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Sample records for singly charged peptide

  1. Fragmentation of phosphorylated and singly charged peptide ions via interaction with metastable atoms

    PubMed Central

    Berkout, Vadym D.; Doroshenko, Vladimir M.

    2008-01-01

    Fragmentation of phosphorylated peptide ions via interaction with electronically excited metastable argon atoms was studied in a linear trap – time-of-flight mass spectrometer. Doubly charged ions of phosphorylated peptides from an Enolase digest were produced by electrospray ionization and subjected to a metastable atom beam in the linear trap. The metastable argon atoms were generated using a glow-discharge source. An intensive series of c- and z- ions were observed in all cases, with the phosphorylation group intact. The formation of molecular radical cations with reduced charge indicated that an electron transfer from a highly excited metastable state of argon to the peptide cation occurred. Additionally, singly charged Bradykinin, Substance P and Fibrinopeptide A molecular ions were fragmented via interaction with electronically excited metastable helium atoms. The fragmentation mechanism was different in this case and involved Penning ionization. PMID:19956340

  2. Fragmentation of phosphorylated and singly charged peptide ions via interaction with metastable atoms.

    PubMed

    Berkout, Vadym D; Doroshenko, Vladimir M

    2008-12-01

    Fragmentation of phosphorylated peptide ions via interaction with electronically excited metastable argon atoms was studied in a linear trap - time-of-flight mass spectrometer. Doubly charged ions of phosphorylated peptides from an Enolase digest were produced by electrospray ionization and subjected to a metastable atom beam in the linear trap. The metastable argon atoms were generated using a glow-discharge source. An intensive series of c- and z- ions were observed in all cases, with the phosphorylation group intact. The formation of molecular radical cations with reduced charge indicated that an electron transfer from a highly excited metastable state of argon to the peptide cation occurred. Additionally, singly charged Bradykinin, Substance P and Fibrinopeptide A molecular ions were fragmented via interaction with electronically excited metastable helium atoms. The fragmentation mechanism was different in this case and involved Penning ionization.

  3. Adsorption of insulin peptide on charged single-walled carbon nanotubes: significant role of ordered water molecules.

    PubMed

    Shen, Jia-Wei; Wu, Tao; Wang, Qi; Kang, Yu; Chen, Xin

    2009-06-02

    Ordered hydration shells: The more ordered hydration shells outside the charged CNT surfaces prevent more compact adsorption of the peptide in the charged CNT systems [picture: see text], but peptide binding strengths on the charged CNT surfaces are stronger due to the electrostatic interaction.Studies of adsorption dynamics and stability for peptides/proteins on single-walled carbon nanotubes (SWNTs) are of great importance for a better understanding of the properties and nature of nanotube-based biosystems. Herein, the dynamics and mechanism of the adsorption of the insulin chain B peptide on different charged SWNTs are investigated by explicit solvent molecular dynamics simulations. The results show that all types of surfaces effectively attract the model peptide. Water molecules play a significant role in peptide adsorption on the surfaces of charged carbon nanotubes (CNTs). Compared to peptide adsorption on neutral CNT surfaces, the more ordered hydration shells outside the tube prevent more compact adsorption of the peptide in charged CNT systems. This shield effect leads to a smaller conformational change and van der Waals interaction between the peptide and surfaces, but peptide binding strengths on charged CNT surfaces are stronger than those on the neutral CNT surface due to the strong electrostatic interaction. The result of these simulations implies the possibility of improving the binding strength of peptides/proteins on CNT surfaces, as well as keeping the integrity of the peptide/protein conformation in peptide/protein-CNT complexes by charging the CNTs.

  4. A collision cross-section database of singly-charged peptide ions.

    PubMed

    Tao, Lei; McLean, Janel R; McLean, John A; Russell, David H

    2007-07-01

    A database of ion-neutral collision cross-sections for singly-charged peptide ions is presented. The peptides included in the database were generated by enzymatic digestion of known proteins using three different enzymes, resulting in peptides that differ in terms of amino acid composition as well as N-terminal and C-terminal residues. The ion-neutral collision cross-sections were measured using ion mobility (IM) spectrometry that is directly coupled to a time-of-flight (TOF) mass spectrometer. The ions were formed by a matrix-assisted laser desorption ionization (MALDI) ion source operated at pressures (He bath gas) of 2 to 3 torr. The majority (63%) of the peptide ion collision cross-sections correlate well with structures that are best described as charge-solvated globules, but a significant number of the peptide ions exhibit collision cross-sections that are significantly larger or smaller than the average, globular mobility-mass correlation. Of the peptide ions having larger than average collision cross-sections, approximately 71% are derived from trypsin digestion (C-terminal Arg or Lys residues) and most of the peptide ions that have smaller (than globular) collision cross-sections are derived from pepsin digestion (90%).

  5. Factors that Influence Helical Preferences for Singly-Charged Gas-Phase Peptide Ions: The Effects of Multiple Potential Charge-Carrying Sites

    PubMed Central

    McLean, Janel R.; McLean, John A.; Wu, Zhaoxiang; Becker, Christopher; Pérez, Lisa M; Pace, C. Nick; Scholtz, J. Martin; Russell, David H.

    2009-01-01

    Ion mobility-mass spectrometry is used to investigate the structure(s) of a series of model peptide [M + H]+ ions to better understand how intrinsic properties affect structure in low dielectric environments. The influence of peptide length, amino acid sequence and composition on gas-phase structure is examined for a series of model peptides that have been previously studied in solution. Collision cross-sections for the [M + H]+ ions of Ac-(AAKAA)nY-NH2 (n = 3 – 6) and Ac-Y(AEAAKA)nF-NH2 (n = 2 – 5) are reported and correlated with candidate structures generated obtained using molecular modeling techniques. The [M + H]+ ions of the AAKAA peptide series each exhibit a single, dominant ion mobility arrival time distribution (ATD) which correlates to partial helical structures, whereas the [M + H]+ ions of the AEAAKA ion series are composed of ATDs which correlate to charge-solvated globules (i.e. the charge is coordinated or solvated by polar peptide functional groups). These data raise numerous questions concerning intrinsic properties (amino acid sequence and composition as well as charge location) that dictate gas-phase peptide ion structure, which may reflect trends for peptide ion structure in low dielectric environments, such as transmembrane segments. PMID:20000372

  6. Study of Charge-Dependent Transport and Toxicity of Peptide-Functionalized Silver Nanoparticles Using Zebrafish Embryos and Single Nanoparticle Plasmonic Spectroscopy

    PubMed Central

    Lee, Kerry J.; Browning, Lauren M.; Nallathamby, Prakash D.; Xu, Xiao-Hong Nancy

    2013-01-01

    Nanomaterials possess unusually high surface area-to-volume ratios, and surface-determined physicochemical properties. It is essential to understand their surface-dependent toxicity in order to rationally design biocompatible nanomaterials for a wide variety of applications. In this study, we have functionalized the surfaces of silver nanoparticles (Ag NPs, 11.7 ± 2.7 nm in diameters) with three biocompatible peptides (CALNNK, CALNNS, CALNNE) to prepare positively (Ag-CALNNK NPs+ζ), negatively (Ag-CALNNS NPs−2ζ), and more negatively charged NPs (Ag-CALNNE NPs−4ζ), respectively. Each peptide differs in a single amino acid at its C-terminus, which minimizes the effects of peptide sequences and serves as a model molecule to create positive, neutral and negative charges on the surface of the NPs at pH 4–10. We have studied their charge-dependent transport into early-developing (cleavage-stage) zebrafish embryos and their effects on embryonic development using dark-field optical microscopy and spectroscopy (DFOMS). We found that all three Ag-peptide NPs passively diffused into the embryos via their chorionic pore canals, and stayed inside the embryos throughout their entire development (120 h), showing charge-independent diffusion modes and charge-dependent diffusion coefficients. Notably, the NPs create charge-dependent toxic effects on embryonic development, showing that the Ag-CALNNK NPs+ζ (positively charged) are the most biocompatible while the Ag-CALNNE NPs–4ζ (more negatively charged) are the most toxic. By comparing with our previous studies of the same sized citrated Ag and Au NPs, the Ag-peptide NPs are much more biocompatible than the citrated Ag NPs, and nearly as biocompatible as the Au NPs, showing the dependence of nanotoxicity upon the surface charges, surface functional groups and chemical compositions of the NPs. This study also demonstrates powerful applications of single NP plasmonic spectroscopy for quantitative analysis of single NPs

  7. Study of charge-dependent transport and toxicity of peptide-functionalized silver nanoparticles using zebrafish embryos and single nanoparticle plasmonic spectroscopy.

