Determination of kinetic parameters for interfacial enzymatic reactions on self-assembled monolayers

Concentration-Dependent Inhibition of Mesophilic PETases on Poly(ethylene terephthalate) Can Be Eliminated by Enzyme Engineering

Enzyme-based depolymerization is a viable approach for recycling of poly(ethylene terephthalate) (PET). PETase from Ideonella sakaiensis (IsPETase) is capable of PET hydrolysis under mild conditions but suffers from concentration-dependent inhibition. In this study, this inhibition is found to be dependent on incubation time, the solution conditions, and PET surface area. Furthermore, this inhibition is evident in other mesophilic PET-degrading enzymes to varying degrees, independent of the level of PET depolymerization activity. The inhibition has no clear structural basis, but moderately thermostable IsPETase variants exhibit reduced inhibition, and the property is completely absent in the highly thermostable HotPETase, previously engineered by directed evolution, which simulations suggest results from reduced flexibility around the active site. This work highlights a limitation in applying natural mesophilic hydrolases for PET hydrolysis and reveals an unexpected positive outcome of engineering these enzymes for enhanced thermostability.

Human Neutrophil Elastase Activated Fluorescent Probe for Pulmonary Diseases Based on Fluorescence Resonance Energy Transfer Using CdSe/ZnS Quantum Dots

There is an increasing demand for effective noninvasive diagnosis against common pulmonary diseases, which are rising sharply due to the serious air pollution. Human neutrophil elastase (HNE), a typical protease highly involved in pulmonary inflammatory diseases and lung cancer, is a potential predictor for disease progression. Currently, few of the HNE-targeting probes are applicable in vivo due to the limitation in sensitivity and biocompatibility. Herein, we reported the achievement of in vitro detection and in vivo imaging of HNE by incorporating the HNE-specific peptide substrate, quantum dots (QDs), and organic dyes into the fluorescence resonance energy transfer (FRET) system. The refined nanoprobe, termed QDP, could specifically measure the HNE with excellent sensitivity of 7.15 pM in aqueous solution and successfully image the endogenous and exogenous HNE in living cells. In addition, this nanoprobe enabled HNE imaging in mouse models of lung cancer and acute lung injury, and the HNE activity at high temporal and spatial resolution was continuously monitored. Most importantly, QDP successfully discriminated the serums of patients with lung diseases from those of the healthy controls based on the HNE activity determination. Overall, this study demonstrates the advantages of a FRET-system-based nanoprobe in imaging performance and provides an applicable tool for in vivo HNE detection and pulmonary disease diagnosis.

Dynamically Tunable Cell Culture Platforms for Tissue Engineering and Mechanobiology

Human tissues are sophisticated ensembles of many distinct cell types embedded in the complex, but well-defined, structures of the extracellular matrix (ECM). Dynamic biochemical, physicochemical, and mechano-structural changes in the ECM define and regulate tissue-specific cell behaviors. To recapitulate this complex environment in vitro, dynamic polymer-based biomaterials have emerged as powerful tools to probe and direct active changes in cell function. The rapid evolution of polymerization chemistries, structural modulation, and processing technologies, as well as the incorporation of stimuli-responsiveness, now permit synthetic microenvironments to capture much of the dynamic complexity of native tissue. These platforms are comprised not only of natural polymers chemically and molecularly similar to ECM, but those fully synthetic in origin. Here, we review recent in vitro efforts to mimic the dynamic microenvironment comprising native tissue ECM from the viewpoint of material design. We also discuss how these dynamic polymer-based biomaterials are being used in fundamental cell mechanobiology studies, as well as towards efforts in tissue engineering and regenerative medicine.

Gold nanodome SERS platform for label-free detection of protease activity

Surface-enhanced Raman scattering provides a promising technology for sensitive and selective detection of protease activity by monitoring peptide cleavage. Not only are peptides and plasmonic hotspots similarly sized, Raman fingerprints also hold large potential for spectral multiplexing. Here, we use a gold-nanodome platform for real-time detection of trypsin activity on a CALNNYGGGGVRGNF substrate peptide. First, we investigate the spectral changes upon cleavage through the SERS signal of liquid-chromatography separated products. Next, we show that similar patterns are detected upon digesting surface-bound peptides. We demonstrate that the relative intensity of the fingerprints from aromatic amino acids before and after the cleavage site provides a robust figure of merit for the turnover rate. The presented method offers a generic approach for measuring protease activity, which is illustrated by developing an analogous substrate for endoproteinase Glu-C.

