Differential presentation of a single antimicrobial peptide is sufficient to identify LPS from distinct bacterial samples.

Rapid detection and identification of bacteria is important for human health, biodefense, and food safety. Small arrays of different antimicrobial peptides (AMPs) enable the identification of lipopolysaccharide (LPS) samples from a variety of bacterial species and strains. A model system for examining how peptide presentation affects LPS detection is the sheep myeloid antimicrobial peptide (SMAP-29), which contains a helix-turn-helix motif. Varying the cysteine attachment site on SMAP-29 controls the three-dimensional presentation of the peptide on the surface, altering the ability of the peptide to discriminate between LPS samples. A small array of only SMAP-29 variants-and no other peptides-is capable of discriminating among LPS samples from multiple bacterial species, as well as between different strains within the same species, with high accuracy.

Selection of RNA Aptamers Against Botulinum Neurotoxin Type A Light Chain Through a Non-Radioactive Approach.

Botulinum neurotoxin (BoNT), a category A agent, is the most toxic molecule known to mankind. The endopeptidase activity of light chain domain of BoNT is the cause for the inhibition of the neurotransmitter release and the flaccid paralysis that leads to lethality in botulism. Currently, antidotes are not available to reverse the flaccid paralysis caused by BoNT. In the present study, a non-radioactive-based systematic evolution of ligands by exponential enrichment (SELEX) process is developed by utilizing surface plasmon resonance to monitor the binding enrichment. Two RNA aptamers have been identified as strong binders against light chain of botulinum neurotoxin type A. These two aptamers showed strong inhibition activity on LCA, with IC50 in nanomolar range. Inhibition kinetic studies reveal mid nanomolar KI and non-competitive nature of their inhibition, suggesting that they have strong potential as antidotes that can reverse the symptom caused by BoNT/A. More importantly, we observed that the 2'-fluorine-pyrimidine-modified RNA aptamers identified here do not change their binding and biological activities. This observation could lead to a cost-effective way for SELEX, by using regular nucleotide during SELEX, and 2'-fluorine-pyrimidine-modified nucleotide for final application to enhance their RNase-resistance.

Bactericidal Hydrogels via Surface Functionalization with Cecropin A.

The immobilization of antimicrobial peptides (AMPs) to surfaces, enabling their utilization in biosensor and antibacterial/antifouling coating applications, is typically performed using rigid, solid support materials such as glass or gold and may require lengthy, temperamental protocols. Here, we employ a hydrogel immobilization platform to afford facile fabrication and surface functionalization while offering improved biocompatibility for evaluating the influence of linker length, surface density, and AMP conjugation site on retained peptide activity. Rapid, interfacial photo-polymerization using the radical-mediated thiol-ene addition mechanism was used to generate cross-linked, polymeric coatings bearing residual thiol moieties on prefabricated poly(ethylene glycol) (PEG)-based hydrogel supports. The photo-polymerized coatings were 60 µm thick and contained 0.55 nmol of unreacted free thiols, corresponding to a concentration of 410 µM, for use as cecropin A (CPA) immobilization handles via thiol-maleimide conjugation, where the CPA-bound maleimide moiety was localized at either the carboxyl terminus or midsequence between Ala22 and Gly23. Surface presentation of the thiol handles was controlled by varying the thiolated PEG monomer (PEGSH) used in the photo-polymerizable formulation. Bactericidal activity of CPA functionalized hydrogels against E. coli K235 indicated that CPA immobilized at the carboxyl terminus killed 94 ± 6% of the inoculated pathogens when coatings were prepared with high molecular weight PEGSH and 99 ± 1% when prepared with low molecular weight PEGSH. E. coli cell death demonstrated a stronger dependence on peptide concentration than PEG linker length or degree of thiol functionalization, with activity ranging from 34 ± 13% to 99 ± 1% bacterial cells killed as the prefunctionalization thiol concentration in the coatings was increased from 90 to 990 µM. Finally, the immobilization site on the surface-bound CPA strongly affected antibacterial activity; when midsequence modified CPA was bound to a hydrogel coating bearing 990 µM thiol, only 20 ± 4% of the E. coli population was killed.

Different interfacial behaviors of peptides chemically immobilized on surfaces with different linker lengths and via different termini.