    PubMed

    Lee, Kerry J; Browning, Lauren M; Nallathamby, Prakash D; Xu, Xiao-Hong Nancy

    2013-06-17

    Nanomaterials possess unusually high surface area-to-volume ratios and surface-determined physicochemical properties. It is essential to understand their surface-dependent toxicity in order to rationally design biocompatible nanomaterials for a wide variety of applications. In this study, we have functionalized the surfaces of silver nanoparticles (Ag NPs, 11.7 ± 2.7 nm in diameter) with three biocompatible peptides (CALNNK, CALNNS, CALNNE) to prepare positively (Ag-CALNNK NPs(+ζ)), negatively (Ag-CALNNS NPs(-2ζ)), and more negatively charged NPs (Ag-CALNNE NPs(-4ζ)), respectively. Each peptide differs in a single amino acid at its C-terminus, which minimizes the effects of peptide sequences and serves as a model molecule to create positive, neutral, and negative charges on the surface of the NPs at pH 4-10. We have studied their charge-dependent transport into early developing (cleavage-stage) zebrafish embryos and their effects on embryonic development using dark-field optical microscopy and spectroscopy (DFOMS). We found that all three Ag-peptide NPs passively diffused into the embryos via their chorionic pore canals, and stayed inside the embryos throughout their entire development (120 h), showing charge-independent diffusion modes and charge-dependent diffusion coefficients. Notably, the NPs create charge-dependent toxic effects on embryonic development, showing that the Ag-CALNNK NPs(+ζ) (positively charged) are the most biocompatible while the Ag-CALNNE NPs(-4ζ) (more negatively charged) are the most toxic. By comparing with our previous studies of the same sized citrated Ag and Au NPs, the Ag-peptide NPs are much more biocompatible than the citrated Ag NPs, and nearly as biocompatible as the Au NPs, showing the dependence of nanotoxicity upon the surface charges, surface functional groups, and chemical compositions of the NPs. This study also demonstrates powerful applications of single NP plasmonic spectroscopy for quantitative analysis of single

  8. Electron induced dissociation of singly deprotonated peptides.

    PubMed

    Kalli, Anastasia; Grigorean, Gabriela; Håkansson, Kristina

    2011-12-01

    Dissociation of singly charged species is more challenging compared with that of multiply charged precursor ions because singly charged ions are generally more stable. In collision activated dissociation (CAD), singly charged ions also gain less kinetic energy in a fixed electric field compared with multiply charged species. Furthermore, ion-electron and ion-ion reactions that frequently provide complementary and more extensive fragmentation compared with CAD typically require multiply charged precursor ions. Here, we investigate electron induced dissociation (EID) of singly deprotonated peptides and compare the EID fragmentation patterns with those observed in negative ion mode CAD. Fragmentation induced upon electron irradiation and collisional activation is not specific and results in the formation of a wide range of product ions, including b-, y-, a-, x-, c-, and z-type ions. Characteristic amino acid side chain losses are detected in both techniques. However, differences are also observed between EID and CAD spectra of the same species, including formation of odd-electron species not seen in CAD, in EID. Furthermore, EID frequently results in more extensive fragmentation compared with CAD. For modified peptides, EID resulted in retention of sulfonation and phosphorylation, allowing localization of the modification site. The observed differences are likely due to both vibrational and electronic excitation in EID, whereas only the former process occurs in CAD.

  9. Electron Induced Dissociation of Singly Deprotonated Peptides

    NASA Astrophysics Data System (ADS)

    Kalli, Anastasia; Grigorean, Gabriela; Håkansson, Kristina

    2011-12-01

    Dissociation of singly charged species is more challenging compared with that of multiply charged precursor ions because singly charged ions are generally more stable. In collision activated dissociation (CAD), singly charged ions also gain less kinetic energy in a fixed electric field compared with multiply charged species. Furthermore, ion-electron and ion-ion reactions that frequently provide complementary and more extensive fragmentation compared with CAD typically require multiply charged precursor ions. Here, we investigate electron induced dissociation (EID) of singly deprotonated peptides and compare the EID fragmentation patterns with those observed in negative ion mode CAD. Fragmentation induced upon electron irradiation and collisional activation is not specific and results in the formation of a wide range of product ions, including b-, y-, a-, x-, c-, and z-type ions. Characteristic amino acid side chain losses are detected in both techniques. However, differences are also observed between EID and CAD spectra of the same species, including formation of odd-electron species not seen in CAD, in EID. Furthermore, EID frequently results in more extensive fragmentation compared with CAD. For modified peptides, EID resulted in retention of sulfonation and phosphorylation, allowing localization of the modification site. The observed differences are likely due to both vibrational and electronic excitation in EID, whereas only the former process occurs in CAD.

  10. Selective isolation of multiply charged peptides: a confident strategy for protein identification using a linear trap quadrupole mass spectrometer.

    PubMed

    Sanchez, Aniel; Sun, Wei; Ma, Jie; Betancourt, Lazaro; Perez-Riverol, Yasset; de-Cossio, Jorge Fernandez; Padron, Gabriel; Jiang, Ying; He, Fuchu; Gonzalez, Luis Javier; Besada, Vladimir

    2012-01-01

    In this work, a method devised for the selective isolation of multiply-charged peptide applied to a complex protein mixture was evaluated for the first time using a mass spectrometer with low resolution (LTQ). In this procedure, all primary amino groups of tryptic peptides derived from human Liver tissue interstitial fluid (TIF) are blocked, restricting their positive charge, at acidic pH, to the presence of histidine and arginine residues. After strong cation exchange chromatography, multiply-charged peptides (#R+#H > 1) are retained in the column and separated with high selectivity from singly (#R+#H = 1) and neutral peptides (#R +#H = 0) which are collected together in the flow-through. Using Liquid chromatography electrospray ionization tandem mass spectrometry analysis the retained fraction displayed a 95% enrichment of multiply charged peptides while in the flow-through; only 4% of multiply-charged peptides were identified.

  11. The partial charge of the nitrogen atom in peptide bonds.

    PubMed Central

    Milner-White, E. J.

    1997-01-01

    A majority of the standard texts dealing with proteins portray the peptide link as a mixture of two resonance forms, in one of which the nitrogen atom has a positive charge. As a consequence, it is often believed that the nitrogen atom has a net positive charge. This is in apparent contradiction with the partial negative charge on the nitrogen that is used in force fields for molecular modeling. However, charges on resonance forms are best regarded as formal rather than actual charges and current evidence clearly favors a net negative charge for the nitrogen atom. In the course of the discussion, new ideas about the electronic structure of amides and the peptide bond are presented. PMID:9385654

  12. Electron Transport in Short Peptide Single Molecules

    NASA Astrophysics Data System (ADS)

    Cui, Jing; Brisendine, Joseph; Ng, Fay; Nuckolls, Colin; Koder, Ronald; Venkarataman, Latha

    We present a study of the electron transport through a series of short peptides using scanning tunneling microscope-based break junction method. Our work is motivated by the need to gain a better understanding of how various levels of protein structure contribute to the remarkable capacity of proteins to transport charge in biophysical processes such as respiration and photosynthesis. We focus here on short mono, di and tri-peptides, and probe their conductance when bound to gold electrodes in a native buffer environment. We first show that these peptides can bind to gold through amine, carboxyl, thiol and methyl-sulfide termini. We then focus on two systems (glycine and alanine) and show that their conductance decays faster than alkanes terminated by the same linkers. Importantly, our results show that the peptide bond is less conductive than a sigma carbon-carbon bond. This work was supported in part by NSF-DMR 1507440.

  13. Statistical Characterization of the Charge State and Residue Dependence of Low Energy CID Peptide Dissociation Patterns

    PubMed Central

    Huang, Yingying; Triscari, Joseph M.; Tseng, George C.; Pasa-Tolic, Ljiljana; Lipton, Mary S.; Smith, Richard D.; Wysocki, Vicki H.

    2013-01-01

    Data mining was performed on 28,330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pair-wise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly-charged Arg- and Lys- ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially-mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton(s) and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton(s). When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions and/or y ions depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially-mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion

  14. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    SciTech Connect

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; Rose, Kristie L.; Tabb, David L.

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.

  15. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    PubMed Central

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel C.; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; Rose, Kristie L.; Tabb, David L.

    2013-01-01

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification. PMID:23499924

  16. Correlation of charge, hydrophobicity, and structure with antimicrobial activity of S1 and MIRIAM peptides.

    PubMed

    Leptihn, Sebastian; Har, Jia Yi; Wohland, Thorsten; Ding, Jeak Ling

    2010-11-02

    Antimicrobial peptides are key elements of the innate immune system. Many of them interact with membranes of bacteria leading to perturbation of the lipid bilayer and eventually to inactivation of the pathogen. The emergence of multidrug-resistant bacteria has necessitated innovations of new and more powerful classes of antimicrobials. Here we present the in-depth study of an antimicrobial peptide, MIRIAM, derived from Sushi1 (S1), a well-characterized peptide from the horseshoe crab. MIRIAM interacts strongly with negatively charged lipids, forming an α-helical structure. MIRIAM was found to neutralize LPS and kill Gram-negative bacteria with high efficiency, while not releasing LPS. The promising therapeutic potential of MIRIAM is shown by hemolytic assays, which demonstrate that eukaryotic membranes are unaffected at bactericidal concentrations. Nanoparticle-conjugated MIRIAM used in single-molecule fluorescence and electron microscopy experiments showed that MIRIAM targets bacterial membranes to kill bacteria similarly to parental S1. Furthermore, fragments derived from MIRIAM and S1 provided insights on their molecular mechanisms of action, in particular, the relationships of functional motifs comprised by charge, hydrophobicity, and structure within each peptide. We conclude that the combination of charge, hydrophobicity, and length of the peptide is important. A close interaction of amino acids in a single molecule in a carefully balanced ensemble of sequence position and secondary structure is crucial.

  17. Single-electron charging effects

    SciTech Connect

    Ruggiero, S.T.

    1991-12-15

    The status of our project on single-electron tunneling is, again, excellent. As outlined in our original proposal, a key goal for this project has been the development of a scanning tunneling instrument for the purpose of imaging individual particles and tunneling into these particles at high magnetic fields. Further progress is discussed in this report.

  18. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    DOE PAGES

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; ...

