - a tetrameric GBP that binds to mannosides multivalently - was measured by fluorescence microscopy. We observed that the fluorescence decreased nonlinearly with increasing spacer concentration in the features, and we present a model that relates the average mannoside-mannoside spacing to the abrupt drop-off in ConA binding. Applying these recent advances in microscale photolithography to the challenge of mimicking the architecture of the glycocalyx could lead to a rapid understanding of how information is trafficked on the cell surface.

Photoactivatable Reaction for Covalent Nanoscale Patterning of Multiple Proteins

This article describes a photochemical approach for independently patterning multiple proteins to an inert substrate, particularly for studies of cell adhesion. A photoactivatable chloropyrimidine ligand was employed for covalent immobilization of SnapTag fusion proteins on self-assembled monolayers of alkanethiolates on gold. A two-step procedure was used: first, patterned UV illumination of the surface activated protein capture ligands, and second, incubation with a SnapTag fusion protein bound to the surface in illuminated regions. Two different fluorescent proteins were patterned in registry with features of 400 nm in size over a 1 mm2 area. An example is given wherein an anti-carcinoembryonic antigen (anti-CEA) scFv antibody was patterned to direct the selective attachment of a human cancer cell line that express the CEA antigen. This method enables the preparation of surfaces with control over the density and activity of independently patterned proteins.

VUV Photodeposition of Thiol-Terminated Films: A Wavelength-Dependent Study

Photoinitiated chemical vapor deposition (PICVD) has become attractive for selective and specific surface functionalization, because it relies on a single energy source, the photons, to carry out (photo-) chemistry. In the present wavelength (λ)-dependent study, thiol (SH)-terminated thin film deposits have been prepared from gas mixtures of acetylene (C₂H₂) and hydrogen sulfide (H₂S) via PICVD using four different vacuum-ultraviolet (VUV) sources, namely, KrL (λ_peak = 123.6 nm), XeL (λ_peak = 147.0 nm), XeE (λ_peak = 172.0 nm), and Hg (λ = 184.9 nm) lamps. Different λ influence the deposition kinetics and film composition, reflecting that photolytic reactions are governed by the gases' absorption coefficients, k(λ). Thiol concentrations, [SH], up to ∼7.7%, were obtained with the XeL source, the highest reported in the literature so far. Furthermore, all films showed islandlike surface morphology, regardless of λ.

Fabrication of antibody-loaded microgels using microfluidics and thiol-ene photoclick chemistry

Reducing burst effects, providing controlled release, and safeguarding biologics against degradation are a few of several highly attractive applications for microgels in the field of controlled release. However, the incorporation of proteins into microgels without impairing stability is highly challenging. In this proof of concept study, the combination of microfluidics and thiol-ene photoclick chemistry was evaluated for the fabrication of antibody-loaded microgels with narrow size distribution. Norbornene-modified eight-armed poly(ethylene glycol) with an average molecular mass of 10,000 Da, 20,000 Da, or 40,000 Da were prepared as macromonomers for microgel formation. For functionalization, either hydrolytically cleavable ester or stable amide bonds were used. A microfluidic system was employed to generate precursor solution droplets containing macromonomers, the cross-linker dithiothreitol and the initiator Eosin-Y. Irradiation with visible light was used to trigger thiol-ene reactions which covalently cross-linked the droplets. For all bond-types, molecular masses, and concentrations gelation was very rapid (<20 s) and a plateau for the complex shear modulus was reached after only 5 min. The generated microgels had a rod-like shape and did not show considerable cellular toxicity. Stress conditions during the fabrication process were simulated and it could be shown that fabrication did not impair the activity of the model proteins lysozyme and bevacizumab. It was confirmed that the average hydrogel network mesh size was similar or smaller than the hydrodynamic diameter of bevacizumab which is a crucial factor for restricting diffusion and delaying release. Finally, microgels were loaded with bevacizumab and a sustained release over a period of 30 ± 4 and 47 ± 7 days could be achieved in vitro.

One-step purification and oriented attachment of protein A on silica and graphene oxide nanoparticles using sortase-mediated immobilization

One-step purification and oriented immobilization of protein A on functionalized carriers.

Core functionalization of semi-crystalline polymeric cylindrical nanoparticles using photo-initiated thiol-ene radical reactions

Sequential ring-opening and reversible addition-fragmentation chain transfer (RAFT) polymerization was used to form a triblock copolymer of tetrahydropyran acrylate (THPA), 5-methyl-5-allyloxycarbonyl-1,3-dioxan-2-one (MAC) and l-lactide. Concurrent deprotection of the THPA block and crystallization-driven self-assembly (CDSA) was undertaken and allowed for the formation of cylindrical micelles bearing allyl handles in a short outer core segment. These handles were further functionalized by different thiols using photo-initiated thiol-ene radical reactions to demonstrate that the incorporation of an amorphous PMAC block within the core does not disrupt CDSA and can be used to load the cylindrical nanoparticles with cargo.

Investigation into the photolytic stability of RAFT agents and the implications for photopolymerization reactions

The photolytic stability of RAFT agents under blue LED irradiation has been investigated with regard to photopolymerization reactions.

