A novel approach to chemical microarray using ketone-modified macromolecular scaffolds: Application in micro cell-adhesion assay

This paper describes a novel strategy for the preparation of chemical microarrays using macro-molecular scaffolds. The macromolecular scaffolds are first functionalized with ketone groups and compounds of interest containing an aminooxy group are conjugated onto the ketone-modified scaffolds through a chemoselective oxime ligation. The conjugate mixtures are then spotted directly onto a plastic or glass surface to form compound microarrays. Because a constant amount of scaffold is used in the presence of excess compound in the ligation reaction, the amount of compound actually immobilized per microarray spot is constant and dependent on the scaffold concentration. Using this approach, 60 different peptides were ligated to human serum albumin or agarose scaffolds, and the peptide conjugates subsequently printed on glass or polystyrene surface to form microarrays. These peptide microarrays were subsequently evaluated and optimized for binding of Jurkat leukemic cancer cells.     

UV resonance Raman spectroscopy probes the amide II′p band position in short breast milk peptides with antioxidant activity

UV resonance Raman spectroscopic study of six short proline‐containing peptides with antioxidant activity isolated from human breast milk was performed. The amide II′ proline spectroscopic band was used to estimate relative cis trans isomerization state of proline amide bonds in the different peptides. Antioxidant activity of the peptides was determined using 1,1‐diphenyl‐2‐picryl‐hydrazyl (DPPH) assay and linoleic acid emulsion assay. Although no clear correlation between the amide II′p position and antioxidant activity of the peptides was observed, they both were found to be sensitive to the presence and/or relative position of proline and tyrosine residues in the peptide. Copyright © 2011 John Wiley & Sons, Ltd.     

Profiling of generic anti-phosphopeptide antibodies and kinases with peptide microarrays using radioactive and fluorescence-based assays

Kinases represent one of the largest enzyme families and key regulatory proteins in the cell. Only a small subset of these enzymes has been characterised so far. We have prepared different types of phosphopeptide and peptide microarrays displaying peptides deduced from annotated human phosphorylation sites and cytoplasmic domains of all annotated human membrane proteins. This approach was enabled by fully-automated high throughput micro-scale synthesis of peptides by the SPOT technology combined with chemo-selective immobilisation on modified glass slides. The phosphopeptide microarrays displaying 2923 peptides in total have been used for the characterisation of commercially available generic anti-phosphopeptide antibodies. This enabled us to detect Abl kinase activity on a microarray with anti-phosphotyrosine antibodies yielding results comparable to those obtained from a radioactive assay. More than 13 000 peptides deposited on six glass slides were used to profile casein kinase 2 (CK2) using a radioactive assay, since no generic antibody for the reliable detection of serine or threonine phosphorylation could be identified. All previously identified substrates were detected in the microarray experiment. In order to confirm whether substrates on the microarray are substrates in solution phase assays, more than 700 peptides were synthesised and tested with CK2 in a solution phase assay. All substrates identified in the solution phase assay were also detected on the microarray.     

Peptide arrays with designed α-helical structures for characterization of proteins from FRET fingerprint patterns

A practical high-throughput protein detection system is described, based on synthetic peptide arrays consisting of designed alpha-helical peptides, detected by fluorescence resonance energy transfer (FRET). Initially a model alpha-helical peptide known to interact with a structured protein, calmodulin, was selected to establish the strategy for high-throughput detection. In comparison to peptides with a single probe, a much higher FRET response has been observed with two fluorescent probes (7-diethylaminocoumarin-3-carboxylic acid and 5(6)-carboxy-fluorescein) at both termini of the synthetic peptides. To establish a reproducible high-throughput detection system, peptides were also immobilized onto a solid surface for detection of the target proteins. A small library of 112 different peptides was constructed, based on a model of the alpha-helical peptide with systematic replacement of residues carrying specific charges and/or hydrophobicities. The library was used to effectively characterize various proteins, giving their own 'protein fingerprint' patterns. The resulting 'protein fingerprints' correlate with the recognition properties of the proteins. The present microarray with designed synthetic peptides as the capturing agents is promising for the development of protein detection chips.     