Buffers more than buffering agent: introducing a new class of stabilizers for the protein BSA

In this study, we have analyzed the influence of four biological buffers on the thermal stability of bovine serum albumin (BSA) using dynamic light scattering (DLS).

Enzymatic reactions on immobilised substrates

This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.

Investigation of an electrochemically switched heterocyclization reaction on gold surface

We report an investigation of an electrochemically switched heterocyclization reaction on hydroquinone-terminated self-assembled monolayers (SAMs). This reaction involves an electrochemically modulated hydroquinone/benzoquinone transformation step in the SAMs and a subsequent heterocyclization step taking place between the electrochemically generated benzoquinone moieties in SAMs and l-cysteine in solution. The reaction process was monitored by XPS and electrochemical surface-enhanced Raman spectroscopy (EC-SERS). The surface reaction proceeds as a two-step reaction to give a benzothiazine product, which is in contrast to the much more complicated multiple step reactions in solution. This result suggests that the tight molecular packing in the SAMs does not hinder the intramolecular heterocylization reaction, but prevents the intermolecular coupling reaction from happening. This work provides insights to the control and detection of biomolecule related multistep reactions occurring at solid-liquid interface.

Kinetics of enzyme action on surface-attached substrates: a practical guide to progress curve analysis in any kinetic situation

In the present work, exact kinetic equations describing the action of an enzyme in solution on a substrate attached to a surface have been derived in the framework of the Michaelis-Menten mechanism but without resorting to the often-used steady-state approximation. The here-derived kinetic equations are cast in a workable format, allowing us to introduce a simple and universal procedure for the quantitative analysis of enzyme surface kinetics that is valid for any kinetic situation. The results presented here should allow experimentalists studying the kinetics of enzyme action on immobilized substrates to analyze their data in a perfectly rigorous way.

Thin-layer matrix sublimation with vapor-sorption induced co-crystallization for sensitive and reproducible SAMDI-TOF MS analysis of protein biosensors

Coupling immunoassays on self-assembled monolayers (SAMs) to matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) provides improved assay selectivity compared with traditional photometric detection techniques. We show that thin-layer-transfer (TLT) of α-cyano-4-hydroxycinnaminic acid (CHCA) MALDI matrix via vacuum sublimation followed by organic solvent-based vapor-sorption induced co-crystallization (VIC) results in unique matrix/analyte co-crystallization tendencies that optimizes assay reproducibility and sensitivity. Unique matrix crystal morphologies resulted from VIC solvent vapors, indicating nucleation and crystal growth characteristics depend upon VIC parameters. We observed that CHCA microcrystals generated by methanol VIC resulted in >10× better sensitivity, increased analyte charging, and improved precision compared with dried droplet measurements. The uniformity of matrix/analyte co-crystallization across planar immunoassays directed at intact proteins yielded low spectral variation for single shot replicates (18.5 % relative standard deviation, RSD) and signal averaged spectra (<10 % RSD). We envision that TLT and VIC for MALDI-TOF will enable high-throughput, reproducible array-based immunoassays for protein molecular diagnostic assays in diverse biochemical and clinical applications.

Enzyme responsive materials: design strategies and future developments

Enzyme responsive materials (ERMs) are a class of stimuli responsive materials with broad application potential in biological settings. This review highlights current and potential future design strategies for ERMs and provides an overview of the present state of the art in the area.

Proteolytic activity at quantum dot-conjugates: kinetic analysis reveals enhanced enzyme activity and localized interfacial "hopping"

Recent studies show that polyvalent, ligand-modified nanoparticles provide significantly enhanced binding characteristics compared to isolated ligands. Here, we assess the ability of substrate-modified nanoparticles to provide enhanced enzymatic activity. Energy transfer assays allowed quantitative, real-time measurement of proteolytic digestion at polyvalent quantum dot-peptide conjugates. Enzymatic progress curves were analyzed using an integrated Michaelis-Menten (MM) formalism, revealing mechanistic details, including deviations from classic MM-behavior. A "hopping" mode of proteolysis at the nanoparticle was identified, confirming enhanced activity.