Molecular structures such as conformation and orientation are crucial in determining the activity of peptides immobilized to solid supports. In this study, sum frequency generation (SFG) vibrational spectroscopy was applied to investigate such structures of peptides immobilized on self-assembled monolayers (SAMs). Here cysteine-modified antimicrobial peptide cecropin P1 (CP1) was chemically immobilized onto SAM with a maleimide terminal group. Two important characteristics, length of the poly(ethylene glycol) (PEG) segment in the SAM and location of the cysteine residue in the peptide, were examined using SFG spectroscopy to determine the effect of each on surface immobilization as well as peptide secondary structure and its orientation in the immobilized state. Results have shown that while each length of PEG chain studied promotes chemical immobilization of the target peptide and prevents nonspecific adsorption, CP1 immobilized on long-chain (PEG2k) maleimide SAMs shows random coil structure in water, whereas CP1 demonstrates α-helical structure when immobilized on short-chain (with four ethylene glycol units - (EG4)) maleimide SAMs. Placement of the cysteine residue at the C-terminus promotes the formation of α-helical structure of CP1 with a single orientation when tethered to EG4 maleimide SAM surfaces. In contrast, immobilization via the N-terminal cysteine of CP1 results in a random coil or lying-down helical structure. The bacteria capturing/killing capability was tested, showing that the surface-immobilized CP1 molecules via C- and N- terminal cysteine exhibit only slight difference, even though they have different secondary structures and orientations.

RNA aptasensor for rapid detection of natively folded type A botulinum neurotoxin.

A surface plasmon resonance based RNA aptasensor for rapid detection of natively folded type A botulinum neurotoxin is reported. Using detoxified recombinant type A botulinum neurotoxin as the surrogate, the aptasensor detects active toxin within 90 min. The detection limit of the aptasensor in phosphate buffered saline, carrot juice, and fat free milk is 5.8 ng/ml, 20.3 ng/ml and 23.4 ng/ml, respectively, while that in 5-fold diluted human serum is 22.5 ng/ml. Recovery of toxin from disparate sample matrices are within 91-116%. Most significant is the ability of this aptasensor to effectively differentiate the natively folded toxin from denatured, inactive toxin, which is important for homeland security surveillance and threat assessment. The aptasensor is stable for more than 30 days and over 400 injections/regeneration cycles. Such an aptasensor holds great promise for rapid detection of active botulinum neurotoxin for field surveillance due to its robustness, stability and reusability.

Different interfacial behaviors of N- and C-terminus cysteine-modified cecropin P1 chemically immobilized onto polymer surface.

Sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) were used to investigate the orientation of N-terminus cysteine-modified cecropin P1 (cCP1) at the polystyrene maleimide (PS-MA)/peptide phosphate buffer solution interface. The cCP1 cysteine group reacts with the maleimide group on the PS-MA surface to chemically immobilize cCP1. Previously, we found that the C-terminus cysteine-modified cecropin P1 (CP1c) molecules exhibit a multiple-orientation distribution at the PS-MA/peptide phosphate buffer solution interface, due to simultaneous physical adsorption and chemical immobilization of CP1c on the PS-MA surface. Differently, in this research, it was found that the interfacial orientation of cCP1 molecules varied from a horizontal orientation to the "tilting" orientation to the "standing up" orientation and then to the "multiple-orientation" distribution as the peptide concentration increased from 0.19 to 3.74 µM. This research shows the different interaction mechanisms between CP1c and PS-MA and between cCP1 and PS-MA.

Detection and classification of related lipopolysaccharides via a small array of immobilized antimicrobial peptides.

A small array of antimicrobial peptides comprising three cysteine-terminated natural sequences covalently immobilized to pendant surface maleimide groups are used to bind and successfully discriminate five types of lipopolysaccharide (LPS) molecules. Using surface plasmon resonance, LPSs isolated from four strains of Escherichia coli and one strain of Pseudomonas aeruginosa yield distinct binding profiles to the three immobilized peptides. Linear discriminant analysis generated 100% training set and 80% validation set classification success for the 40 samples evaluated. This work demonstrates the discriminatory binding capabilities of immobilized antimicrobial peptides toward LPS molecules and alludes to their use as probes in pathogen sensing devices potentially superior to the current state-of-the-art.

Supramolecular electrostatic nanoassemblies for bacterial forensics.