Covalent and non-covalent binding in the ion/ion charge inversion of peptide cations with benzene-disulfonic acid anions

Protonated angiotensin II and protonated leucine enkephalin-based peptides, which included YGGFL, YGGFLF, YGGFLH, YGGFLK and YGGFLR, were subjected to ion/ion reactions with the doubly deprotonated reagents 4-formyl-1,3-benzenedisulfonic acid (FBDSA) and 1,3-benzenedisulfonic acid (BDSA). The major product of the ion/ion reaction is a negatively charged complex of the peptide and reagent. Following dehydration of [M + FBDSA-H](-) via collisional-induced dissociation (CID), angiotensin II (DRVYIHPF) showed evidence for two product populations, one in which a covalent modification has taken place and one in which an electrostatic modification has occurred (i.e. no covalent bond formation). A series of studies with model systems confirmed that strong non-covalent binding of the FBDSA reagent can occur with subsequent ion trap CID resulting in dehydration unrelated to the adduct. Ion trap CID of the dehydration product can result in cleavage of amide bonds in competition with loss of the FBDSA adduct. This scenario is most likely for electrostatically bound complexes in which the peptide contains both an arginine residue and one or more carboxyl groups. Otherwise, loss of the reagent species from the complex, either as an anion or as a neutral species, is the dominant process for electrostatically bound complexes. The results reported here shed new light on the nature of non-covalent interactions in gas phase complexes of peptide ions that can be used in the rationale design of reagent ions for specific ion/ion reaction applications.     

Characterization of bioactive RGD peptide immobilized onto poly(acrylic acid) thin films by plasma polymerization

Plasma surface modification can be used to improve the surface properties of commercial pure Ti by creating functional groups to produce bioactive materials with different surface topography. In this study, a titanium surface was modified with acrylic acid (AA) using a plasma treatment and immobilized with bioactive arginine-glycine-aspartic acid (RGD) peptide, which may accelerate the tissue integration of bone implants. Both terminals containing the -NH₂ of RGD peptide sequence and -COOH of poly(acrylic acid) (PAA) thin film were combined with a covalent bond in the presence of 1-ethyl-3-3-dimethylaminopropyl carbodiimide (EDC). The chemical structure and morphology of AA film and RGD immobilized surface were investigated by X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FT-IR), atomic force microscopy (AFM), and scanning electron microscopy (SEM). All chemical analysis showed full coverage of the Ti substrate with the PAA thin film containing COOH groups and the RGD peptide. The MC3T3-E1 cells were cultured on each specimen, and the cell alkaline phosphatase (ALP) activity were examined. The surface-immobilized RGD peptide has a significantly increased the ALP activity of MC3T3-E1 cells. These results suggest that the RGD peptide immobilization on the titanium surface has an effect on osteoblastic differentiation of MC3T3-E1 cells and potential use in osteo-conductive bone implants.     

Identification of cyclized calmodulin antagonists from a phage display random peptide library

Summary To isolate peptide ligands that bound calmodulin (CaM) specifically, we screened an M13 phage library displaying cyclized octamer random peptides with immobilized bovine CaM. Isolates were recovered, sequenced, and deduced to express nine independent peptides, five of which contained the sequence Trp-Gly-Lys (WGK). Four of the nine peptide sequences were synthesized in cyclized, biotinylated form. All of the peptides required Ca²⁺ to bind CaM. The cyclized, disulfide-bonded form of one such peptide, SCLRWGKWSNCGS, bound CaM better than its reduced form or an analogue in which the cysteine residues were replaced by serine. The cyclized peptide also exhibited the ability to inhibit CaM-dependent kinase activity. Systematic alanine substitution of residues in this peptide sequence implicate the tryptophan residue as being critical for binding, with other residues contributing to binding to varying degrees. Cloning of ligand targets (COLT) confirmed the specificity of one of the cyclized peptides, yielding full-length and C-terminal CaM clones, in addition to a full-length clone of troponin C, a CaM-related protein. This study has demonstrated that conformationally constrained peptides isolated from a phage library acted as specific, Ca²⁺-dependent CaM ligands.     

Asymmetry of calmodulin revealed by peptide binding

The binding of amphiphilic peptides to calmodulin has been studied using fluorescence energy transfer techniques. Calmodulin has no tryptophan residues but possesses two tyrosines (at positions 99 and 138) in the C-terminal half of the protein. The peptides have a single tryptophan which serves as energy acceptor for the protein tyrosine fluorescence. For the binding of mastoparan or peptide Baa17, with a tryptophan at position 3, the observed quenching of the tyrosine fluorescence of over a factor of 2 corresponds to an average tyrosine-trytophan distance of less than 14 Å. These results indicate that the peptides binds preferentially with the tryptophan in the C-terminal half of the protein.     