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

  19. Roles of Hydrophobicity and Charge Distribution of Cationic Antimicrobial Peptides in Peptide-Membrane Interactions*

    PubMed Central

    Yin, Lois M.; Edwards, Michelle A.; Li, Jessica; Yip, Christopher M.; Deber, Charles M.

    2012-01-01

    Cationic antimicrobial peptides (CAPs) occur as important innate immunity agents in many organisms, including humans, and offer a viable alternative to conventional antibiotics, as they physically disrupt the bacterial membranes, leading to membrane lysis and eventually cell death. In this work, we studied the biophysical and microbiological characteristics of designed CAPs varying in hydrophobicity levels and charge distributions by a variety of biophysical and biochemical approaches, including in-tandem atomic force microscopy, attenuated total reflection-FTIR, CD spectroscopy, and SDS-PAGE. Peptide structural properties were correlated with their membrane-disruptive abilities and antimicrobial activities. In bacterial lipid model membranes, a time-dependent increase in aggregated β-strand-type structure in CAPs with relatively high hydrophobicity (such as KKKKKKALFALWLAFLA-NH2) was essentially absent in CAPs with lower hydrophobicity (such as KKKKKKAAFAAWAAFAA-NH2). Redistribution of positive charges by placing three Lys residues at both termini while maintaining identical sequences minimized self-aggregation above the dimer level. Peptides containing four Leu residues were destructive to mammalian model membranes, whereas those with corresponding Ala residues were not. This finding was mirrored in hemolysis studies in human erythrocytes, where Ala-only peptides displayed virtually no hemolysis up to 320 μm, but the four-Leu peptides induced 40–80% hemolysis at the same concentration range. All peptides studied displayed strong antimicrobial activity against Pseudomonas aeruginosa (minimum inhibitory concentrations of 4–32 μm). The overall findings suggest optimum routes to balancing peptide hydrophobicity and charge distribution that allow efficient penetration and disruption of the bacterial membranes without damage to mammalian (host) membranes. PMID:22253439

  20. Dynamic Peptide Library for the Discovery of Charge Transfer Hydrogels.

    PubMed

    Berdugo, Cristina; Nalluri, Siva Krishna Mohan; Javid, Nadeem; Escuder, Beatriu; Miravet, Juan F; Ulijn, Rein V

    2015-11-25

    Coupling of peptide self-assembly to dynamic sequence exchange provides a useful approach for the discovery of self-assembling materials. In here, we demonstrate the discovery and optimization of aqueous, gel-phase nanostructures based on dynamically exchanging peptide sequences that self-select to maximize charge transfer of n-type semiconducting naphthalenediimide (NDI)-dipeptide bioconjugates with various π-electron-rich donors (dialkoxy/hydroxy/amino-naphthalene or pyrene derivatives). These gel-phase peptide libraries are characterized by spectroscopy (UV-vis and fluorescence), microscopy (TEM), HPLC, and oscillatory rheology and it is found that, of the various peptide sequences explored (tyrosine Y-NDI with tyrosine Y, phenylalanine F, leucine L, valine V, alanine A or glycine G-NH2), the optimum sequence is tyrosine-phenylalanine in each case; however, both its absolute and relative yield amplification is dictated by the properties of the donor component, indicating cooperativity of peptide sequence and donor/acceptor pairs in assembly. The methodology provides an in situ discovery tool for nanostructures that enable dynamic interfacing of supramolecular electronics with aqueous (biological) systems.

  1. Influence of the Length and Charge on the Activity of α-Helical Amphipathic Antimicrobial Peptides.

    PubMed

    Gagnon, Marie-Claude; Strandberg, Erik; Grau-Campistany, Ariadna; Wadhwani, Parvesh; Reichert, Johannes; Bürck, Jochen; Rabanal, Francesc; Auger, Michèle; Paquin, Jean-François; Ulrich, Anne S

    2017-03-21

    Hydrophobic mismatch is important for pore-forming amphipathic antimicrobial peptides, as demonstrated recently [Grau-Campistany, A., et al. (2015) Sci. Rep. 5, 9388]. A series of different length peptides have been generated with the heptameric repeat sequence KIAGKIA, called KIA peptides, and it was found that only those helices sufficiently long to span the hydrophobic thickness of the membrane could induce leakage in lipid vesicles; there was also a clear length dependence of the antimicrobial and hemolytic activities. For the original KIA sequences, the cationic charge increased with peptide length. The goal of this work is to examine whether the charge also has an effect on activity; hence, we constructed two further series of peptides with a sequence similar to those of the KIA peptides, but with a constant charge of +7 for all lengths from 14 to 28 amino acids. For both of these new series, a clear length dependence similar to that of KIA peptides was observed, indicating that charge has only a minor influence. Both series also showed a distinct threshold length for peptides to be active, which correlates directly with the thickness of the membrane. Among the longer peptides, the new series showed activities only slightly lower than those of the original KIA peptides of the same length that had a higher charge. Shorter peptides, in which Gly was replaced with Lys, showed activities similar to those of KIA peptides of the same length, but peptides in which Ile was replaced with Lys lost their helicity and were less active.

  2. Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns

    SciTech Connect

    Huang, Yingying; Triscari, Joseph M.; Tseng, George C.; Pasa-Tolic, Ljiljana; Lipton, Mary S.; Smith, Richard D.; Wysocki, Vicki H.

    2005-09-01

    Data mining was performed on 28 330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pairwise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly charged Arg- and Lys-ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton. When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions, y ions, or both depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion

  3. Laserspray ionization on a commercial atmospheric pressure-MALDI mass spectrometer ion source: selecting singly or multiply charged ions.

    PubMed

    McEwen, Charles N; Larsen, Barbara S; Trimpin, Sarah

    2010-06-15

    Multiply charged ions, similar to those obtained with electrospray ionization, are produced at atmospheric pressure (AP) using standard MALDI conditions of laser fluence and reflective geometry. Further, the charge state can be switched to singly charged ions nearly instantaneously by changing the voltage applied to the MALDI target plate. Under normal AP-MALDI operating conditions in which a voltage is applied to the target plate, primarily singly charged ions are observed, but at or near zero volts, highly charged ions are observed for peptides and proteins. Thus, switching between singly and multiply charged ions requires only manipulation of a single voltage. As in ESI, multiple charging, produced using the AP-MALDI source, allows compounds with molecular weights beyond the mass-to-charge limit of the mass spectrometer to be observed and improves the fragmentation relative to singly charged ions.

  4. Interactions of Cationic Peptides and Ions with Negatively Charged Lipid Bilayers

    NASA Astrophysics Data System (ADS)

    Taheri-Araghi, Sattar

    In this thesis we study the interactions of ions and cationic peptides with a negatively charged lipid bilayer in an ionic solution where the electrostatic interactions are screened. We first examine the problem of charge renormalization and inversion of a highly charged bilayer with low dielectric constant. To be specific, we consider an asymmetrically charged lipid bilayer, in which only one layer is negatively charged. In particular, we study how dielectric discontinuities and charge correlations among lipid charges and condensed counterions influence the effective charge of the surface. When counterions are monovalent, e. g. , Na+, our mean-field approach implies that dielectric discontinuities can enhance counterion condensation. A simple scaling picture shows how the effects of dielectric discontinuities and surface-charge distributions are intertwined: Dielectric discontinuities diminish condensation if the backbone charge is uniformly smeared out while counterions are localized in space; they can, however, enhance condensation when the backbone charge is discrete. In the presence of asymmetric salts such as CaCl2, we find that the correlation effect, treated at the Gaussian level, is more pronounced when the surface has a lower dielectric constant, inverting the sign of the charge at a smaller value of Ca2+ concentration. In the last chapter we study binding of cationic peptides onto a lipid-bilayer membrane. The peptide not only interacts electrostatically with anionic lipids, rearranging their spatial distributions, but it can also insert hydrophobically into the membrane, expanding the area of its binding layer (i. e. , the outer layer). We examine how peptide charges and peptide insertion (thus area expansion) are intertwined. Our results show that, depending on the bilayer's surface charge density and peptide hydrophobicity, there is an optimal peptide charge yielding the maximum peptide penetration. Our results shed light on the physics behind the

  5. Charge transport in single crystal organic semiconductors

    NASA Astrophysics Data System (ADS)

    Xie, Wei

    Organic electronics have engendered substantial interest in printable, flexible and large-area applications thanks to their low fabrication cost per unit area, chemical versatility and solution processability. Nevertheless, fundamental understanding of device physics and charge transport in organic semiconductors lag somewhat behind, partially due to ubiquitous defects and impurities in technologically useful organic thin films, formed either by vacuum deposition or solution process. In this context, single-crystalline organic semiconductors, or organic single crystals, have therefore provided the ideal system for transport studies. Organic single crystals are characterized by their high chemical purity and outstanding structural perfection, leading to significantly improved electrical properties compared with their thin-film counterparts. Importantly, the surfaces of the crystals are molecularly flat, an ideal condition for building field-effect transistors (FETs). Progress in organic single crystal FETs (SC-FETs) is tremendous during the past decade. Large mobilities ~ 1 - 10 cm2V-1s-1 have been achieved in several crystals, allowing a wide range of electrical, optical, mechanical, structural, and theoretical studies. Several challenges still remain, however, which are the motivation of this thesis. The first challenge is to delineate the crystal structure/electrical property relationship for development of high-performance organic semiconductors. This thesis demonstrates a full spectrum of studies spanning from chemical synthesis, single crystal structure determination, quantum-chemical calculation, SC-OFET fabrication, electrical measurement, photoelectron spectroscopy characterization and extensive device optimization in a series of new rubrene derivatives, motivated by the fact that rubrene is a benchmark semiconductor with record hole mobility ~ 20 cm2V-1s-1. With successful preservation of beneficial pi-stacking structures, these rubrene derivatives form

  6. Charge States of y Ions in the Collision-Induced Dissociation of Doubly Charged Tryptic Peptide Ions

    NASA Astrophysics Data System (ADS)

    Neta, Pedatsur; Stein, Stephen E.

