Molecular templates for bio-specific recognition by low-energy electron beam lithography

Protein patterning has become an important topic as advances are made in biologically integrated devices and protein chip technology. Versatile and effective patterning requires substrates that can be quantified, with active presentation of proteins and control over protein density and orientation. Herein we describe a model system and the use of low-energy electron beam lithography to pattern molecular templates for immobilization of antibodies through ligand recognition. The templates were patterned over a background of poly(ethylene glycol) (PEG) modified silicon oxide (SiO _x ). These substrates were exposed to a low-voltage (2 keV) electron beam to remove PEG selectively from exposed regions. These regions were then functionalized with a dinitrophenyl (DNP) ligand and tested for specific binding of fluorescently labeled anti-DNP antibodies. The PEG modified regions in conjunction with ligand-presenting regions in the patterned arrays substantially reduces non-specific adsorption of proteins, yielding a specific/nonspecific ratio of approx 10. The surface coverage of the biologically active DNP groups on SiO _x and the amount of immobilized antibody on DNP were measured with a fluorescence-based, enzyme-linked immunosorbent assay. The specificity of the interaction between DNP ligand and fluorescently labeled anti-DNP antibodies was evaluated with fluorescence microscopy. This approach to patterning of molecular templates and assays for quantification are generally applicable to immobilization of any ligand-receptor pair on a wide range of substrates.     

Purification and properties of a diisopropyl-fluorophosphatase from squid Todarodes pacificus steenstrup

A diisopropyl-fluorophosphatase (DFPase) was purified from brain and ganglia of squid Todarodes pacificus steenstrup. The DFPase had a preference in hydrolysis toward diisopropylphosphorofluoridate (DFP). It also was able to hydrolyze O-1,2,2-trimethylpropyl methylphosphofluoridate (soman) and O-isopropyl methylphosphonofluoridate (sarin) at nearly equal hydrolytic rates but only 1/10 that of DFP. The hydrolytic activity toward diethyl-p-nitrophenylphosphate (paraoxon) was very low compared with DFP, so man, and sarin. The DFPase was purified 330-fold to a specific activity of 18,300 n mol/min/mg protein. Its molecular weight was 34,000 dalton determined by gel-filtration chromatography. Mn²⁺ stimulation of the DFPase was not observed when DFP and soman were the substrates, but with sarin, the rate increased onefold in the presence of 1.0 mM of Mn²⁺. Ethylenediamine tetraacetic acid disodium (EDTA-Na₂) at 0.05 M inhibited the DFPase activity about 30%. It could be concluded that this DFPase belongs to the squid-type DFPase.     

High-activity enzyme-polyurethane coatings

The synthesis of water-borne polyurethane coatings in the presence of diisopropylfluorophosphatase (DFPase, E.C. 3.8.2.1) enabled the irreversible attachment of the enzyme to the polymeric matrix. The distribution of immobilized DFPase as well as activity retention are homogeneous within the coating. The resulting enzyme-containing coating (ECC) film hydrolyzes diisopropylfluorophosphate (DFP) in buffered media at high rates, retaining approximately 39% intrinsic activity. Decreasing ECC hydrophilicity, via the use of a less hydrophilic polyisocyanate during polymerization, significantly enhanced the intrinsic activity of the ECC. DFPase-ECC has biphasic deactivation kinetics, where the initial rapid deactivation of DFPase-ECC leads to the formation of a hyperstable and active form of enzyme.     

Site-specific, covalent attachment of poly(dT)-modified peptides to solid surfaces for microarrays

The present study reported proof-of-principle for a kinase assay approach that can detect specific peptide phosphorylation events. The method involves attachment of peptides onto commercial aminosilane and polycarbodiimide-coated glass slides, using a newly developed DNattach linker system that consists of a poly(dT) tail (Nisshinbo Industries Inc.), followed by a detection step using fluorescently labeled antiphosphoamino acid antibodies. The linker-modified peptides are efficiently synthesized by Michael addition between maleimido-modified peptides and thiol-containing DNattach. Specific covalent immobilization of the modified peptides onto aminosilane and poly carbodiimide-coated slides is then achieved by short exposure to UV-light. Highly selective and quantitative recognition by standard antiphosphoamino acid antibodies (antiphosphotyrosine and anti-phosphoGFAP) and kinases (c-Src and PKA) to the corresponding modified peptides on the microarray spots is demonstrated. Furthermore, we found that this immobilization method provides greater signal-to-noise ratio and better discrimination ability of phosphorylated amino acids than does the conventional immobilization technique. The phosphorylation pattern of target sequences, detected using fluorescently labeled antiphosphoamino acid antibodies, revealed that the linker system preference of the kinase is determined by its activity profile.     

