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Find video protocols related to scientific articles indexed in Pubmed.
Different interfacial behaviors of peptides chemically immobilized on surfaces with different linker lengths and via different termini.
J Phys Chem B
PUBLISHED: 03-06-2014
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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 ?-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 ?-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.
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Different interfacial behaviors of N- and C-terminus cysteine-modified cecropin P1 chemically immobilized onto polymer surface.
Langmuir
PUBLISHED: 09-03-2013
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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 ?M. This research shows the different interaction mechanisms between CP1c and PS-MA and between cCP1 and PS-MA.
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RNA aptasensor for rapid detection of natively folded type A botulinum neurotoxin.
Talanta
PUBLISHED: 06-14-2013
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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.
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Effect of interaction with coesite silica on the conformation of Cecropin P1 using explicit solvent molecular dynamics simulation.
J Chem Phys
PUBLISHED: 02-08-2013
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Explicit solvent molecular dynamics (MD) simulation was carried out for the antimicrobial peptides (i) Cecropin P1 and C-terminus cysteine modified Cecropin P1 (Cecropin P1 C) in solution, (ii) Cecropin P1 and Cecropin P1 C adsorbed onto coesite -Si - O - and Si - O - H surfaces, and (iii) Cecropin P1 C tethered to coesite -Si - O - surface with either (PEO)(3) or (PEO)(6) linker. Low energy structures for Cecropin P1 and Cecropin P1 C in solution consists of two regions of high ? helix probability with a sharp bend, consistent with the available structures of other antimicrobial peptides. The structure of Cecropin P1 C at low ionic strength of 0.02 M exhibits two regions of high ? helix probability (residues AKKLEN and EGI) whereas at higher ionic strength of 0.12 M, the molecule was more compact and had three regions of higher ? helix probability (residues TAKKLENSA, ISE, and AIQG) with an increase in ? helical content from 15.6% to 18.7% as a result of shielding of electrostatic interactions. In the presence of Cecropin P1 C in the vicinity of -Si - O - surface, there is a shift in the location of two peaks in H - O - H density profile to larger distances (2.95 Å and 7.38 Å compared to 2.82 Å and 4.88 Å in the absence of peptide) with attenuated peak intensity. This attenuation is found to be more pronounced for the first peak. H-bond density profile in the vicinity of -Si - O - surface exhibited a single peak in the presence of Cecropin P1 C (at 2.9 Å) which was only slightly different from the profile in the absence of polypeptide (2.82 Å) thus indicating that Cecropin P1 C is not able to break the H-bond formed by the silica surface. The ? helix probability for different residues of adsorbed Cecropin P1 C on -Si - O - surface is not significantly different from that of Cecropin P1 C in solution at low ionic strength of 0.02 M whereas there is a decrease in the probability in the second (residues ISE) and third (residues AIQG) ? helical regions at higher ionic strength of 0.12 M. Though the total ? helical content of adsorbed and tethered Cecropin P1 C was lower for hydrophilic Si - O - H surface compared to hydrophobic -Si - O -, hydrophobicity of the surface did not significantly affect the ? helix probability of different residues. The conformation of Cecropin P1 C in solution is closer to that of tethered to -Si - O - with (PEO)(6) than that tethered with (PEO)(3) as a result of less surface interaction of tethered polypeptide with a longer linker. At low ionic strength of 0.02 M, tethered Cecropin P1 C to -Si - O - is found to exhibit lower ? helix (13.0%) compared to adsorbed (15.6%) for (PEO)(3) linker with this difference being insignificant for larger (PEO)(6) linker molecule. Experimental values of % ? helix inferred from circular dichroism spectra of Cecropin P1 in solution as well as in adsorbed state on silica surface compared well with the corresponding values obtained from MD simulation thereby validating the simulation procedure.
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Characterization of supported lipid bilayer disruption by chrysophsin-3 using QCM-D.
J Phys Chem B
PUBLISHED: 12-05-2011
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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 ?M demonstrated changes in frequency (?f) and energy dissipation (?D) that were near zero, indicating little change in the membrane. At higher concentrations of chyrsophsin-3 (0.25-4 ?M), decreases in ?f 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 ?M, 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.
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Supramolecular electrostatic nanoassemblies for bacterial forensics.
Chemistry
PUBLISHED: 07-13-2011
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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).
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Solvent effect and time-dependent behavior of C-terminus-cysteine-modified cecropin P1 chemically immobilized on a polymer surface.
Langmuir
PUBLISHED: 05-09-2011
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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.
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Chemical modification of M13 bacteriophage and its application in cancer cell imaging.
Bioconjug. Chem.
PUBLISHED: 05-27-2010
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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.
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In vitro selection of RNA aptamers that inhibit the activity of type A botulinum neurotoxin.
Biochem. Biophys. Res. Commun.
PUBLISHED: 04-29-2010
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The category A agent, botulinum neurotoxin (BoNT), 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, we have identified three RNA aptamers through SELEX-process, which bind strongly to the light chain of type A BoNT (BoNT/A) and inhibit the endopeptidase activity, with IC(50) in low nM range. Inhibition kinetic studies reveal low nM K(I) and non-competitive nature of their inhibition. Aptamers are unique group of molecules as therapeutics, and this is first report of their development as an antidote against botulism. These data on K(I) and IC(50) strongly suggest that the aptamers have strong potential as antidotes that can reverse the symptom caused by BoNT/A.
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Binding, inactivation, and adhesion forces between antimicrobial peptide cecropin P1 and pathogenic E. coli.
Colloids Surf B Biointerfaces
PUBLISHED: 05-06-2009
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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.
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Atomic force microscopy study of germination and killing of Bacillus atrophaeus spores.
J. Mol. Recognit.
PUBLISHED: 03-05-2009
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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.
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Detection and classification of related lipopolysaccharides via a small array of immobilized antimicrobial peptides.
Anal. Chem.
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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.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.