Peptidoglycan Metabolite Photoaffinity Reporters Reveal Direct Binding to Intracellular Pattern Recognition Receptors and Arf GTPases.

The peptidoglycan fragments γ-d-glutamyl- meso-diaminopimelic acid (iE-DAP) and muramyl-dipeptide (MDP) are microbial-specific metabolites that activate intracellular pattern recognition receptors and stimulate immune signaling pathways. While extensive structure-activity studies have demonstrated that these bacterial cell wall metabolites trigger NOD1- and NOD2-dependent signaling, their direct binding to these innate immune receptors or other proteins in mammalian cells has not been established. To characterize these fundamental microbial metabolite-host interactions, we synthesized a series of peptidoglycan metabolite photoaffinity reporters and evaluated their cross-linking to NOD1 and NOD2 in mammalian cells. We show that active iE-DAP and MDP photoaffinity reporters selectively cross-linked NOD1 and NOD2, respectively, and not their inactive mutants. We also discovered MDP reporter cross-linking to Arf GTPases, which interacted most prominently with GTP-bound Arf6 and coimmunoprecipitated with NOD2 upon MDP stimulation. Notably, MDP binding to NOD2 and Arf6 was abrogated with loss-of-function NOD2 mutants associated with Crohn's disease. Our studies demonstrate peptidoglycan metabolite photoaffinity reporters can capture their cognate immune receptors in cells and reveal unpredicted ligand-induced interactions with other cellular cofactors. These photoaffinity reporters should afford useful tools to discover and characterize other peptidoglycan metabolite-interacting proteins.

Chemical proteomics reveals ADP-ribosylation of small GTPases during oxidative stress.

ADP-ribosylation is a post-translational modification that is known to be involved in cellular homeostasis and stress but has been challenging to analyze biochemically. To facilitate the detection of ADP-ribosylated proteins, we show that an alkyne-adenosine analog, N6-propargyl adenosine (N6pA), is metabolically incorporated in mammalian cells and enables fluorescence detection and proteomic analysis of ADP-ribosylated proteins. Notably, our analysis of N6pA-labeled proteins that are upregulated by oxidative stress revealed differential ADP-ribosylation of small GTPases. We discovered that oxidative stress induced ADP-ribosylation of Hras on Cys181 and Cys184 in the C-terminal hypervariable region, which are normally S-fatty-acylated. Downstream Hras signaling is impaired by ADP-ribosylation during oxidative stress, but is rescued by ADP-ribosyltransferase inhibitors. Our study demonstrates that ADP-ribosylation of small GTPases not only is mediated by bacterial toxins but is endogenously regulated in mammalian cells. N6pA provides a useful tool to characterize ADP-ribosylated proteins and their regulatory mechanisms in cells.

Chemical reporters for exploring ADP-ribosylation and AMPylation at the host-pathogen interface.

Bacterial pathogens secrete protein toxins and effectors that hijack metabolites to covalently modify host proteins and interfere with their function during infection. Adenosine metabolites, such as nicotinamide adenine dinucleotide (NAD) and adenosine triphosphate (ATP), have in particular been coopted by these secreted virulence factors to reprogram host pathways. While some host targets for secreted virulence factors have been identified, other toxin and effector substrates have been elusive, which require new methods for their characterization. In this review, we focus on chemical reporters based on NAD and ATP that should facilitate the discovery and characterization of adenosine diphosphate (ADP)-ribosylation and adenylylation/AMPylation in bacterial pathogenesis and cell biology.

Dynamic 3D cell culture via a chemoselective photoactuated ligand.

A new strategy to create a dynamic scaffold for three-dimensional (3D) cell experiments based on a photo-activated cell adhesive peptide ligand is described. After polymerization, the inert matrix becomes cell adhesive by chemoselective modification through the conjugation of oxyamine-terminated ligands. Furthermore, spatial and temporal control of cell culture within the 3D matrix was achieved by the use of a biospecific photoprotected peptide and visualized by confocal microscopy.

Controlling cell behavior with peptide nano-patterns.

Proper cell polarization and division are critical for a developing organism and a number of downstream biological processes including cancer metastasis, cell migration, and organelle organization. Both cell behaviors are complex and influenced by a number of external factors including, the extracellular matrix (ECM), physical-mechanical and hydrodynamic forces. In particular, the ECM functions as a dynamic 3-dimensional scaffold support for tissue segregation and cell adhesion. Although cells are microns in size, they sense and respond to dynamic nanoarchitecture changes of the ECM. To further understand these complex processes model substrates have been developed to recapitulate the spatial presentation of ligands as gradients and single cell patterns. However, until now, the interplay between ligand affinity, ligand density and ligand area at the nanoscale on cell behavior has received little attention due to the lack of synergistic surface chemistry, microscopy, cell biology, and nanopatterning technologies. In this report, we develop biospecific nanopatterned peptide array substrates to examine how the nano-environment controls cell behavior utilizing parallel dip-pen nanolithography.