    2011-05-01

    Bonds that break in collision-induced dissociation (CID) are often weakened by a nearby proton, which can, in principle, be carried away by either of the product fragments. Since peptide backbone dissociation is commonly charge-directed, relative intensities of charge states of product y- and b-ions depend on the final location of that proton. This study examines y-ion charge distributions for dissociation of doubly charged peptide ions, using a large reference library of peptide ion fragmentation generated from ion-trap CID of peptide ions from tryptic digests. Trends in relative intensities of y2+ and y1+ ions are examined as a function of bond cleavage position, peptide length (n), residues on either side of the bond and effects of residues remote from the bond. It is found that yn-2/b2 dissociation is the most sensitive to adjacent amino acids, that y2+/y1+ steadily increase with increasing peptide length, that the N-terminal amino acid can have a major influence in all dissociations, and in some cases other residues remote from the bond cleavage exert significant effects. Good correlation is found between the values of y2+/y1+ for the peptide and the proton affinities of the amino acids present at the dissociating peptide bond. A few deviations from this correlation are rationalized by specific effects of the amino acid residues. These correlations can be used to estimate trends in y2+/y1+ ratios for peptide ions from amino acid proton affinities.

  7. Single Electron Charging Effects in Mesoscopic Systems

    NASA Astrophysics Data System (ADS)

    Hanna, Ashraf Elfar

    1992-01-01

    We report the investigation of two ultra-small tunnel junctions in series. These junctions have capacitances on the order of 10^{-18} -10^{-19}F each. In this regime the charging energy associated with a single electron tunneling event (e^2/2C) can be made significantly larger than thermal fluctuations (k _{rm B}T) at liquid helium temperatures. As such, measurements of the tunneling current as a function of voltage show unique features associated individual electron tunneling events. In this thesis we present high-resolution data from measurements on a two ultra-small tunnel junctions in series. The junctions are created by using a scanning tunneling microscope vacuum tunneling into a small (10 -100A) gold sphere which is separated from a metal electrode by an oxide layer. Our measurements show sharp features, such as the Coulomb blockade and Coulomb staircase, in the I(V) data of two junction systems. We explain our data by use of the orthodox theory of tunneling. The features in the data displayed overwhelming agreement with the predictions of the orthodox theory, which correctly produces the location of linear voltage onsets, current steps and step slopes. The high resolution of our data also allowed the categorizing of the I(V) curves according to the onset of certain features. The orthodox theory, combined with our data, has also shed understanding on the nature of Q_0, the "fractional" charge on the middle electrode. Higher order tunneling processes associated with macroscopic quantum tunneling of charge, q-MQT, have also been observed in our data. This observation is not only of fundamental physical interest, but is an effect which could set the limit of future devices operating on the transfer of single electrons.

  8. Structural Heterogeneity of Doubly-Charged Peptide b-Ions

    PubMed Central

    Li, Xiaojuan; Huang, Yiqun; O’Connor, Peter B.; Lin, Cheng

    2011-01-01

    Performing collisionally activated dissociation (CAD) and electron capture dissociation (ECD) in tandem has shown great promise in providing comprehensive sequence information that was otherwise unobtainable by using either fragmentation method alone or in duet. However, the general applicability of this MS3 approach in peptide sequencing may be undermined by the formation of non-direct sequence ions, as sometimes observed under CAD, particularly when multiple stages of CAD are involved. In this study, varied-sized doubly-charged b-ions from three tachykinin peptides were investigated by ECD. Sequence scrambling was observed in ECD of all b-ions from neurokinin A (HKTDSFVGLM-NH2), suggesting the presence of N- and C-termini linked macro-cyclic conformers. On the contrary, none of the b-ions from eledoisin (pEPSKDAFIGLM-NH2) produced non-direct sequence ions under ECD, as it does not contain a free N-terminal amino group. ECD of several b-ions from Substance P (RPKPQQFFGLM-NH2) showed series of cm-Lys fragment ions which suggested that the macro-cyclic structure may also be formed by connecting the C-terminal carbonyl group and the ε-amino group of the lysine side chain. Theoretical investigation of selected Substance P b-ions revealed several low energy conformers, including both linear oxazolones and macro-ring structures, in corroboration with the experimental observation. This study showed that a b-ion may exist as a mixture of several forms, with their propensities influenced by its N-terminus, length, and certain side-chain groups. Further, the presence of several macro-cyclic structures may result in erroneous sequence assignment when the combined CAD and ECD methods are used in peptide sequencing. PMID:21472584

  9. A Novel Triethylphosphonium Charge Tag on Peptides: Synthesis, Derivatization, and Fragmentation

    NASA Astrophysics Data System (ADS)

    DeGraan-Weber, Nick; Ward, Sarah A.; Reilly, James P.

    2017-09-01

    Charge tagging is a peptide derivatization process that commonly localizes a positive charge on the N-terminus. Upon low energy activation (e.g., collision-induced dissociation or post-source decay) of charge tagged peptides, relatively few fragment ions are produced due to the absence of mobile protons. In contrast, high energy fragmentation, such as 157 nm photodissociation, typically leads to a series of a-type ions. Disadvantages of existing charge tags are that they can produce mobile protons or that they are undesirably large and bulky. Here, we investigate a small triethylphosphonium charge tag with two different linkages: amide (158 Da) and amidine bonds (157 Da). Activation of peptides labeled with a triethylphosphonium charge tag through an amide bond can lead to loss of the charge tag and the production of protonated peptides. This enables low intensity fragment ions from both the protonated and charge tagged peptides to be observed. Triethylphosphonium charge tagged peptides linked through an amidine bond are more stable. Post-source decay and photodissociation yield product ions that primarily contain the charge tag. Certain amidine induced fragments are also observed. The previously reported tris(trimethoxyphenyl) phosphonium acetic acid N-hydroxysuccinimidyl ester charge tag shows a similar fragment ion distribution, but the mass of the triethylphosphonium tag label is 415 Da smaller. [Figure not available: see fulltext.

  10. Short Peptides Enhance Single Cell Adhesion and Viability on Microarrays

    PubMed Central

    Veiseh, Mandana; Veiseh, Omid; Martin, Michael C.; Asphahani, Fareid; Zhang, Miqin

    2011-01-01

    Single cell patterning holds important implications for biology, biochemistry, biotechnology, medicine, and bioinformatics. The challenge for single cell patterning is to produce small islands hosting only single cells and retaining their viability for a prolonged period of time. This study demonstrated a surface engineering approach that uses a covalently-bound short peptide as a mediator to pattern cells with improved single cell adhesion and prolonged cellular viability on gold patterned SiO2 substrates. The underlying hypothesis is that cell adhesion is regulated by the type, availability and stability of effective cell adhesion peptides, and thus covalently bound short peptides would promote cell spreading and thus, single cell adhesion and viability. The effectiveness of this approach and the underlying mechanism for the increased probability of single cell adhesion and prolonged cell viability by short peptides were studied by comparing cellular behavior of human umbilical cord vein endothelial cells on three model surfaces whose gold electrodes were immobilized with fibronectin, physically adsorbed Arg-Glu-Asp-Val-Tyr, and covalently-bound Lys-Arg-Glu-Asp-Val-Tyr, respectively. The surface chemistry and binding properties were characterized by reflectance Fourier transform infrared spectroscopy. Both short peptides were superior to fibronectin in producing adhesion of only single cells, while the covalently bound peptide also reduced apoptosis and necrosis of adhered cells. Controlling cell spreading by peptide binding domains to regulate apoptosis and viability represents a fundamental mechanism in cell-materials interaction and provides an effective strategy in engineering arrays of single cells. PMID:17371055

  11. Role of peptide--peptide interactions in stabilizing peptide-wrapped single-walled carbon nanotubes: a molecular dynamics study.

    PubMed

    Chiu, Chi-Cheng; Dieckmann, Gregg R; Nielsen, Steven O

    2009-01-01

    Single-walled carbon nanotubes (SWNTs) have unique properties and are projected to have a major impact in nanoscale electronics, materials science, and nanomedicine. Yet, these potential applications are hindered by the need for sample purification to separate SWNTs from each other and from metallic catalyst and amorphous carbon present in as-synthesized samples. Common purification strategies involve dispersing SWNTs as individual tubes in aqueous solution. Towards this end, a designed helical peptide was shown to be excellent at dispersing SWNTs. However, the molecular details of the peptide-SWNT and peptide-peptide interactions await elucidation. Here we explore these molecular interactions using fully atomistic molecular dynamics simulations of peptide-wrapped SWNTs. We characterize the interactions by measuring the aromatic residue-to-SWNT surface distance, the peptide amphiphilicity, the peptide-SWNT crossing angle, the peptide-SWNT contact area, the peptide helix axis-to-axis distance, and the inter-peptide hydrogen bonding. We find that the peptides collectively tilt with respect to the SWNT long axis, are alpha-helical, and form interpeptide hydrogen bonds through their lysine and glutamate residues, which helps to stabilize the multipeptide/SWNT complex. All hydrophobic residues interact with the SWNT and are sequestered from water. The picture that emerges from this study gives insight into subsequent peptide design. (c) 2009 Wiley Periodicals, Inc.