Microwave-Assisted Syntheses in Recyclable Ionic Liquids: Photoresists Based on Renewable Resources

The copoly(2-oxazoline) pNonOx80 -stat-pDc(=) Ox20 can be synthesized from the cationic ring-opening copolymerization of 2-nonyl-2-oxazoline NonOx and 2-dec-9'-enyl-2-oxazoline Dc(=) Ox in the ionic liquid n-hexyl methylimidazolium tetrafluoroborate under microwave irradiation in 250 g/batch quantities. The polymer precipitates upon cooling, enabling easy recovery of the polymer and the ionic liquid. Both monomers can be obtained from fatty acids from renewable resources. pNonOx80 -stat-pDc(=) Ox20 can be used as polymer in a photoresist (resolution of 1 μm) based on UV-induced thiol-ene reactions.

Versatile thiol-based reactions for micrometer- and nanometer-scale photopatterning of polymers and biomolecules

Thiol-based reactions were applied to enable the photochemical patterning of polymer brushes and green fluorescent protein on silicon oxide surfaces.

Facile functionalization of PDMS elastomer surfaces using thiol-ene click chemistry

A variety of methods have been developed for polydimethylsiloxane (PDMS) elastomer surface functionalization, particularly for the improvement of hydrophilicity. However, in addition to difficulties in avoiding undesired physical changes to the modified surface, including surface cracking, "hydrophobic recovery" frequently leads hydrophilically modified surfaces to completely return over time to their hydrophobic nature, with accompanying loss of accessible functional groups. Thiol-ene chemistry provides a mild and robust technology for synthetic elaboration. We demonstrate the introduction of thiol groups onto the PDMS surface via base-catalyzed equilibration of MTS ((MeO)3Si(CH2)3SH). Thiols in the product elastomer were shown to be located primarily at the air interface using EDX, XPS, and fluorescence labeling initially, and after extended periods of time: total thiol concentrations at the surface and in the bulk were established by complementary chemical titrations with DTDP (4,4'-dithiodipyridine) and iodine titrations in different solvents. The surface density of thiols was readily controlled by reaction conditions: the rate of hydrophobic recovery, which led to incomplete loss of accessible functional groups, was determined. Thiol-ene click chemistry was then used to introduce a variety of hydrophilic moieties onto the surface including a silicone surfactant and maleic anhydride, respectively. In the latter case, molecular functionalization with both small (fluorescent labels) and polymeric nucleophiles (poly(ethylene glycol), chitosan) could be subsequently induced by simple ring-opening nucleophilic attack leading to permanently functional surfaces.

Site-specific labeling of proteins with a chemically stable, high-affinity tag for protein study

Site-specific labeling of proteins with paramagnetic lanthanides offers unique opportunities by virtue of NMR spectroscopy in structural biology. In particular, these paramagnetic data, generated by the anisotropic paramagnetism including pseudocontact shifts (PCS), residual dipolar couplings (RDC), and paramagnetic relaxation enhancement (PRE), are highly valuable in structure determination and mobility studies of proteins and protein-ligand complexes. Herein, we present a new way to label proteins in a site-specific manner with a high-affinity and chemically stable tag, 4-vinyl(pyridine-2,6-diyl)bismethylenenitrilo tetrakis(acetic acid) (4VPyMTA), through thiol alkylation. Its performance has been demonstrated in G47C and E64C mutants of human ubiquitin both in vitro and in a crowded environment. In comparison with the published tags, 4VPyMTA has several interesting features: 1) it has a very high binding affinity for lanthanides (higher than EDTA), 2) there is no heterogeneity in complexes with lanthanides, 3) the derivatized protein is stable and potentially applicable to the in situ analysis of proteins.

Patterning of functional compounds by multicomponent Langmuir-Blodgett transfer and subsequent chemical modification

The multicomponent transfer of functional molecules by Langmuir-Blodgett (LB) technique onto solid substrates offers an interesting route for generation of functionalized patterns by self-assembly over large surface areas. In the present paper, we discuss LB transfer of mixed LB films containing different functional amphiphiles (an azide, an estrone derivate, a lithocholic acid derivative, or an alkoxyamine) in combination with dipalmitoylphosphatidyl choline (DPPC). The effect of the mixing ratio on pattern formation is discussed, and we provide some general design rules for the synthesis of functional molecules to be applicable for the multicomponent LB transfer process. We show that these functional compounds can be successfully transferred to oxidized Si wafers in stripe pattern. Covalent attachment of the functional entities is easily achieved, and the patterned surfaces are then ready for further chemical manipulation. This is demonstrated by site-specifically covalent attaching dye molecules applying the copper(l)-catalyzed alkyne azide click reaction (CuAAC), the thiol-ene reaction, and a surface-initiated radical polymerization.

Preparation of biomolecule microstructures and microarrays by thiol-ene photoimmobilization

A mild, fast and flexible method for photoimmobilization of biomolecules based on the light-initiated thiol-ene reaction has been developed. After investigation and optimization of various surface materials, surface chemistries and reaction parameters, microstructures and microarrays of biotin, oligonucleotides, peptides, and MUC1 tandem repeat glycopeptides were prepared with this photoimmobilization method. Furthermore, MUC1 tandem repeat glycopeptide microarrays were successfully used to probe antibodies in mouse serum obtained from vaccinated mice. Dimensions of biomolecule microstructures were shown to be freely controllable through photolithographic techniques, and features down to 5 microm in size covering an area of up to 75x25 mm were created. Use of a confocal laser microscope with a UV laser as UV-light source enabled further reduction of biotin feature size opening access to nanostructured biochips.

Bioorthogonal chemistry: fishing for selectivity in a sea of functionality

The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.

Chemical strategies for generating protein biochips

Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.