General chemoselective and redox-responsive ligation and release strategy.

We report a switchable redox click and cleave reaction strategy for conjugating and releasing a range of molecules on demand. This chemoselective redox-responsive ligation (CRRL) and release strategy is based on a redox switchable oxime linkage that is controlled by mild chemical or electrochemical redox signals and can be performed at physiological conditions without the use of a catalyst. Both conjugation and release reactions are kinetically well behaved and quantitative. The CRRL strategy is synthetically modular and easily monitored and characterized by routine analytical techniques. We demonstrate how the CRRL strategy can be used for the dynamic generation of cyclic peptides and the ligation of two different peptides that are stable but can be selectively cleaved upon changes in the redox environment. We also demonstrate a new redox based delivery of cargoes to live cells strategy via the CRRL methodology by synthesizing a FRET redox-responsive probe that is selectively activated within a cellular environment. We believe the ease of the CRRL strategy should find wide use in a range of applications in biology, tissue engineering, nanoscience, synthetic chemistry, and material science and will expand the suite of current conjugation and release strategies.

Fabrication of dynamic self-assembled monolayers for cell migration and adhesion studies.

How cells interact with the extracellular matrix (ECM) is important for a number of fundamental -processes in cell biology. However, the ECM is highly complex and in order to simplify the matrix for cell biological studies, it has been modeled with self-assembled monolayers (SAMs) of alkanethiolates on gold substrates. In this chapter, we outline procedures to create dynamic surfaces by functionalizing SAMs. SAMs based on quinone, oxyamine, and alcohol-terminated thiols were used to immobilize cell adhesive peptides with spatial control. Cells were seeded to these surfaces to provide cell co-culture -patterns suitable for biological studies.

Chemoselective ligand patterning of electroactive surfaces using microfluidics.

To generate model substrates for cell adhesion, we have developed two different biocompatible strategies based on self-assembled monolayers (SAMs) of alkanethiolates on gold terminated with latent ketones and aldehydes. Under spatial control, the hydroquinone and alcohol-terminated SAMs can be oxidized to allow for oxyamine ligand patterning on the surface with microfluidic cassettes. These immobilization strategies were characterized by electrochemistry, fluorescence, and utilizing a cell adhesive peptide, cell patterns were generated.

Patterned hybrid nanohole array surfaces for cell adhesion and migration.

We report the fabrication of hybrid nanohole array surfaces to study the role of the surface nanoevironment on cell adhesion and cell migration. We use polystyrene beads and reactive ion etching to control the size and the spacing between nanoholes on a tailored self-assembled monolayer inert gold surface. The arrays were characterized by scanning electron microscopy and brightfield microscopy. For cell adhesion studies, cells were seeded to these substrates to study the effect of ligand spacing on cell spreading, stress fiber formation, and focal adhesion structure and size. Finally, comparative cell migration rates were examined on the various nanohole array surfaces using time-lapse microscopy.

Rapid in situ generation of two patterned chemoselective surface chemistries from a single hydroxy-terminated surface using controlled microfluidic oxidation.

In this work, we develop a new, rapid and inexpensive method to generate spatially controlled aldehyde and carboxylic acid surface groups by microfluidic oxidation of 11-hydroxyundecylphosphonic acid self-assembled monolayers (SAMs) on indium tin oxide (ITO) surfaces. SAMs are activated and patterned using a reversibly sealable, elastomeric polydimethylsiloxane cassette, fabricated with preformed micropatterns by soft lithography. By flowing the mild oxidant pyridinium chlorochromate through the microchannels, only selected areas of the SAM are chemically altered. This microfluidic oxidation strategy allows for ligand immobilization by two chemistries originating from a single SAM composition. ITO is robust, conductive, and transparent, making it an ideal platform for studying interfacial interactions. We display spatial control over the immobilization of a variety of ligands on ITO and characterize the resulting oxime and amide linkages by electrochemistry, X-ray photoelectron spectroscopy, contact angle, fluorescence microscopy, and atomic force microscopy. This general method may be used with many other materials to rapidly generate patterned and tailored surfaces for studies ranging from molecular electronics to biospecific cell-based assays and biomolecular microarrays.

Electrochemical and chemical microfluidic gold etching to generate patterned and gradient substrates for cell adhesion and cell migration.