Synthesis and solid state NMR characterization of novel peptide/silica hybrid materials

The successful synthesis and solid state NMR characterization of silica-based organic–inorganic hybrid materials is presented. For this, collagen-like peptides are immobilized on carboxylate functionalized mesoporous silica (COOH/SiO_x) materials. A pre-activation of the silica material with TSTU (O-(N-Succinimidyl)-N,N,N′,N′-tetramethyluronium tetrafluoroborate) is performed to enable a covalent binding of the peptides to the linker. The success of the covalent immobilization is indicated by the decrease of the ¹³C CP-MAS NMR signal of the TSTU moiety. A qualitative distinction between covalently bound and adsorbed peptide is feasible by ¹⁵N CP-MAS Dynamic Nuclear Polarization (DNP). The low-field shift of the ¹⁵N signal of the peptide's N-terminus clearly identifies it as the binding site. The DNP enhancement allows the probing of natural abundance ¹⁵N nuclei, rendering expensive labeling of peptides unnecessary.     

Intraarticular application of superparamagnetic nanoparticles and their uptake by synovial membrane—an experimental study in sheep

A superparamagnetic iron oxide nanoparticle, coated with polyvinyl alcohol, (PVA-SPION) and its fluorescently functionalized analogue (amino-PVA-Cy3.5-SPION) were compared in vivo as proof of principle for future use in magnetic drug targeting in inflammatory joint diseases. They were injected either intraarticularly or periarticularly and their uptake by cells of the synovial membrane was evaluated. Uptake was completed in 48 h and was enforced by an extracorporally applied magnet.     

Use of peptide for selective and sensitive detection of an Anthrax biomarker via peptide recognition and surface‐enhanced Raman scattering

A short 16‐amino acid peptide has been used in place of an antibody to selectively detect the specific Anthrax biomarker, protective antigen (PA), using surface‐enhanced Raman scattering (SERS). Peptides are more stable than antibodies under various biological conditions and are easily synthesized for a specific target. A peptide that has high affinity to PA was conjugated onto gold nanoparticles along with a Raman reporter and then incubated in various concentrations of PA. Parallel studies in which the peptide sequence was replaced with an antibody were performed to compare the performance of the two methodologies. Both the peptide and antibody functionalized nanoparticles were able to specifically detect PA concentrations down to 6.1 fM . These results demonstrate that these short, robust peptides can be used in the place of traditional antibodies to specifically recognize target biomarkers in the field for the potential diagnosis of disease. Copyright © 2010 John Wiley & Sons, Ltd.     

Utilization of multiple phage display libraries for the identification of dissimilar peptide motifs that bind to a B7-1 monoclonal antibody

Summary Seven random peptide libraries (two displaying linear peptides and five displaying cysteine-constrained peptides) were constructed as gene III fusion proteins of the bacteriophage fd-tet. These libraries were used to screen a blocking monoclonal antibody raised against B7-1 (CD80), a human cell surface antigen that binds two T cell receptors, CD28 and CTLA-4. After three rounds of screening against the immobilized antibody, 1000-fold enrichment was observed in libraries displaying both linear and cysteineconstrained peptides. DNA sequencing of the enriched phage revealed two distinct consensus sequences: HXG(A/Y)XH and DVCXXGGPGC. Phage expressing these consensus sequences bound to L307.4 but not to an isotype matched antibody, indicating that binding was antibody specific. Synthetic peptides corresponding to both motifs inhibited phage binding to L307.4, indicating that the gene III protein is not required for peptide binding. In addition, the cyclized forms of synthetic peptides containing the DVCXXGGPGC motif were capable of inhibiting L307.4 binding to soluble B7-1/Fc fusion. Moreover, phage expressing only the HXG(A/Y)XH consensus sequence were inhibited from binding to L307.4 by the presence of chelating agents. These results indicate that the framework within which the peptide is presented on the surface of the phage may allow the identification of unique peptide motifs with distinct binding characteristics. These peptide motifs could be used for the design of peptidomimetics with therapeutic applications if they inhibit the binding of B7-1 to its T cell receptors.     