Comparison of coatings from reactive star shaped PEG-stat-PPG prepolymers and grafted linear PEG for biological and medical applications

Grafting of poly(ethylene glycol) (PEG) is a common strategy for reducing nonspecific interactions of surfaces with proteins. We have used grafting at "cloud point" solution conditions that ensures maximum grafting density of linear methoxy terminated PEG-aldehyde (mPEG-ald, M(w) = 5000 and 30000). In an alternative approach, surfaces were modified with layers prepared from isocyanate terminated, star shaped poly(ethylene glycol-stat-propylene glycol) prepolymers (80% ethylene glycol, six arms, M(w) = 3000, 12,000, and 18,000; this compound will be referred to as "Star PEG" in the text). Due to the highly reactive endgroups, these molecules form a dense network on the substrate with a high polymer surface coverage. The two systems were compared regarding their ability to prevent unspecific adsorption of insulin and lysozyme. The layers were analyzed by ellipsometry, contact angle measurements, and XPS. Protein adsorption was monitored by surface MALDI-TOF MS and fluorescence microscopy. No protein adsorption could be detected on Star PEG coatings and on mPEG-ald 5000, whereas mPEG-ald 30,000 could only prevent adsorption of lysozyme but not of the smaller insulin.     

Activity and Stability of Native and Modified Subtilisins in Various Media

The activity and stability of native subtilisin 72, its complex with poly(acrylic acid), and subtilisin covalently attached to poly(vinyl alcohol) cryogel were studied in aqueous and organic media by hydrolysis of specific chromogenic peptide substrates. Kinetic parameters of the hydrolysis of Glp-Ala-Ala-Leu-pNA by native subtilisin and its complex with poly(acrylic acid) were determined. Based on the comparative study of stability of native and modified subtilisins in media of various compositions, it was established that covalent immobilization of subtilisin on poly(vinyl alcohol) cryogel is the most effective approach to improve enzyme stability in water as well as in mixtures with low water content.     

Surface functionalized electrospun biodegradable nanofibers for immobilization of bioactive molecules

A blend mixture of biodegradable poly(epsilon-caprolactone) (PCL) and poly(d,l-lactic-co-glycolic acid)-poly(ethylene glycol)-NH(2) (PLGA-b-PEG-NH(2)) block copolymer was electrospun to produce surface functionalized nanofibers. The resulting nanofibrous mesh with primary amine groups on the surface was applied for immobilization of biologically active molecules using lysozyme as a model enzyme. Lysozyme was immobilized via covalent conjugation by using a homobifunctional coupling agent. The nanofibrous mesh could immobilize a far greater amount of lysozyme on the surface with concomitantly increased activity, primarily due to its larger surface area, compared to that of the solvent casting film. It was also found that the enzyme immobilization process slightly altered thermal and pH-dependent catalytic activity profiles compared to those of native lysozyme. The results demonstrated the surface functionalized electrospun nanofibrous mesh could be used as a promising material for immobilizing a wide range of bioactive molecules.     

Thermal stability studies of a globular protein in aqueous poly(ethylene glycol) by (1)H NMR

The reversible folding destabilization of hen lysozyme has been confirmed by a melting temperature (T(m)) decrease in aqueous poly(ethylene glycol) (PEG). The percent denatured, extracted from the histidine 15 C2H (H15 C2H) native and denatured peak areas from 500-MHz one-dimensional proton nuclear magnetic resonance (1D (1)H NMR) spectra in D(2)O, was analyzed through denaturation temperatures at 0% and 20% (w/w) PEG 1000. The lysozyme (3.5 mM) T(m) decreased by 4.2 degrees C and 7.1 degrees C in 20% (w/w) PEG 1000 at pH 3.8 and 3.0, respectively. The T(m) decreased with increasing lysozyme concentration. Additionally, the temperature-induced resonance migrations of 17 protons from 8 residues indicate that the native lysozyme structure undergoes temperature-induced conformational changes. The changes were essentially identical in both 0% and 20% (w/w) PEG 1000 at both pH 3.0 and 3.8. This small, local restructuring of the hydrophobic box region may be a manifestation of temperature-dependent solution hydrophobicity, whereas active-site cleft fluctuations may be due to the inherent active-site flexibility. The lysozyme structure in PEG at 35 degrees C was determined to be essentially native from the (1)H nuclear Overhauser effect spectroscopy (NOESY) fingerprint regions. Additionally, lysozyme chemical shifts, from 1D spectra, in PEG 200, 300, and 1000 at 35 degrees C and various concentrations were essentially identical, further confirming that the conformation remains native in various PEG solutions. (c) 1996 John Wiley & Sons, Inc.     