Optimizing electrode-attached redox-peptide systems for kinetic characterization of protease action on immobilized substrates. Observation of dissimilar behavior of trypsin and thrombin enzymes

In this work, we experimentally address the issue of optimizing gold electrode attached ferrocene (Fc)-peptide systems for kinetic measurements of protease action. Considering human α-thrombin and bovine trypsin as proteases of interest, we show that the recurring problem of incomplete cleavage of the peptide layer by these enzymes can be solved by using ultraflat template-stripped gold, instead of polished polycrystalline gold, as the Fc-peptide bearing electrode material. We describe how these fragile surfaces can be mounted in a rotating disk configuration so that enzyme mass transfer no longer limits the overall measured cleavage kinetics. Finally, we demonstrate that, once the system has been optimized, in situ real-time cyclic voltammetry monitoring of the protease action can yield high-quality kinetic data, showing no sign of interfering effects. The cleavage progress curves then closely match the Langmuirian variation expected for a kinetically controlled surface process. Global fit of the progress curves yield accurate values of the peptide cleavage rate for both trypsin and thrombin. It is shown that, whereas trypsin action on the surface-attached peptide closely follows Michaelis-Menten kinetics, thrombin displays a specific and unexpected behavior characterized by a nearly enzyme-concentration-independent cleavage rate in the subnanomolar enzyme concentration range. The reason for this behavior has still to be clarified, but its occurrence may limit the sensitivity of thrombin sensors based on Fc-peptide layers.

Rate enhancement of an interfacial biochemical reaction through localization of substrate and enzyme by an adaptor domain

This paper describes a model system to characterize the rate enhancement that stems from localization of an enzyme with its substrate. The approach is based on a self-assembled monolayer that presents a substrate for the serine esterase cutinase along with a peptide ligand for an SH2 adaptor domain. The monolayer is treated with a fusion protein of cutinase and the SH2 domain, and the rate for the interfacial reaction is monitored using cyclic voltammetry. The rate is approximately 30-fold greater for monolayers that present the ligand for the SH2 domain than for those that omit the ligand. The rate enhancement is due to the interaction of the adaptor domain with the immobilized ligand. Further, the rate enhancement increases with the densities of both the ligand and the substrate. This example provides a well-defined model system for quantitatively assessing the magnitude of rate enhancement that is possible with colocalization of an enzyme with its substrate and may be particularly significant for understanding the signaling events that rely on enzyme localization at the cell membrane.

Peptide reporters of kinase activity in whole cell lysates

Kinase assays are used to screen for small-molecule inhibitors that may show promise as targeted pharmaceutical therapies. Using cell lysates instead of purified kinases provides a more accurate estimate of inhibitor sensitivity and selectivity in a biological setting. This review summarizes the range of homogeneous (solution-phase) and heterogeneous (solid-supported) formats available for using peptide substrates to monitor kinase activities in cell lysates. With a focus on heterogeneous kinase assays, the peptide substrate Abltide is used as a model to optimize presentation geometries and the modular arrangement of short sequences for kinase recognition. We present results from peptides immobilized on two- and three-dimensional surfaces such as hydrogels on 96-well plates and glass slides, and fluorescent Luminex beads. We discuss methods to increase assay sensitivity using chemifluorescent ELISAs, antibody-based recognition, and label-free mass spectrometry. Monitoring the activity of specific kinases in cell lysates presents challenges that can be overcome by manipulating peptide substrates to optimize assay conditions. In particular, signal-to-background ratios were improved by (1) adding long branched hydrophilic linkers between the substrate and the surface, (2) changing the orientation of peptides relative to the surface, and (3) including peptide ligands in cis or in trans to recruit kinases to the surface. By improving the accessibility of immobilized peptide substrates to kinases in solution, the apparent rate of phosphorylation increased and assays were more sensitive to changes in endogenous kinase activities. These strategies can be generalized to improve the reactivity of most peptide substrates used in heterogeneous kinase assays with cell lysates.