Electrostatic nanoassemblies were employed to identify bacterial growth conditions. They comprise a cationic conjugated oligoelectrolyte and fluorescein-tagged ssDNA and were optimized with a hybrid, computational neural network model. The photoluminescence spectra contained the oligomer and sensitized fluorescein emission. The spectra changed depending on the growth history of the bacteria introduced (see figure).

Characterization of supported lipid bilayer disruption by chrysophsin-3 using QCM-D.

Antimicrobial peptides (AMPs) are naturally occurring polymers that can kill bacteria by destabilizing their membranes. A quartz crystal microbalance with dissipation monitoring (QCM-D) was used to better understand the action of the AMP chrysophsin-3 on supported lipid bilayers (SLB) of phosphatidylcholine. Interaction of the SLB with chrysophsin-3 at 0.05 µM demonstrated changes in frequency (Δf) and energy dissipation (ΔD) that were near zero, indicating little change in the membrane. At higher concentrations of chyrsophsin-3 (0.25-4 µM), decreases in Δf of up to 7 Hz were measured. These negative frequency changes suggest that mass was being added to the SLB, possibly due to peptide insertion into the membrane. At a chrysophsin-3 concentration of 10 µM, there was a net mass loss, which was attributed to pore formation in the membrane. QCM-D can be used to describe a mechanistic relationship between AMP concentration and interaction with a model cell membrane.

Solvent effect and time-dependent behavior of C-terminus-cysteine-modified cecropin P1 chemically immobilized on a polymer surface.

Sum frequency generation (SFG) vibrational spectroscopy has been applied to the investigation of peptide immobilization on a polymer surface as a function of time and peptide conformation. Surface immobilization of biological molecules is important in many applications such as biosensors, antimicrobial materials, biobased fuel cells, nanofabrication, and multifunctional materials. Using C-terminus-cysteine-modified cecropin P1 (CP1c) as a model, we investigated the time-dependent immobilization behavior in situ in real time. In addition, potassium phosphate buffer (PB) and mixtures of PB and trifluoroethanol were utilized to examine the effect of peptide secondary structure on CP1c immobilization to polystyrene maleimide (PS-MA). The orientation of immobilized CP1c on PS-MA was determined using polarized SFG spectra. It was found that the peptide solution concentration, solvent composition, and assembly state (monomer vs dimer) prior to immobilization all influence the orientation of CP1c on a PS-MA surface. The detailed relationship between the interfacial peptide orientation and these immobilization conditions is discussed.

Chemical modification of M13 bacteriophage and its application in cancer cell imaging.

The M13 bacteriophage has been demonstrated to be a robust scaffold for bionanomaterial development. In this paper, we report on the chemical modifications of three kinds of reactive groups, i.e., the amino groups of lysine residues or N-terminal, the carboxylic acid groups of aspartic acid or glutamic acid residues, and the phenol group of tyrosine residues, on M13 surface. The reactivity of each group was identified through conjugation with small fluorescent molecules. Furthermore, the regioselectivity of each reaction was investigated by HPLC-MS-MS. By optimizing the reaction condition, hundreds of fluorescent moieties could be attached to create a highly fluorescent M13 bacteriophage. In addition, cancer cell targeting motifs such as folic acid could also be conjugated onto the M13 surface. Therefore, dual-modified M13 particles with folic acid and fluorescent molecules were synthesized via the selective modification of two kinds of reactive groups. Such dual-modified M13 particles showed very good binding affinity to human KB cancer cells, which demonstrated the potential applications of M13 bacteriophage in bioimaging and drug delivery.

Orientation difference of chemically immobilized and physically adsorbed biological molecules on polymers detected at the solid/liquid interfaces in situ.

A surface sensitive second order nonlinear optical technique, sum frequency generation vibrational spectroscopy, was applied to study peptide orientation on polymer surfaces, supplemented by a linear vibrational spectroscopy, attenuated total reflectance Fourier transform infrared spectroscopy. Using the antimicrobial peptide Cecropin P1 as a model system, we have quantitatively demonstrated that chemically immobilized peptides on polymers adopt a more ordered orientation than less tightly bound physically adsorbed peptides. These differences were also observed in different chemical environments, for example, air versus water. Although numerous studies have reported a direct correlation between the choice of immobilization method and the performance of an attached biological molecule, the lack of direct biomolecular structure and orientation data has made it difficult to elucidate the relationship between structure, orientation, and function at a surface. In this work, we directly studied the effect of chemical immobilization method on biomolecular orientation/ordering, an important step for future studies of biomolecular activity. The methods for orientation analysis described within are also of relevance to understanding biosensors, biocompatibility, marine-antifouling, membrane protein functions, and antimicrobial peptide activities.