  12. How Peptide Molecular Structure and Charge Influence the Nanostructure of Lipid Bicontinuous Cubic Mesophases: Model Synthetic WALP Peptides Provide Insights.

    PubMed

    van 't Hag, Leonie; Li, Xu; Meikle, Thomas G; Hoffmann, Søren V; Jones, Nykola C; Pedersen, Jan Skov; Hawley, Adrian M; Gras, Sally L; Conn, Charlotte E; Drummond, Calum J

    2016-07-12

    Nanostructured bicontinuous lipidic cubic phases are used for the encapsulation of proteins in a range of applications such as in meso crystallization of transmembrane proteins and as drug delivery vehicles. The retention of the nanoscale order of the cubic phases subsequent to protein incorporation, as well as retention of the protein structure and function, is essential for all of these applications. Herein synthetic peptides (WALP21, WALPS53, and WALPS73) with a common α-helical hydrophobic domain, but varying hydrophilic loop size, were designed to systematically examine the effect of peptide structure and charge on bicontinuous cubic phases. The effect of the cubic phases on the secondary structure of the peptides was also investigated. The incorporation of the WALP peptides in cubic phases formed by a range of lipids showed that hydrophobic mismatch of the peptides with the lipid bilayers, the hydrophilic domain size, and peptide charge were all significant factors determining the response of the lipid nanomaterial to protein insertion. As charge repulsion had the most significant effect on the phase transitions observed, we suggest that buffer pH and salt concentration must be carefully considered to ensure cubic mesophase retention. Importantly, the WALP peptides were found to have a different conformation depending on the local lipid environment. Such structural changes could potentially affect membrane protein function, which is crucial for both current and prospective applications.

  13. Heat dissipation in relativistic single charged fluids

    NASA Astrophysics Data System (ADS)

    Garcia-Perciante, A. L.; Sandoval-Villalbazo, A.; Brun-Battistini, D.

    2015-11-01

    When the temperature of a fluid is increased its out of equilibrium behavior is significantly modified. In particular kinetic theory predicts that the heat flux is not solely driven by a temperature gradient but can also be coupled to other thermodynamic vector forces. We explore the nature of heat conduction in a single component charged fluid in special relativity, where the electromagnetic field is introduced as an external force. We obtain an electrothermal effect, similar to the mixture's cross-effect, which is not present in the non-relativistic simple fluid. The general lines of the corresponding calculation will be shown, emphasizing the importance of reference frame invariance and the origin of the extra heat sources, in particular the role of the modified inertia and the difference in fluid's and molecules' proper times. The constitutive equation for the heat flux obtained using Chapman-Enskog's expansion in Marle's approximation will be analyzed together with the corresponding transport coefficients.The impact of this effect in the overall dynamics of the system here considered will be briefly discussed. The authors acknowledge support from CONACyT through grant CB2011/167563.

  14. Insertion of TAT peptide and perturbation of negatively charged model phospholipid bilayer revealed by neutron diffraction.

    PubMed

    Chen, Xiaochao; Sa'adedin, Farid; Deme, Bruno; Rao, Pingfan; Bradshaw, Jeremy

    2013-08-01

    TAT peptide is one of the best-characterized cell penetrating peptides derived from the transactivator of transcription protein from the human immunodeficiency virus 1. The aim of this study was to investigate the interaction between TAT peptide and partially negatively-charged phospholipid bilayer by using lamellar neutron diffraction. The main findings are the existence of a contiguous water channel across the bilayer in the presence of TAT peptide. Taken in combination with other observations, including thinning of the lipid bilayer, this unambiguously locates the peptide within the lipid bilayer. The interaction of TAT peptide with anionic lipid bilayer, composed of an 80:20 mixture of DOPC and DOPS, takes place at two locations. One is in the peripheral aqueous phase between adjacent bilayers and the second is below the glycerol backbone region of bilayer. A membrane thinning above a peptide concentration threshold (1mol%) was found, as was a contiguous transbilayer water channel at the highest peptide concentration (10mol%). This evidence leads to the suggestion that the toroidal pore model might be involved in the transmembrane of TAT peptide. We interpret the surface peptide distribution in the peripheral aqueous phase to be a massive exclusion of TAT peptide from its intrinsic location below the glycerol backbone region of the bilayer, due to the electrostatic attraction between the negatively-charged headgroups of phospholipids and the positively charged TAT peptides. Finally, we propose that the role that negatively-charged headgroups of DOPS lipids play in the transmembrane of TAT peptide is less important than previously thought. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Hydration, charge, size, and shape characteristics of peptides from their CZE analyses.

    PubMed

    Peirotti, Marta B; Piaggio, Maria V; Deiber, Julio A

    2008-02-01

    A CZE model is presented for peptide characterization on the basis of well-established physicochemical equations. The effective mobility is used as basic data in the model to estimate relevant peptide properties such as, for instance, hydration, net and total electrical charge numbers, hydrodynamic size and shape, particle average orientation, and pH-microenvironment from the charge regulation phenomenon. Therefore 102 experimental effective mobilities of different peptides are studied and discussed in relation to previous work. An equation for the estimation of peptide hydration as a function of ionizing, polar, and non-polar amino acid residues is included in the model. It is also shown that the shape-orientation factor of peptides may be either lower or higher than one, and its value depends on a complex interplay among total charge number, molar mass, hydration, and amino acid sequence.

  16. Determination of Peptide and Protein Ion Charge States by Fourier Transformation of Isotope-Resolved Mass Spectra

    SciTech Connect

    Tabb, Dave L; Shah, Manesh B; Strader, Michael B; Connelly, Heather M; Hettich, Robert {Bob} L; Hurst, Gregory {Greg} B

    2006-01-01

    We report an automated method for determining charge states from high-resolution mass spectra. Fourier transforms of isotope packets from high-resolution mass spectra are compared to Fourier transforms of modeled isotopic peak packets for a range of charge states. The charge state for the experimental ion packet is determined by the model isotope packet that yields the best match in the comparison of the Fourier transforms. This strategy is demonstrated for determining peptide ion charge states from 'zoom scan' data from a linear quadrupole ion trap mass spectrometer, enabling the subsequent automated identification of singly-through quadruply-charged peptide ions, while reducing the numbers of conflicting identifications from ambiguous charge state assignments. We also apply this technique to determine the charges of intact protein ions from LC-FTICR data, demonstrating that it is more sensitive under these experimental conditions than two existing algorithms. The strategy outlined in this paper should be generally applicable to mass spectra obtained from any instrument capable of isotopic resolution.

  17. Surface nanostructures by single highly charged ions.

    PubMed

    Facsko, S; Heller, R; El-Said, A S; Meissl, W; Aumayr, F

    2009-06-03

    It has recently been demonstrated that the impact of individual, slow but highly charged ions on various surfaces can induce surface modifications with nanometer dimensions. Generally, the size of these surface modifications (blisters, hillocks, craters or pits) increases dramatically with the potential energy of the highly charged ion, while the kinetic energy of the projectile ions seems to be of little importance. This paper presents the currently available experimental evidence and theoretical models and discusses the circumstances and conditions under which nanosized features on different surfaces due to the impact of slow highly charged ions can be produced.

  18. Design of single peptides for self-assembled conduction channels

    NASA Astrophysics Data System (ADS)

    Yew, Sok Yee; Shekhawat, Gajendra; Wangoo, Nishima; Mhaisalkar, Subodh; Raman Suri, C.; Dravid, Vinayak P.; Lam, Yeng Ming

    2011-05-01

    Self-assembly of peptides provides the possibility of achieving relatively long range order on surfaces. These ordered peptides can also form channels that can be used as conduction channels. In the past, studies were focused on electron conduction through the secondary structure and amine bond of peptides and these restrict conduction of electrons over a short range (a few nanometers). In this work, we demonstrate the realization of electron conduction over a longer range of a few hundred nanometers via π-π stacking of the phenyl groups in the tyrosine residue of a single peptide. The peptide used in this work was designed with a phenyl ring for π-π stacking at one end and a carboxylic group at the other end for binding to aminopropyltriethoxysilane (APTES) treated silicon wafer. The distance between the peptides is controlled by a disulfide bond formed between neighboring cysteine residue and also by the amine groups of aminopropyltriethoxysilane. We demonstrate that the self-assembled peptide is conducting in the dry state over hundreds of nanometers, realizing the possibility of using peptide as a molecular wire.

  19. Charge Effect on the Quantum Dots-Peptide Self-Assembly Using Fluorescence Coupled Capillary Electrophoresis.

    PubMed

    Wang, Jianhao; Li, Jingyan; Teng, Yiwan; Bi, Yanhua; Hu, Wei; Li, Jinchen; Wang, Cheli; Qiu, Lin; Jiang, Pengju

    2016-04-01

    We present a molecular characterization of metal-affinity driven self-assembly between CdSe-ZnS quantum dots and a series of hexahistidine peptides with different charges. In particular, we uti- lized fluorescence coupled capillary electrophoresis to test the self-assembly process of quantum dots with peptides in solution. Four peptides with different charges can be efficiently separated by fluorescence coupled capillary electrophoresis. The migration time appeared to be influenced by the charges of the peptide. In addition, the kinetics of self-assembly process of quantum dots with one of the peptides manifested a bi-phasic kinetics followed by a saturating stage. This work revealed that there exist two types of binding sites on the surface of quantum dots for peptide 1: one type termed "high priority" binding site and a "low priority" site which is occupied after the first binding sites are fully occupied. The total self-assembly process finishes in solution within 80 s. Our work represents the systematic investigation of the details of self-assembly kinetics utilizing high-resolution fluorescence coupled capillary electrophoresis. The charge effect of peptide coating quantum dots provides a new way of preparing bioprobes.