Interactions of lactoferricin B derivatives with model cell membrane studied by Raman spectroscopy

In this work, we employed Raman spectroscopy to study the effect of the antimicrobial peptide lactoferricin B (LfB) on model cell membranes. We used two derivatives of LfB (RRWQWRMKKLG and RRWQWR) with broad‐spectrum activity against gram‐positive and gram‐negative bacteria, fungus, viruses and tumors. Raman spectra of the peptides showed no conformational change in the temperature range 4–60 °C. The positions of the amide I and amide III bands suggest that in an aqueous solution these peptides preferentially adopt a random coil‐like conformation. We also investigated the effect the peptides had on the melting behavior of model cell membranes composed of zwitterionic lipid dipalmitoylglycero‐phosphocholine (DPPC) and anionic lipid dipalmitoylglycero‐phosphoglycerol (DPPG). Raman CH stretching bands were used to follow the melting of the lipid vesicles. We found that the melting of DPPC lipid vesicles is not affected by the presence of the peptides, while the presence of the peptides reduced cooperativity of the phase transition for anionic DPPG vesicle, suggesting that both peptides interact strongly and specifically with this model cell membrane composed of anionic lipid. Copyright © 2006 John Wiley & Sons, Ltd.     

Effect of ultrasonic treatment on the stability and release of selenium-containing peptide TSeMMM-encapsulated nanoparticles in vitro and in vivo

Rice selenium-containing peptide TSeMMM (T) with immunomodulatory functions was isolated from selenium-enriched rice protein hydrolysates. However, its biological activity is difficult to be protected in complex digestive environments. In this study, T was encapsulated within zein and gum arabian (GA) through ultrasound treatment to improve its bioactivity and bioavailability. The zein@T/GA nanoparticles were formed using ultrasonic treatment at 360 W for 5 min with a 59.9% T-encapsulation efficiency. In vitro digestion showed that the cumulative release rate of zein@T/GA nanoparticles reached a maximum of 80.69% after 6 h. In addition, short-term animal studies revealed that the nanoparticles had an effect on the levels of tissue glutathione and improved peptides’ oral bioavailability. Conclusively, these findings suggest that the ultrasonicated polysaccharide/protein system is suitable for encapsulating active small molecular peptides. Furthermore, it provides a novel foundation for studying the bioavailability of active substances in functional foods.     

Functionalized TiO<Subscript>2</Subscript> nanoparticles labelled with <Superscript>225</Superscript>Ac for targeted alpha radionuclide therapy

The ²²⁵Ac radioisotope exhibits very attractive nuclear properties for application in radionuclide therapy. Unfortunately, the major challenge for radioconjugates labelled with ²²⁵Ac is that traditional chelating moieties are unable to sequester the radioactive daughters in the bioconjugate which is critical to minimize toxicity to healthy, non-targeted tissues. In the present work, we propose to apply TiO₂ nanoparticles (NPs) as carrier for ²²⁵Ac and its decay products. The surface of TiO₂ nanoparticles with 25 nm diameter was modified with Substance P (5-11), a peptide fragment which targets NK1 receptors on the glioma cells, through the silan-PEG-NHS linker. Nanoparticles functionalized with Substance P (5-11) were synthesized with high yield in a two-step procedure, and the products were characterized by transmission electron microscopy (TEM), dynamic light scattering (DLS) and thermogravimetric analysis (TGA). The obtained results show that one TiO₂-bioconjugate nanoparticle contains in average 80 peptide molecules on its surface. The synthesized TiO₂-PEG-SP(5-11) conjugates were labelled with ²²⁵Ac by ion-exchange reaction on hydroxyl (OH) functional groups on the TiO₂ surface. The labelled bioconjugates almost quantitatively retain ²²⁵Ac in phosphate-buffered saline (PBS), physiological salt and cerebrospinal fluid (CSF) for up to 10 days. The leaching of ²²¹Fr, a first decay daughter of ²²⁵Ac, in an amount of 30% was observed only in CSF after 10 days. The synthesized ²²⁵Ac-TiO₂-PEG-SP(5-11) has shown high cytotoxic effect in vitro in T98G glioma cells; therefore, it is a promising new radioconjugate for targeted radionuclide therapy of brain tumours.     