Binding, inactivation, and adhesion forces between antimicrobial peptide cecropin P1 and pathogenic E. coli.

The antimicrobial peptide cecropin P1 (CP1) exhibits broad spectrum activity against planktonic bacteria, including Escherichia coli (E. coli). However, its activity when attached to a substrate has not been thoroughly studied. We immobilized CP1 to gold or silicon nitride, and studied how the method of attachment of peptide to the surface affected peptide interaction with and killing of the bacteria. Using the quartz crystal microbalance with dissipation monitoring (QCM-D), we characterized non-specific binding between CP1 to silicon nitride and gold, and covalent binding of cysteine-terminated CP1 (CP1-cys) to gold. The density of CP1-cys adsorbed on gold was more than the density of CP1 on silicon nitride, and activity against E. coli also depended on the method of attachment used to anchor the peptide to the surface. Twelve E. coli strains with known lipopolysaccharide (LPS) structures were studied. Bacterial adhesion with CP1 was strongest for E. coli with long O-antigens, as determined by atomic force microscopy (AFM). This may be caused by CP1 interacting with the hydrophilic part of the LPS, while control bacteria or those with short O-antigens had their hydrophobic lipid A region more exposed. Killing of E. coli due to contact with CP1 was dependent on the method by which the peptide was immobilized. Four out of 12 E. coli strains were killed when contacted with CP1-cys bound to gold via a thiol bond, while all 12 strains could be killed when in contact with CP1 on silicon nitride. In summary, both QCM-D adsorption experiments and adhesion forces measured by AFM showed a relationship between bacteria LPS length and binding or interaction with the antimicrobial peptide, but killing of E. coli by the peptide was most strongly dependent on how the peptide was attached to the surface.

Atomic force microscopy study of germination and killing of Bacillus atrophaeus spores.

Bacterial spores such as Bacillus atrophaeus are one of the most resistant life forms known and are extremely resistant to chemical and environmental factors in the dormant state. During germination, as bacterial spores progress towards the vegetative state, they become susceptible to anti-sporal agents. B. atrophaeus spores were exposed to the non-nutritive germinant dodecylamine (DDA), a cationic surfactant that can also be used as a killing agent, for up to 60 min, or to the nutrient germinant L-alanine. In kinetic studies, 99% of the spores were killed within 5 min of exposure to DDA. Atomic force microscopy (AFM) can be used as a sensitive tool to assess how the structure of the spore coat changes upon exposure to germinants or killing agents. Changes in cell height and roughness over time of exposure to DDA were examined using AFM. DDA caused the spore height to decrease by >50%, which may have been due to a partial breakdown of the spore coat. Treatment of B. atrophaeus with the nutrient germinant resulted in a decrease in height of spores after 2 h of incubation, from 0.7 +/- 0.1 microm to 0.3 +/- 0.2 microm. However, treatment with L-alanine did not change the surface roughness of the spores, indicating that the changes that occur during germination take place underneath the spore coat. We propose that exposure to DDA at high concentrations causes pores to form in the coat layer, killing B. atrophaeus without the need to fully germinate spores.

Antimicrobial peptide preferential binding of E. coli O157:H7.

The studies presented here explore antimicrobial peptide preferential binding behavior for a target pathogen, Escherichia coli O157:H7. A modified immunoassay and surface plasmon resonance were employed to evaluate immobilized peptide binding of whole bacterial cells. The knowledge gained may guide the rational design of peptides with enhanced species binding selectivity.

Oriented cell growth on self-assembled bacteriophage M13 thin films.

Fibrillar M13 bacteriophages were used as basic building blocks to generate thin films with aligned nanogrooves, which, upon chemical grafting with RGD peptides, guide cell alignment and orient the cell outgrowth along defined directions.

The effects of solution structure on the surface conformation and orientation of a cysteine-terminated antimicrobial peptide cecropin P1.