Immobilization of peptides with distinct biological activities onto stem cell culture substrates using orthogonal chemistries

We have used the orthogonal carbodiimide condensation and copper-catalyzed azide-alkyne "click" cycloaddition (CuAAC) reactions to prepare self-assembled monolayers that present distinct peptides to stem cells in a bioinert background. The approach involved first forming mixed SAMs with three components: (i) an azide-terminated hexaethylene glycol alkanethiolate (HS-EG6-N3), (ii) a carboxylate-terminated hexaethylene glycol alkanethiolate (HS-EG6-COOH), and (iii) a triethylene glycol alkanethiolate (HS-EG3). An acetylene-bearing peptide and an amine-terminated peptide were then immobilized to these substrates using a "click" CuAAC reaction and a carbodiimide condensation reaction, respectively. Polarization-modulated infrared reflectance-absorbance spectroscopic analysis demonstrated formation of well-ordered, close-packed self-assembled monolayers (SAMs), chemoselective conjugation of amine-terminated peptides to surface carboxylate groups, and subsequent conjugation of acetylene-terminated peptides to the azide groups on SAMs. Varying the mole fraction of HS-EG6-N3, HS-EG6-COOH, and HS-EG3 during SAM formation allowed for control over the densities of each peptide on the substrate. Substrates presenting varying surface densities of RGESP (a nonfunctional peptide), RGDSP (a cell adhesion peptide), or TYRSRKY (a heparin/heparan sulfate-binding peptide) were then used to characterize the relationship between peptide surface density and human mesenchymal stem cell (hMSC) adhesion. Results demonstrate that RGESP does not influence RGDSP-mediated adhesion of hMSCs, which indicates that a second peptide with distinct bioactivity can be immobilized alongside RGDSP to characterize the influence of two peptides on hMSC behavior. Our results also demonstrate that RGDSP and TYRSRKY act synergistically to promote hMSC adhesion in the absence of serum. Interestingly, heparin sequestered by TYRSRKY inhibits cell adhesion on substrates presenting RGDSP = 0.1% and > or = 0.1% TYRSRKY or RGDSP = 1% and > or = 0.5% TYRSRKY. Taken together, these results indicate that two peptides can be controllably presented to stem cells on the same otherwise bioinert SAM substrate, and that multiple, distinct extracellular moieties act in concert to regulate hMSC adhesion.

An adaptor domain-mediated autocatalytic interfacial kinase reaction

This paper describes a model system for studying the autocatalytic phosphorylation of an immobilized substrate by a kinase enzyme. This work uses self-assembled monolayers (SAMs) of alkanethiolates on gold to present the peptide substrate on a planar surface. Treatment of the monolayer with Abl kinase results in phosphorylation of the substrate. The phosphorylated peptide then serves as a ligand for the SH2 adaptor domain of the kinase and thereby directs the kinase activity to nearby peptide substrates. This directed reaction is intramolecular and proceeds with a faster rate than does the initial, intermolecular reaction, making this an autocatalytic process. The kinetic non-linearity gives rise to properties that have no counterpart in the corresponding homogeneous phase reaction: in one example, the rate for phosphorylation of a mixture of two peptides is faster than the sum of the rates for phosphorylation of each peptide when presented alone. This work highlights the use of an adaptor domain in modulating the activity of a kinase enzyme for an immobilized substrate and offers a new approach for studying biochemical reactions in spatially inhomogeneous settings.

The Janus-SAM approach for the flexible functionalization of gold and titanium oxide surfaces

A novel approach is developed to address the requirement of multiple stamps and inks for microcontact printing (microCP) onto different substrate surfaces. This approach relies on microCP one divalent molecule, which is able to form Janus self-assembled monolayers (JSAMs) with a labile cleavable centre, thus providing a facile method for the chemical derivatization of different substrate surfaces. This study presents an answer to the challenges presented within a highly versatile application, microCP. N-(3-diethylphosphatoxy)propyl-11-mercaptoundecanamide is used for the first time as an ink for microCP onto both gold and titanium oxide surfaces, utilizing the same polydimethylsiloxane stamp. Following printing, the JSAMs are enzymatically treated on these two different substrates to reveal different functional groups. The newly formed surfaces are subjected to additional surface reactions and used for the chemisorption of bovine serum albumin. At each stage, these JSAMs are characterized by X-ray photoelectron spectroscopy and dynamic water-contact-angle measurements. Confocal laser scanning microscopy is used for the characterization of the adsorbed proteins.