  20. The effect of reagent charge state on the charge inversion efficiency of singly charged polyatomic ions in the gas phase.

    PubMed

    Hassell, Kerry M; Hilger, Ryan T; McLuckey, Scott A

    2011-11-07

    A variety of combinations of oppositely charged ions have been reacted to examine the role of the charge state from a multiply protonated or multiply deprotonated reagent ion on the efficiency of conversion of a singly charged ion of opposite polarity to a singly charged ion of the same polarity as the reagent. Maximum efficiencies on the order of tens of percent were observed. A threshold for charge inversion was noted in all cases and, with one exception, a clear decrease in efficiency was also noted at high charge states. A model was developed to predict charge inversion efficiency based on charge states, cross-sections of the reactants, and relevant thermodynamic ion affinity values for the reactants and products. The model predicts a threshold for charge inversion, although the prediction does not match the observed threshold quantitatively. This discrepancy is likely due to a simplifying assumption that is not justified on a quantitative basis but which does reproduce the qualitative trend. The model does not predict the major decrease in efficiency at high charge states. However, calculations show that the kinetic energies of the charge inversion products can lead to significant scattering losses at high charge states of the ion-ion collision complex.

  1. Peptide nucleic acid probes with charged photocleavable mass markers

    PubMed Central

    Ball, Rachel J; Green, Philip S; Gale, Nittaya; Langley, G John

    2010-01-01

    Halogen-labelled peptide organic acid (HPOA) monomers have been synthesised and incorporated into sequence-specific peptide nucleic acid (PNA) probes. Three different types of probe have been prepared; the unmodified PNA probe, the PNA probe with a mass marker, and the PNA probe with photocleavable mass marker. All three types of probe have been used in model studies to develop a mass spectrometry-based hybridisation assay for detection of point mutations in DNA. PMID:21687524

  2. Use of Doubly Charged Precursors to Validate Dissociation Mechanisms of Singly Charged Poly(Dimethylsiloxane) Oligomers

    NASA Astrophysics Data System (ADS)

    Fouquet, Thierry; Toniazzo, Valérie; Ruch, David; Charles, Laurence

    2013-07-01

    Collision-induced dissociation of doubly charged poly(dimethylsiloxane) (PDMS) molecules was investigated to provide experimental evidence for fragmentation reactions proposed to occur upon activation of singly charged oligomers. This study focuses on two PDMS species holding trimethylsilyl or methoxy end-groups and cationized with ammonium. In both cases, introduction of the additional charge did not induce significant differences in dissociation behavior, and the use of doubly charged precursors enabled the occurrence of charge-separation reactions, allowing molecules always eliminated as neutrals upon activation of singly charged oligomers to be detected as cationized species. In the case of trimethylsilyl-terminated oligomers, random location of the adducted charge combined with rapid consecutive reactions proposed to occur from singly charged precursors could be validated based on MS/MS data of doubly charged oligomers. In the case of methoxy-terminated PDMS, favored interaction of the adducted ammonium with both end-groups, proposed to rationalize the dissociation behavior of singly charged molecules, was also supported by MS/MS data obtained for molecules adducted with two ammonium cations.

  3. Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

    NASA Technical Reports Server (NTRS)

    Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.

    1993-01-01

    The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

  4. Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

    NASA Technical Reports Server (NTRS)

    Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.

    1993-01-01

    The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

  5. Minimal transition state charge stabilization of the oxyanion during peptide bond formation by the ribosome.

    PubMed

    Carrasco, Nicolas; Hiller, David A; Strobel, Scott A

    2011-12-06

    Peptide bond formation during ribosomal protein synthesis involves an aminolysis reaction between the aminoacyl α-amino group and the carbonyl ester of the growing peptide via a transition state with a developing negative charge, the oxyanion. Structural and molecular dynamic studies have suggested that the ribosome may stabilize the oxyanion in the transition state of peptide bond formation via a highly ordered water molecule. To biochemically investigate this mechanistic hypothesis, we estimated the energetic contribution to catalytic charge stabilization of the oxyanion using a series of transition state mimics that contain different charge distributions and hydrogen bond potential on the functional group mimicking the oxyanion. Inhibitors containing an oxyanion mimic that carried a neutral charge and a mimic that preserved the negative charge but could not form hydrogen bonds had less than a 3-fold effect on inhibitor binding affinity. These observations argue that the ribosome provides minimal transition state charge stabilization to the oxyanion during peptide bond formation via the water molecule. This is in contrast to the substantial level of oxyanion stabilization provided by serine proteases. This suggests that the oxyanion may be neutralized via a proton shuttle, resulting in an uncharged transition state.

  6. Interaction of the Antimicrobial Peptide Aurein 1.2 and Charged Lipid Bilayer

    DOE PAGES

    Rai, Durgesh K.; Qian, Shuo

    2017-06-16

    Aurein 1.2 is a potent antimicrobial peptide secreted by frog Litoria aurea. As a short membrane-active peptide with only 13 amino acids in sequence, it has been found to be residing on the surface of lipid bilayer and permeabilizing bacterial membranes at high concentration. However, the detail at the molecular level is largely unknown. Here in this study, we investigated the action of Aurein 1.2 in charged lipid bilayers composed of DMPC/DMPG. Oriented Circular Dichroism results showed that the peptide was on the surface of lipid bilayer regardless of the charged lipid ratio. Only at a very high peptide-to-lipid ratiomore » (~1/10), the peptide became perpendicular to the bilayer, however no pore was detected by neutron in-plane scattering. To further understand how it interacted with charged lipid bilayers, we employed Small Angle Neutron Scattering to probe lipid distribution across bilayer leaflets in lipid vesicles. The results showed that Aurein 1.2 interacted strongly with negatively charged DMPG, causing strong asymmetry in lipid bilayer. At high concentration, while the vesicles were intact, we found additional structure feature on the bilayer. Finally, our study provides a glimpse into how Aurein 1.2 disturbs anionic lipid-containing membranes without pore formation.« less

  7. Interaction of the Antimicrobial Peptide Aurein 1.2 and Charged Lipid Bilayer.

    PubMed

    Rai, Durgesh K; Qian, Shuo

    2017-06-16

    Aurein 1.2 is a potent antimicrobial peptide secreted by frog Litoria aurea. As a short membrane-active peptide with only 13 amino acids in sequence, it has been found to be residing on the surface of lipid bilayer and permeabilizing bacterial membranes at high concentration. However, the detail at the molecular level is largely unknown. In this study, we investigated the action of Aurein 1.2 in charged lipid bilayers composed of DMPC/DMPG. Oriented Circular Dichroism results showed that the peptide was on the surface of lipid bilayer regardless of the charged lipid ratio. Only at a very high peptide-to-lipid ratio (~1/10), the peptide became perpendicular to the bilayer, however no pore was detected by neutron in-plane scattering. To further understand how it interacted with charged lipid bilayers, we employed Small Angle Neutron Scattering to probe lipid distribution across bilayer leaflets in lipid vesicles. The results showed that Aurein 1.2 interacted strongly with negatively charged DMPG, causing strong asymmetry in lipid bilayer. At high concentration, while the vesicles were intact, we found additional structure feature on the bilayer. Our study provides a glimpse into how Aurein 1.2 disturbs anionic lipid-containing membranes without pore formation.

  8. Chiral Sulfoxide-Induced Single Turn Peptide α-Helicity

    PubMed Central

    Zhang, Qingzhou; Jiang, Fan; Zhao, Bingchuan; Lin, Huacan; Tian, Yuan; Xie, Mingsheng; Bai, Guoyun; Gilbert, Adam M.; Goetz, Gilles H.; Liras, Spiros; Mathiowetz, Alan A.; Price, David A.; Song, Kun; Tu, Meihua; Wu, Yujie; Wang, Tao; Flanagan, Mark E.; Wu, Yun-Dong; Li, Zigang

    2016-01-01

    Inducing α-helicity through side-chain cross-linking is a strategy that has been pursued to improve peptide conformational rigidity and bio-availability. Here we describe the preparation of small peptides tethered to chiral sulfoxide-containing macrocyclic rings. Furthermore, a study of structure-activity relationships (SARs) disclosed properties with respect to ring size, sulfur position, oxidation state, and stereochemistry that show a propensity to induce α-helicity. Supporting data include circular dichroism spectroscopy (CD), NMR spectroscopy, and a single crystal X-ray structure for one such stabilized peptide. Finally, theoretical studies are presented to elucidate the effect of chiral sulfoxides in inducing backbone α-helicity. PMID:27934919

  9. Single molecule detection using charge-coupled device array technology

    SciTech Connect

    Denton, M.B.

    1992-07-29

    A technique for the detection of single fluorescent chromophores in a flowing stream is under development. This capability is an integral facet of a rapid DNA sequencing scheme currently being developed by Los Alamos National Laboratory. In previous investigations, the detection sensitivity was limited by the background Raman emission from the water solvent. A detection scheme based on a novel mode of operating a Charge-Coupled Device (CCD) is being developed which should greatly enhance the discrimination between fluorescence from a single molecule and the background Raman scattering from the solvent. Register shifts between rows in the CCD are synchronized with the sample flow velocity so that fluorescence from a single molecule is collected in a single moving charge packet occupying an area approaching that of a single pixel while the background is spread evenly among a large number of pixels. Feasibility calculations indicate that single molecule detection should be achieved with an excellent signal-to-noise ratio.