Use of immobilized Streptomyces griseus proteases (pronase) as a probe of structural transitions of lysozyme, β-lactoglobulin and casein

The native - denatured (N U) structural transition in lysozyme (mucopeptide N-acetylmuramoylhydrolase, EC 3.2.1.17), β-lactoglobulin and caseins have been studied by proteolysis using immobilized Streptomyces griseus proteases (pronase) as a probe. A diverse range of susceptibility to urea denaturation was revealed by evaluation of initial rates and pseudo first-order rate constants for hydrolysis of these proteins. Comparison of the rate of hydrolysis of lysozyme vis-à-vis performic acid oxidized-lysozyme showed that the degree of backbone accessibility for native lysozyme, even in concentrated urea solutions, was less than that of the oxidized protein. At pH 7.5, native lysozyme appeared to possess the most stable structure, followed by β-lactoglobulin and, finally, the caseins. It is postulated that the proteolytic rate depends upon accessibility of a susceptible bond(s) or subtle conformational changes in the least stable domain. Following cleavage of this bond(s), K_D increases thus exposing more backbone. Use of pronase immobilized on porous succinamidopropyl-glass beads resulted in increased enzyme stability and eliminated autolysis. Consequently, immobilized proteases are an excellent probe of structural transitions of protein substrates in denaturants.     

Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS

To examine phylogenetic identity and metabolic activity of individual cells in complex microbial communities, we developed a method which combines rRNA-based in situ hybridization with stable isotope imaging based on nanometer-scale secondary-ion mass spectrometry (NanoSIMS). Fluorine or bromine atoms were introduced into cells via 16S rRNA-targeted probes, which enabled phylogenetic identification of individual cells by NanoSIMS imaging. To overcome the natural fluorine and bromine backgrounds, we modified the current catalyzed reporter deposition fluorescence in situ hybridization (FISH) technique by using halogen-containing fluorescently labeled tyramides as substrates for the enzymatic tyramide deposition. Thereby, we obtained an enhanced element labeling of microbial cells by FISH (EL-FISH). The relative cellular abundance of fluorine or bromine after EL-FISH exceeded natural background concentrations by up to 180-fold and allowed us to distinguish target from non-target cells in NanoSIMS fluorine or bromine images. The method was optimized on single cells of axenic Escherichia coli and Vibrio cholerae cultures. EL-FISH/NanoSIMS was then applied to study interrelationships in a dual-species consortium consisting of a filamentous cyanobacterium and a heterotrophic alphaproteobacterium. We also evaluated the method on complex microbial aggregates obtained from human oral biofilms. In both samples, we found evidence for metabolic interactions by visualizing the fate of substrates labeled with (13)C-carbon and (15)N-nitrogen, while individual cells were identified simultaneously by halogen labeling via EL-FISH. Our novel approach will facilitate further studies of the ecophysiology of known and uncultured microorganisms in complex environments and communities.     

Design of high-affinity peptide conjugates with optimized fluorescence quantum yield as markers for small peptide transporter PEPT1 (SLC15A1)

We employed a computational approach to design and synthesize a series of fluorescently labeled hPEPT1 substrates. Five Alexa Fluor-350-labeled peptides were assessed for their in vitro inhibitory activity in hPEPT1-transfected CHO cells. At least four labeled peptides show potent inhibitory activity toward hPEPT1-mediated uptake of [(3)H]-GlySar and three compounds displayed a significant cellular uptake specifically mediated by hPEPT1.     

Preparation of lysozyme immobilized on textile carriers and its use in treating suppurative wounds

Immobilized forms of lysozyme were prepared by its covalent binding on dialdehyde cellulose and polycaproamide fibres as woven and knitted fabrics respectively. The preparations were estimated by the content of protein and bacteriolytic activity. The lysozyme activity per 1 g of the carrier and the protein content on dialdehyde cellulose were several times higher than those on polycaproamide while the specific activity of lysozyme on the polycaproamide carrier was somewhat higher than that on dialdehyde cellulose. The effect of the immobilized lysozyme in treatment of purulent wounds was studied on albino rats. It was shown that the periods of the wound healing with the use of the immobilized lysozyme were shorter than those with the use of native lysozyme. Cytological and morphological investigation of the wound wall confirmed the higher efficacy of the lysozyme immobilized forms in treatment of purulent wounds as compared to the use of the native enzyme.     