PEGylation modulates the interfacial kinetics of proteases on peptide-capped gold nanoparticles

Fluorescence unquenching measurements of protease-dependent release of fluorescent biomolecules from peptide-capped gold nanoparticles reveal the effect of the monolayer composition on enzyme kinetics.

Enzyme-activated RGD ligands on functionalized poly(ethylene glycol) monolayers: surface analysis and cellular response

We report on the design, stepwise synthesis, and surface analysis of enzyme-responsive surfaces that present cell adhesive RGD sequences on-demand, that is, by enzymatic hydrolysis of inactive RGD containing precursors that carry cleavable steric blocking groups. These surfaces, incorporating poly(ethylene glycol) (PEG) monolayers coupled via epoxy silanes to glass, are functionalized via stepwise solid phase synthesis, presenting a versatile and straightforward approach to preparation of peptide surfaces. Successive amino acid coupling and deprotection steps using fluorenylmethoxycarbonyl (Fmoc) chemistry are verified using surface analysis with time-of-flight secondary-ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy (XPS). Exposure of surfaces to elastase results in activation of cell binding ligands as demonstrated using osteoblast cells. These surfaces may have applications in spatiotemporally controlled attachment of cells as relevant for three-dimensional tissue engineering scaffolds and cell-based biosensors.

Kinetics of enzyme attack on substrates covalently attached to solid surfaces: influence of spacer chain length, immobilized substrate surface concentration and surface charge

The use of alpha-chymotrypsin to cleave covalently bound N-acetyl- l-tryptophan (Ac-Trp-OH) from the surfaces of aminopropylated controlled pore glass (CPG) and the polymer PEGA 1,900 was investigated. Oligoglycine spacer chains were used to present the covalently attached Ac-Trp-OH substrate to the aqueous enzyme. In the absence of the oligoglycine spacer chain, the rate of release was relatively slow, especially from the PEGA 1,900. These slow rates reflect the position of the amino group to which Ac-Trp-OH is covalently attached. On the glass there was a clear optimum with a chain of four glycine residues. For PEGA 1,900 there is no real apparent change beyond two glycine residues. The decline in rate beyond these optima are a possible result of changes in oligoglycine structure. Comparing different surface loadings of bound substrate the rate of release of Ac-Trp-OH from CPG with a pore diameter of 1,200 A was optimal when using 83% of the maximum that can be coupled, then fell again at higher loading. The rate of Ac-Trp-OH release from CPG was the same for surface coverages of 0.4 and 1.0. The introduction of permanent surface charges on CPG 1,200 exhibits a distinct influence on enzymatic cleavage with an increase in the rate of biocatalysis at the surface. Optimal presentation of covalently immobilized substrate on different supports by use of appropriate linkers leads to favorable biocatalysis from the support.

Kinetics of adsorption and proteolytic cleavage of a multilayer ovalbumin film by subtilisin Carlsberg

Adsorption and proteolytic activity of the enzyme subtilisin Carlsberg have been studied on an immobilized, multilayer ovalbumin film. The cross-linked multilayer substrate permits protease adsorption to be examined unencumbered by the surface inhomogeneity typically observed in monolayer studies of protease surface kinetics. Decline of the protein film was measured over time using ellipsometry. Resulting kinetic data as a function of aqueous enzyme concentration and temperature were well fit by a Langmuir-Michaelis-Menten model for surface proteolysis. We observed that both the protein degradation kinetics and the in situ adsorption data were well described by the proposed model. The temperature dependence of the kinetic rate parameter yielded an activation energy of 12 kcal/mol. Further, the apparent Langmuir adsorption equilibrium constant of the enzyme at the protein/aqueous interface was 0.11 L/mg at 22 degrees C, 0.034 L/mg at 36 degrees C, and 0.011 L/mg at 50 degrees C. Although enzyme adsorption at a given aqueous enzyme concentration decreased at higher temperature, the enzyme cleaved the substrate more rapidly, leading to a net increase in the ovalbumin film degradation rate. We observed that the maximum enzyme coverage on the immobilized protein surface was approximately 40% of a close-packed monolayer at ambient temperature (22 degrees C).