  10. Field Regulation of Single Molecule Conductivity by a Charged Atom

    NASA Astrophysics Data System (ADS)

    Wolkow, Robert

    2006-03-01

    A new concept for a single molecule transistor is demonstrated [1]. A single chargeable atom adjacent to a molecule shifts molecular energy levels into alignment with electrode levels, thereby gating current through the molecule. Seemingly paradoxically, the silicon substrate to which the molecule is covalently attached provides 2, not 1, effective contacts to the molecule. This is achieved because the single charged silicon atom is at a substantially different potential than the remainder of the substrate. Charge localization at one dangling bond is ensured by covalently capping all other surface atoms. Dopant level control and local Fermi level control can change the charge state of that atom. The same configuration is shown to be an effective transducer to an electrical signal of a single molecule detection event. Because the charged atom induced shifting results in conductivity changes of substantial magnitude, these effects are easily observed at room temperature. [1] Paul G. Piva1,Gino A. DiLabio, Jason L. Pitters, Janik Zikovsky, Moh'd Rezeq, Stanislav Dogel, Werner A. Hofer & Robert A. Wolkow, Field regulation of single-molecule conductivity by a charged surface atom, NATURE 435, 658-661 (2005)

  11. Promotion of alpha-cyano-4-hydroxycinnamic acid and peptide cocrystallization within levitated droplets with net charge.

    PubMed

    Bogan, Michael J; Bakhoum, Samuel F W; Agnes, George R

    2005-02-01

    Many reactions occur as a result of charge imbalance within or between reactive species in reaction vessels that have zero net charge. Here, chemical processes taking place within reaction vessels having net excess charge were studied. For mass spectroscopists, a familiar example of vessels that defy electroneutrality are the charged droplets produced by an electrospray ion source. Evidence is presented that control of the magnitude of the net charge contained in a reaction vessel, in this case a levitated droplet, can be used to promote nucleation and crystal growth of a mixture of an organic acid, alpha-cyano-4-hydroxycinnamic acid (CHCA), with one or more peptides. This phenomenon was first observed during our ongoing development of wall-less sample preparation (WaSP), electrodynamic charged droplet processing methodology capable of creating micrometer-sized sample spots for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) from subnanoliter volumes of sample material. Peptide ion signal-to-noise (S/N) ratios obtained by MALDI-TOF-MS from sample spots created from droplets that had high relative magnitude of net charge were consistently greater than those detected from sample spots created from droplets that had lower net charge. To study this unexpected phenomenon further, WaSP methodology was developed to process different mass-to-charge (m/z) droplets levitated in an electrodynamic balance (EDB), facilitating their deposition onto different positions of a target to create arrays of droplet residues ordered from highest to lowest m/z. This capability allowed simultaneous levitation with subsequent separation of a population of droplets created from a single starting solution, but the droplets had varied magnitudes of net charge. After the droplets were ejected from the EDB and collected on a glass slide or MALDI plate, the solids contained in the deposited droplets were characterized using microscopy and MALDI

  12. Charged two-exciton emission from a single semiconductor nanocrystal

    SciTech Connect

    Hu, Fengrui; Zhang, Qiang; Zhang, Chunfeng; Wang, Xiaoyong; Xiao, Min

    2015-03-30

    Here, we study the photoluminescence (PL) time trajectories of single CdSe/ZnS nanocrystals (NCs) as a function of the laser excitation power. At the low laser power, the PL intensity of a single NC switches between the “on” and “off” levels arising from the neutral and positively charged single excitons, respectively. With the increasing laser power, an intermediate “grey” level is formed due to the optical emission from a charged multiexciton state composed of two excitons and an extra electron. Both the inter-photon correlation and the PL decay measurements demonstrate that lifetime-indistinguishable photon pairs are emitted from this negatively charged two-exciton state.

  13. Charge transport in vertically aligned, self-assembled peptide nanotube junctions

    NASA Astrophysics Data System (ADS)

    Mizrahi, Mordechay; Zakrassov, Alexander; Lerner-Yardeni, Jenny; Ashkenasy, Nurit

    2012-01-01

    The self-assembly propensity of peptides has been extensively utilized in recent years for the formation of supramolecular nanostructures. In particular, the self-assembly of peptides into fibrils and nanotubes makes them promising building blocks for electronic and electro-optic applications. However, the mechanisms of charge transfer in these wire-like structures, especially in ambient conditions, are not yet fully understood. We describe here a layer-by-layer deposition methodology of short self-assembled cyclic peptide nanotubes, which results in vertically oriented nanotubes on gold substrates. Using this novel deposition methodology, we have fabricated molecular junctions with a conductive atomic force microscopy tip as a second electrode. Studies of the junctions' current-voltage characteristics as a function of the nanotube length revealed an efficient charge transfer in these supramolecular structures, with a low current attenuation constant of 0.1 Å-1, which indicate that electron transfer is dominated by hopping. Moreover, the threshold voltage to field-emission dominated transport was found to increase with peptide length in a manner that depends on the nature of the contact with the electrodes. The flexibility in the design of the peptide monomers and the ability to control their sequential order over the nanotube by means of the layer-by-layer assembly process, which is demonstrated in this work, can be used to engineer the electronic properties of self-assembled peptide nanotubes toward device applications.

  14. Charge transport in vertically aligned, self-assembled peptide nanotube junctions.

    PubMed

    Mizrahi, Mordechay; Zakrassov, Alexander; Lerner-Yardeni, Jenny; Ashkenasy, Nurit

    2012-01-21

    The self-assembly propensity of peptides has been extensively utilized in recent years for the formation of supramolecular nanostructures. In particular, the self-assembly of peptides into fibrils and nanotubes makes them promising building blocks for electronic and electro-optic applications. However, the mechanisms of charge transfer in these wire-like structures, especially in ambient conditions, are not yet fully understood. We describe here a layer-by-layer deposition methodology of short self-assembled cyclic peptide nanotubes, which results in vertically oriented nanotubes on gold substrates. Using this novel deposition methodology, we have fabricated molecular junctions with a conductive atomic force microscopy tip as a second electrode. Studies of the junctions' current-voltage characteristics as a function of the nanotube length revealed an efficient charge transfer in these supramolecular structures, with a low current attenuation constant of 0.1 Å(-1), which indicate that electron transfer is dominated by hopping. Moreover, the threshold voltage to field-emission dominated transport was found to increase with peptide length in a manner that depends on the nature of the contact with the electrodes. The flexibility in the design of the peptide monomers and the ability to control their sequential order over the nanotube by means of the layer-by-layer assembly process, which is demonstrated in this work, can be used to engineer the electronic properties of self-assembled peptide nanotubes toward device applications.

  15. Advances in single-charge detectors and their applications

    NASA Astrophysics Data System (ADS)

    Chechik, R.; Breskin, A.; Garty, G.; Shefer, E.; Singh, B. K.; Shchemelinin, S.

    2000-08-01

    Modern gas avalanche detectors are instruments of choice for detecting single charges deposited in gas or emitted from thin solid radiation converters. We discuss principal factors governing the operation of gas avalanche photomultipliers, combining solid photocathodes with advanced micro-pattern gaseous multipliers and summarize the properties of UV photocathodes and film-protected photocathodes for the visible spectral range. We review recent progress and applications of single-charge counting detectors and discuss in some detail their application to nanodosimetry and its relevance to studies of radiation damage to DNA.

  16. Single neutral pion production by charged-current $$\\bar{\

    DOE PAGES

    Le, T.; Paomino, J. L.; Aliaga, L.; ...

    2015-07-21

    We studied single neutral pion production via muon antineutrino charged-current interactions in plastic scintillator (CH) using the MINERvA detector exposed to the NuMI low-energy, wideband antineutrino beam at Fermilab. Measurement of this process constrains models of neutral pion production in nuclei, which is important because the neutral-current analog is a background for appearance oscillation experiments. Furthermore, the differential cross sections for π0 momentum and production angle, for events with a single observed π0 and no charged pions, are presented and compared to model predictions. These results comprise the first measurement of the π0 kinematics for this process.

  17. Sol-gel transition of charged fibrils composed of a model amphiphilic peptide.

    PubMed

    Owczarz, Marta; Bolisetty, Sreenath; Mezzenga, Raffaele; Arosio, Paolo

    2015-01-01

    We characterized the sol-gel transition of positively charged fibrils composed of the model amphiphilic peptide RADARADARADARADA (RADA 16-I) using a combination of microscopy, light scattering, microrheology and rheology techniques, and we investigated the dependence of the hydrogel formation on fibril concentration and ionic strength. The peptide is initially present as a dispersion of short rigid fibrils with average length of about 100 nm. During incubation, the fibrils aggregate irreversibly into longer fibrils and fibrillar aggregates. At peptide concentrations in the range 3-6.5 g/L, the fibrillar aggregates form a weak gel network which can be destroyed upon dilution. Percolation occurs without the formation of a nematic phase at a critical peptide concentration which decreases with increasing ionic strength. The gel structure can be well described in the frame of the fractal gel theory considering the network as a collection of fibrillar aggregates characterized by self-similar structure with a fractal dimension of 1.34.