Chemical synthesis of TASP arrays and their application in protein design

A combinatorial synthesis of de novo proteins is described. The concept of template-assembled synthetic proteins (TASP) has been adapted to an orthogonal assembly of small libraries of purified peptide building blocks. It is combined with the spot synthesis of peptides which is exploited to array cyclic decapeptide templates on cellulose membranes. A cleavable linker on the cellulose allows control of the synthesis. The hydrophilic proteins are constructed by successive cleavage of orthogonal protecting groups on the template, followed by coupling of amphipathic helices in a predefined orientation and finally by incorporation of a cofactor. Libraries of peptides with variation of the amino acids expected to be close to the cofactor were coupled to the cellulose-bound template in all combinations, yielding up to 500 variants of a protein. Cofactors have been inserted either at non-covalent binding sites as heme and Cu2+ or by covalent modification of amino acids as Ru-bipyridine or flavin. The proteins were screened by recording their UV-vis spectra directly on the solid support. The properties screened include the redox potential of heme proteins, charge transfer bands indicating the ligation of Cu-centers, enzymatic activity, and folding stability. Synthesis of the best hits as soluble variants was used for detailed characterization. Iterative improvement in a second screening cycle was efficient in finding novel copper proteins. We discuss the prospects of synthesizing proteins by extending the concept to beta-sandwich proteins and construction of efficient peptide libraries with computer-supported design, as well as the possible usage of improved solid phase materials.     

Controlled immobilization of peptide nanotube-templated metallic wires on Au surfaces

Peptide nanotubes were immobilized on Au substrates functionalized with self-assembled monolayers of 4-mercaptobenzoic acid in a pH 6 citric acid solution via hydrogen bonds between the peptide nanotubes and the monolayers. Subsequently, the immobilized nanotubes were metallized by nickel via the electroless coating process. Received 30 November 2000     

Real-Time Detection of Polymerase Activity Using Supercritical Angle Fluorescence

We investigated the incorporation efficiencies of different fluorescently labelled dNTPs with polymerases by complementary strand synthesis. For this reason single stranded DNA was immobilized on a coverslip and the increase of fluorescence due to the synthesis of the corresponding strand with tagged dNTPs was detected with a supercritical angle fluorescence biosensor in real-time. By comparison of the observed signal intensities it was possible to conclude that the system Cy5-dCTP-Klenow (exonuclease free) fragment gives the best incorporation yield of the investigated enzymes and dNTPs.     

REDOR NMR on a hydrophobic peptide in oriented membranes

A method is presented for the calculation of REDOR dephasing for specifically labeled membrane-spanning peptides in uniformly aligned lipid bilayers under magic angle oriented sample spinning (MAOSS) conditions. Numerical simulations are performed for dephasing of (13)C signal by (15)N when the labels are placed in an alpha-helical peptide at the carbonyl of residue (i) and amide nitrogen of residue (i + 2) to show the dependency of REDOR echo intensity on the peptide tilt angle relative to the membrane normal. The approach was applied to the labeled transmembrane domain of phospholamban ([(15)N-Leu(37), (13)C-Leu(39)]PLBTM) incorporated into dimyristoylphosphatidylcholine bilayers. The dephasing observed for a random membrane dispersion showed that the peptide was alpha-helical in the region including the two labels, and dephasing in oriented membranes showed that the peptide helix was tilted by 25 degrees +/- 7 degrees relative to the bilayer normal. These results agree with those obtained by other spectroscopic methods.     

Nitroxide Side-Chain Dynamics in a Spin-Labeled Helix-Forming Peptide Revealed by High-Frequency (139.5-GHz) EPR Spectroscopy

High-frequency electron paramagnetic resonance (EPR) spectroscopy has been performed on a nitroxide spin-labeled peptide in fluid aqueous solution. The peptide, which follows the single letter sequence, was reacted with the methanethiosulfonate spin label at the cysteine sulfur. The spin sensitivity of high-frequency EPR is excellent with less than 20 pmol of sample required to obtain spectra with good signal-to-noise ratios. Simulation of the temperature-dependent spectral lineshapes reveals the existence of local anisotropic motion about the nitroxide N-O bond with a motional anisotropy tau( perpendicular)/tau( parallel) ( identical with N) approaching 2.6 at 306 K. Comparison with previous work on rigidly labeled peptides suggests that the spin label is reorienting about its side-chain tether. This study demonstrates the feasibility of performing 140-GHz EPR on biological samples in fluid aqueous solution.