Real time visualization of protein kinase activity in living cells.

A library of fluorescently labeled protein kinase C (PKC) peptide substrates was prepared to identify a phosphorylation-induced reporter of protein kinase activity. The lead PKC substrate displays a 2.5-fold change in fluorescence intensity upon phosphorylation. PKC activity is readily sampled in cell lysates containing the activated PKCs. Immunodepletion of conventional PKCs from the cell lysate eliminates the fluorescence response, suggesting that this peptide substrate is selectively phosphorylated by PKCalpha, beta, and gamma. Finally, living cells microinjected with the peptide substrate exhibit a 2-fold increase in fluorescence intensity upon exposure to a PKC activator. These results suggest that peptide-based protein kinase biosensors may be useful in monitoring the temporal and spatial dynamics of PKC activity in living cells.     

Towards single-molecule DNA sequencing: assays with low nonspecific adsorption

New DNA sequencing techniques are currently being developed using single-molecule fluorescence-based detection of enzymatic double-strand synthesis. Such application requires surface architectures on which single-stranded templates can be immobilized. A further important attribute is a very low tendency to attract fluorescently labeled bases nonspecifically. On this account, the adsorption behaviour of Cy5-dNTPs on a variety of surface coatings was studied by performing real-time measurements of the DNA synthesis using a supercritical angle fluorescence biosensor. It is demonstrated that polyacrylic acid coatings are an excellent choice to minimize the nonspecific binding of the bases.     

The DFPase from Loligo vulgaris in sugar surfactant-based bicontinuous microemulsions: structure, dynamics, and enzyme activity

The enzyme diisopropyl fluorophosphatase (DFPase) from the squid Loligo vulgaris is of great interest because of its ability to catalyze the hydrolysis of highly toxic organophosphates. In this work, the enzyme structure in solution (native state) was studied by use of different scattering methods. The results are compared with those from hydrodynamic model calculations based on the DFPase crystal structure. Bicontinuous microemulsions made of sugar surfactants are discussed as host systems for the DFPase. The microemulsion remains stable in the presence of the enzyme, which is shown by means of scattering experiments. Moreover, activity assays reveal that the DFPase still has high activity in this complex reaction medium. To complement the scattering experiments cryo-SEM was also employed to study the microemulsion structure.     

Heat denaturation enhanced immunoglobulin production stimulating activity of lysozyme from hen egg white

Lysozyme from hen egg white was identified as an immunoglobulin production stimulating factor (IPSF) that enhances immunoglobulin production by hybridomas and lymphocytes. The IPSF activity of lysozyme was facilitated by heat treatment. The heat treatment of lysozyme at 83 degrees C for 30 min activated its specific IPSF effect 30.0-fold compared with that of native lysozyme. The IPSF activity of lysozyme heat-treated at 83 degrees C in 4 M urea solution was enhanced 8.4-fold than that of native lysozyme. However, lysozyme that was not heated in 4 M urea solution completely lost its IPSF activity. This means that the IPSF activity of this enzyme in 4 M urea was reactivated by thermal treatment. Moreover, coexistence of 0.5 mM 2-mercaptoethanol (2-ME) during heating in 4 M urea solution extremely enhanced the IPSF activity up to 77.8-fold. The uptake of lysozyme by hybridoma cells was enhanced by heat denaturation in 4 M urea. The hydrophobicity of lysozyme was extremely increased by heat-treatment in 2-ME containing urea solution. It is expected from these findings that the increase in the hydrophobicity caused the enhancement of incorporation of lysozyme into target cells, and resulted in the acceleration of IgM production.     

Immobilized lipase on porous silica particles: Preparation and application for biodegradable polymer syntheses in ionic liquid at higher temperature

Porous silica particles (PSP) modified with different surface active groups were prepared for covalent immobilization of porcine pancreas lipase (PPL). Organosilanes combined with reactive end amino-group or epoxy-group were employed for the modification through silanization process. Polyethylenimine and long chain alkyl silane coupling agent were also used in the modification process. Several modification-immobilization strategies were performed, while good coupling yield could be achieved within the range of 86.2–158.2 mg of native PPL per gram of the carrier. Furthermore, at higher temperature, the resulting immobilized PPL (IPPL) could successfully perform the syntheses of polycaprolactone (PCL) and poly(5,5-dimethyl-1,3-dioxan-2-one) (PDTC) in ionic liquid medium. No polymers could be obtained catalyzed by native PPL, suggesting that IPPL showed much higher catalytic activity than native PPL. Effect of different treatments on the activity of IPPL also showed the long time high temperature stability in ionic liquid medium, contributing to a good combination of immobilization and ionic liquids effect. The catalytic activity of IPPL for polymerization was closely related to both the properties of immobilized enzyme and cyclic monomer. This work would be expected to highlight further careful design of immobilized enzyme for a wide range of application, especially in biodegradable polymers syntheses.     