The surface structure of an antimicrobial peptide, cecropin P1, immobilized to a gold surface via a terminal cysteine residue was investigated. Using reflection-absorption infrared spectroscopy, surface plasmon resonance, and X-ray photoelectron spectroscopy, the effects of pH, solution conformation, and concentration on the immobilized peptide conformation, average orientation, and surface density were determined. Under all conditions investigated, the immobilized peptides were alpha-helical in a predominately flat, random orientation. The addition of the reducing agent Tris(2-carboxyethyl) phosphine hydrochloride to the buffer resulted in a twofold increase in immobilized peptide surface density.

Cy5 labeled antimicrobial peptides for enhanced detection of Escherichia coli O157:H7.

Fluorescently labeled antimicrobial peptides were evaluated as a potential replacement of labeled antibodies in a sandwich assay for the detection of Escherichia coli O157:H7. Antimicrobial peptides naturally bind to the lipopolysaccharide component of bacterial cell walls as part of their mode of action. Because of their small size relative to antibodies peptides can bind to cell surfaces with greater density, thereby increasing the optical signal and improving sensitivity. This method combines the specificity of a capture antibody with the increased sensitivity provided by using a labeled peptide as a detection molecule. The antimicrobial peptides cecropin P1, SMAP29, and PGQ were labeled with the fluorescent dye Cy5 via maleimide linker chemistry. Preliminary screening using a whole-cell solution binding assay revealed that Cy5 cecropin P1 enhanced the detection of E. coli O157:H7 relative to a Cy5 labeled anti-E. coli O157:H7 antibody 10-fold. Detection sensitivity of antibody and peptide were also compared with a prototype immuno-magnetic bead biosensor. Detection using Cy5 cecropin P1 resulted in a 10-fold improvement in sensitivity. Correlation of peptide antimicrobial activity with detection of E. coli O157:H7 indicated that activity was not predictive of the sensitivity of the fluorescent assay.

Synthesis and application of poly(phenylene ethynylene)s for bioconjugation: a conjugated polymer-based fluorogenic probe for proteases.

A set of carboxylate-functionalized poly(phenylene ethynylene)s (PPEs) has been synthesized in which the carboxylic acid groups are separated from the polymer backbone by oligo(ethylene glycol) spacer units. These polymers are soluble in water and organic solvents and have photophysical properties that are sensitive to solvent conditions, with high salt content and the absence of surfactant promoting the formation of aggregates of relatively low quantum yield and long fluorescence lifetime. Quenching of these materials by the dinitrophenyl (DNP) chromophore (K(SV) approximately 10(4)) is also highly solvent-dependent. The presence of carboxylate groups far from the polymer backbone appended to each repeating unit allows for the postpolymerization modification of these PPEs with peptides by methods analogous to those described for carboxylate-functionalized small-molecule dyes. Covalent attachment of the fluorescence-quenching 14-mer Lys(DNP)-GPLGMRGLGGGGK to the PPE results in a nonemissive substrate whose fluorescence is restored upon treatment with trypsin. The rate of fluorescence turn-on in this case is increased 3-fold by the presence of surfactant, though the actual rate of peptide hydrolysis remains the same. A small-molecule mimic of the polymer-peptide system shows a smaller fluorescence enhancement upon treatment with trypsin, illustrating the value of polymer-based amplification in this sensory scheme.

Immobilization of Escherichia coli cells by use of the antimicrobial peptide cecropin P1.

An immobilization scheme for bacterial cells is described, in which the antimicrobial peptide cecropin P1 was used to trap Escherichia coli K-12 and O157:H7 cells on microtiter plate well surfaces. Cecropin P1 was covalently attached to the well surfaces, and E. coli cells were allowed to bind to the peptide-coated surface. The immobilized cells were detected colorimetrically with an anti-E. coli antibody-horseradish peroxidase conjugate. Binding curves were obtained in which the signal intensities were dependent upon the cell concentration and upon the amount of peptide attached to the well surface. After normalization for the amount of peptide coupled to the surface and the relative binding affinity of the antibody for each strain, the binding data were compared, which indicated that there was a strong preference for E. coli O157:H7 over E. coli K-12. The cells could be immobilized reproducibly at pH values ranging from 5 to 10 and at ionic strengths up to 0.50 M.