To generate patterned substrates of self-assembled monolayers (SAMs) for cell adhesion and migration studies, a variety of gold/glass hybrid substrates were fabricated from gold evaporated on glass. A variety of surfaces were generated including gradients of gold height, completely etched gold/glass hybrids, and partially etched gold surfaces for pattern visualization. Etch rates were controlled by the alkanethiol present on the surface. Gradients of gold height were created using an electrochemical etch with control over the position and slope of the gold height gradient. Cells were seeded to these surfaces, and their adhesion to the gold was controlled by the surface chemistry present in the channel regions. In the future, the etched gold surfaces will be used to simulate the varying nanotopology experienced by the migrating cell in vivo.

Renewable and optically transparent electroactive indium tin oxide surfaces for chemoselective ligand immobilization and biospecific cell adhesion.

In this report, we show the successful transfer of a sophisticated electroactive immobilization and release strategy to an indium tin oxide (ITO) surface to generate (1) optically transparent, robust, and renewable surfaces, (2) inert surfaces that resist nonspecific protein adsorption and cell attachment, and (3) tailored biospecific surfaces for live-cell high-resolution fluorescence microscopy of cell culture. By comparing the surface chemistry properties on both ITO and gold surfaces, we demonstrate the ITO surfaces are superior to gold as a renewable surface, in robustness (durability), and as an optically transparent material for live-cell fluorescence microscopy studies of cell behavior. These advantages will make ITO surfaces a desired platform for numerous biosensor and microarray applications and as model substrates for various cell biological studies.

Expedient generation of patterned surface aldehydes by microfluidic oxidation for chemoselective immobilization of ligands and cells.

An expedient and inexpensive method to generate patterned aldehydes on self-assembled monolayers (SAMs) of alkanethiolates on gold with control of density for subsequent chemoselective immobilization from commercially available starting materials has been developed. Utilizing microfluidic cassettes, primary alcohol oxidation of tetra(ethylene glycol) undecane thiol and 11-mercapto-1-undecanol SAMs was performed directly on the surface generating patterned aldehyde groups with pyridinium chlorochromate. The precise density of surface aldehydes generated can be controlled and characterized by electrochemistry. For biological applications, fibroblast cells were seeded on patterned surfaces presenting biospecifc cell adhesive (Arg-Glyc-Asp) RGD peptides.

Microfluidic lithography of SAMs on gold to create dynamic surfaces for directed cell migration and contiguous cell cocultures.

A straightforward, flexible, and inexpensive method to create patterned self-assembled monolayers (SAMs) on gold using microfluidics-microfluidic lithography-has been developed. Using a microfluidic cassette, alkanethiols were rapidly patterned on gold surfaces to generate monolayers and mixed monolayers. The patterning methodology is flexible and, by controlling the solvent conditions and thiol concentration, permeation of alkanethiols into the surrounding PDMS microfluidic cassette can be advantageously used to create different patterned feature sizes and to generate well-defined SAM surface gradients with a single microfluidic chip. To demonstrate the utility of microfluidic lithography, multiple cell experiments were conducted. By patterning cell adhesive regions in an inert background, a combination of selective masking of the surface and centrifugation achieved spatial and temporal control of patterned cells, enabling the design of both dynamic surfaces for directed cell migration and contiguous cocultures. Cellular division and motility resulted in directed, dynamic migration, while the centrifugation-aided seeding of a second cell line produced contiguous cocultures with multiple sites for heterogeneous cell-cell interactions.

Synergistic microfluidic and electrochemical strategy to activate and pattern surfaces selectively with ligands and cells.

We show a straightforward, flexible synergistic approach that combines microfluidics, electrochemistry, and a general immobilization strategy to activate regions of a substrate selectively for the precise immobilization of ligands and cells in patterns for a variety of cell-based assays and cell migration and cell adhesion studies. We develop microfluidic microchips to control the delivery of electrolyte solution to select regions of an electroactive hydroquinone SAM. Once an electrical potential is applied to the substrate, only the hydroquinone exposed to electrolyte solution within the microfluidic channels oxidizes to the corresponding quinone. The quinone form can then react chemoselectively with oxyamine-tethered ligands to pattern the surface. Therefore, this microfluidic/electrochemistry strategy selectively activates the surface for ligand patterning that exactly matches the channel design of the microfluidic channel. We demonstrate the ease of this system by first quantitatively characterizing the electrochemical activation and immobilization of ligands on the surface. Second, we immobilize a fluorescent dye to show the fidelity of the methodology, and third, we show the immobilization of biospecific cell adhesive peptide ligands to pattern cells. This is the first report that combines microfluidics/electrochemistry and a general electroactive immobilization strategy to pattern ligands and cells. We believe that this strategy will be of broad utility for applications ranging from fundamental studies of cell behavior to patterning molecules on a variety of materials for molecular electronic devices.