Ubiquitin-lysozyme conjugates. Purification and susceptibility to proteolysis

To produce ubiquitinated substrates for studies on ATP-dependent proteolysis, 125I-lysozyme was incubated in hemin-inhibited rabbit reticulocyte lysates. A portion of the labeled molecules became linked to ubiquitin in large covalent complexes. When these were partially purified and returned to uninhibited lysates containing ATP, the conjugated lysozyme molecules were degraded 10 times faster than free lysozyme. Purification of covalently modified lysozyme from hemin-inhibited lysates containing 125I-ubiquitin and 131I-lysozyme confirmed that both molecules were present in the complexes. The doubly labeled conjugates also permitted us to determine the fate of each molecule in uninhibited lysates. Besides degradation of lysozyme, there was a progressive release of intact lysozyme molecules from the complexes. This disassembly, which was the only fate of the complexes in the absence of ATP, proceeded through a series of smaller intermediates, several having molecular weights expected for ubiquitin-lysozyme conjugates, and eventually free lysozyme was regenerated. The behavior of labeled ubiquitin was similar, though not identical, to that of lysozyme. Even in lysates containing ATP ubiquitin emerged from the complex undegraded. Furthermore, ubiquitin was present in a greater number of species than was lysozyme. The demonstration that ubiquitin-lysozyme conjugates are rapidly degraded provides support for the hypothesis of Hershko, Rose, Ciechanover, and their colleagues that a key function of ubiquitin is to modify the proteolytic substrate. Further support for the hypothesis is presented in the following paper where we show that the conjugated lysozyme molecules are substrates for an ATP-dependent protease that does not degrade free lysozyme.     

Purification of a DFP-hydrolyzing enzyme from squid head ganglion

An enzyme which hydrolyzes DFP and similar organophosphorus compounds has been purified 1300-fold from squid head ganglion. This enzyme which we term squid nerve DFPase is markedly different from previously reported DFPases from mammalian and microbial sources. The enzyme shows marked selectivity with respect to substrates, permitting some speculation about the nature of its active site. A striking feature of squid nerve DFPase is its relative limitation to cephalopod nerve. Available evidence suggests that a similar distribution may exist for isethionate, the major anion in squid nerve. This tentative parallel between DFPase and isethionate raises the possibility of a function for squid nerve DFPase.     

Solid-phase chemical amination of a lipase from Bacillus thermocatenulatus to improve its stabilization via covalent immobilization on highly activated glyoxyl-agarose

In this paper, the stabilization of a lipase from Bacillus thermocatenulatus (BTL2) by a new strategy is described. First, the lipase is selectively adsorbed on hydrophobic supports. Second, the carboxylic residues of the enzyme are modified with ethylenediamine, generating a new enzyme having 4-fold more amino groups than the native enzyme. The chemical amination did not present a significant effect on the enzyme activity and only reduced the enzyme half-life by a 3-4-fold factor in inactivations promoted by heat or organic solvents. Next, the aminated and purified enzyme is desorbed from the support using 0.2% Triton X-100. Then, the aminated enzyme was immobilized on glyoxyl-agarose by multipoint covalent attachment. The immobilized enzyme retained 65% of the starting activity. Because of the lower p K of the new amino groups in the enzyme surface, the immobilization could be performed at pH 9 (while the native enzyme was only immobilized at pH over 10). In fact, the immobilization rate was higher at this pH value for the aminated enzyme than that of the native enzyme at pH 10. The optimal stabilization protocol was the immobilization of aminated BTL2 at pH 9 and the further incubation for 24 h at 25 degrees C and pH 10. This preparation was 5-fold more stable than the optimal BTL2 immobilized on glyoxyl agarose and around 1200-fold more stable than the enzyme immobilized on CNBr and further aminated. The catalytic properties of BTL2 could be greatly modulated by the immobilization protocol. For example, from (R/S)-2- O-butyryl-2-phenylacetic acid, one preparation of BTL2 could be used to produce the S-isomer, while other preparation produced the R-isomer.