  18. Modulating charge transfer through cyclic D,L-alpha-peptide self-assembly.

    PubMed

    Horne, W Seth; Ashkenasy, Nurit; Ghadiri, M Reza

    2005-02-04

    We describe a concise, solid support-based synthetic method for the preparation of cyclic d,l-alpha-peptides bearing 1,4,5,8-naphthalenetetracarboxylic acid diimide (NDI) side chains. Studies of the structural and photoluminescence properties of these molecules in solution show that the hydrogen bond-directed self-assembly of the cyclic d,l-alpha-peptide backbone promotes intermolecular NDI excimer formation. The efficiency of NDI charge transfer in the resulting supramolecular assemblies is shown to depend on the length of the linker between the NDI and the peptide backbone, the distal NDI substituent, and the number of NDIs incorporated in a given structure. The design rationale and synthetic strategies described here should provide a basic blueprint for a series of self-assembling cyclic d,l-alpha-peptide nanotubes with interesting optical and electronic properties.

  19. Modulating Charge Transfer Through Cyclic D,L α-Peptide Self-Assembly

    PubMed Central

    Horne, W. Seth; Ashkenasy, Nurit; Ghadiri, M. Reza

    2007-01-01

    We describe a concise solid support-based synthetic method for the preparation of cyclic D,L α-peptides bearing 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) side chains. Studies of the structural and photoluminescence properties of these molecules in solution show that the hydrogen bond directed self-assembly of the cyclic D,L α-peptide backbone promotes intermolecular NDI excimer formation. The efficiency of NDI charge transfer in the resulting supramolecular assemblies is shown to depend on the length of the linker between the NDI and the peptide backbone, the distal NDI substituent, and the number of NDIs incorporated in a given structure. The design rationale and synthetic strategies described here should provide a basic blueprint for a series of self-assembling cyclic D,L α-peptide nanotubes with interesting optical and electronic properties. PMID:15624124

  20. Fluoroolefins as peptide mimetics: a computational study of structure, charge distribution, hydration, and hydrogen bonding.

    PubMed

    Urban, Joseph J; Tillman, Brendon G; Cronin, William Andrew

    2006-09-28

    The design of peptide mimetic compounds is greatly facilitated by the identification of functionalities that can act as peptide replacements. The fluoroalkene moiety has recently been employed for that purpose. The purpose of this work is to characterize prototypical fluoroalkenes (fluoroethylene and 2-fluoro-2-butene) with respect to key properties of peptides (amides) including structure, charge distribution, hydration, and hydrogen bonding. The results are compared to those obtained for model peptides (formamide, N-methylacetamide). Calculations have been carried out at the MP2 and B3LYP levels of theory with the 6-311++G(2d,p) and 6-311++G(2d,2p) basis sets. The results suggest that the fluoroalkene is similar in steric requirements to a peptide bond but that there is less charge separation. Calculations of the hydration free energies with the PCM bulk continuum solvent model indicate that the fluoroalkene has much smaller hydration free energies than an amide but that the difference in solvation free energy for cis and trans isomers is comparable. In studies of complexes with water molecules, the fluoroalkene is found to engage in interactions that are analogous to backbone hydrogen-bonding interactions that govern many properties of natural peptides and proteins but with smaller interaction energies. In addition, key structural differences are noted when the fluoroalkene is playing the role of hydrogen-bond acceptor which may have implications in binding, aggregation, and conformational preferences in fluoroalkene peptidomimetics. The issue of cooperativity in hydrogen-bonding interactions in complexes with multiple waters has also been investigated. The fluoroalkene is found to exhibit cooperative effects that mirror those of the peptide but are smaller in magnitude. Thus, pairwise addivitity of interactions appears to more adequately describe the fluoroalkenes than the peptides they are intended to mimic.

  1. Improved sensitivity for quantification of proteins using triply charged cleavable isotope-coded affinity tag peptides.

    PubMed

    Qu, Jun; Straubinger, Robert M

    2005-01-01

    Isotope-coded affinity tag (ICAT) methods, in conjunction with capillary liquid chromatography/tandem mass spectrometry (LC/MS/MS), represent a promising approach for accurate protein quantification. However, sensitivity remains a challenge for the quantification of low-copy proteins in complex biological matrices. Here we investigated the electrospray ionization (ESI) and collision-activated dissociation (CAD) behavior of peptides derivatized with the cleavable ICAT (cICAT) reagent. For cICAT-peptides that were either synthesized or obtained by digestion of model proteins, the cICAT moiety showed a tendency toward protonation under positive ESI, producing relatively intense triply charged cICAT-peptide ions ([IP+3H]3+). [IP+3H]3+ exhibited significantly higher CAD reactivity than did the doubly charged cICAT-peptide ([IP+2H]2+), and produced a greater abundance of fragments at lower collision energies. Fragmentation spectra of [IP+3H]3+ showed variable intensities of doubly charged y and b ions, and the amount of sequence information obtained was dependent on the position of the cICAT-labeled cysteine residue in the peptide sequence. However, the absolute abundances of major fragments of [IP+3H]3+ were much higher than for [IP+2H]2+. Although the efficiency of identification of cICAT-peptides was compromised by their charge distribution toward the triply charged state and by the unique CAD behavior of the [IP+3H]3+ ions, it was found that the triply charged ions provided higher sensitivity than [IP+2H]2+ for quantification using multiple reaction monitoring (MRM). ESI and CAD conditions for MRM of [IP+3H]3+ were optimized, and, for all cICAT-peptides studied, MRM using [IP+3H]3+ as precursors showed 2- to 8-fold higher sensitivity than obtained using [IP+2H]2+, without compromising quantitative accuracy. Using this approach, the time course of tyrosine aminotransferase induction by methylprednisolone was monitored in rat livers. A remarkably better signal

  2. Ionization detector, electrode configuration and single polarity charge detection method

    DOEpatents

    He, Zhong

    1998-01-01

    An ionization detector, an electrode configuration and a single polarity charge detection method each utilize a boundary electrode which symmetrically surrounds first and second central interlaced and symmetrical electrodes. All of the electrodes are held at a voltage potential of a first polarity type. The first central electrode is held at a higher potential than the second central or boundary electrodes. By forming the first and second central electrodes in a substantially interlaced and symmetrical pattern and forming the boundary electrode symmetrically about the first and second central electrodes, signals generated by charge carriers are substantially of equal strength with respect to both of the central electrodes. The only significant difference in measured signal strength occurs when the charge carriers move to within close proximity of the first central electrode and are received at the first central electrode. The measured signals are then subtracted and compared to quantitatively measure the magnitude of the charge.

  3. Ionization detector, electrode configuration and single polarity charge detection method

    DOEpatents

    He, Z.

    1998-07-07

    An ionization detector, an electrode configuration and a single polarity charge detection method each utilize a boundary electrode which symmetrically surrounds first and second central interlaced and symmetrical electrodes. All of the electrodes are held at a voltage potential of a first polarity type. The first central electrode is held at a higher potential than the second central or boundary electrodes. By forming the first and second central electrodes in a substantially interlaced and symmetrical pattern and forming the boundary electrode symmetrically about the first and second central electrodes, signals generated by charge carriers are substantially of equal strength with respect to both of the central electrodes. The only significant difference in measured signal strength occurs when the charge carriers move to within close proximity of the first central electrode and are received at the first central electrode. The measured signals are then subtracted and compared to quantitatively measure the magnitude of the charge. 10 figs.

  4. Single Molecular Demonstration of Modulating Charge Inversion of DNA

    NASA Astrophysics Data System (ADS)

    Wang, Yanwei; Wang, Ruxia; Cao, Bozhi; Guo, Zilong; Yang, Guangcan

    2016-12-01

    Charge inversion of DNA is a counterintuitive phenomenon in which the effective charge of DNA switches its sign from negative to positive in the presence of multivalent counterions. The underlying microscopic mechanism is still controversial whether it is driven by a specific chemical affinity or electrostatic ion correlation. It is well known that DNA shows no charge inversion in normal aqueous solution of trivalent counterions though they can induce the conformational compaction of DNA. However, in the same trivalent counterion condition, we demonstrate for the first time the occurrence of DNA charge inversion by decreasing the dielectric constant of solution to make the electrophoretic mobility of DNA increase from a negative value to a positive value. In contrast, the charge inversion of DNA induced by quadrivalent counterions can be canceled out by increasing the dielectric constant of solution. The physical modulation of DNA effective charge in two ways unambiguously demonstrates that charge inversion of DNA is a predominantly electrostatic phenomenon driven by the existence of a strongly correlated liquid (SCL) of counterions at the DNA surface. This conclusion is also supported by the measurement of condensing and unraveling forces of DNA condensates by single molecular MT.

  5. Single Molecular Demonstration of Modulating Charge Inversion of DNA

    PubMed Central

    Wang, Yanwei; Wang, Ruxia; Cao, Bozhi; Guo, Zilong; Yang, Guangcan

    2016-01-01

    Charge inversion of DNA is a counterintuitive phenomenon in which the effective charge of DNA switches its sign from negative to positive in the presence of multivalent counterions. The underlying microscopic mechanism is still controversial whether it is driven by a specific chemical affinity or electrostatic ion correlation. It is well known that DNA shows no charge inversion in normal aqueous solution of trivalent counterions though they can induce the conformational compaction of DNA. However, in the same trivalent counterion condition, we demonstrate for the first time the occurrence of DNA charge inversion by decreasing the dielectric constant of solution to make the electrophoretic mobility of DNA increase from a negative value to a positive value. In contrast, the charge inversion of DNA induced by quadrivalent counterions can be canceled out by increasing the dielectric constant of solution. The physical modulation of DNA effective charge in two ways unambiguously demonstrates that charge inversion of DNA is a predominantly electrostatic phenomenon driven by the existence of a strongly correlated liquid (SCL) of counterions at the DNA surface. This conclusion is also supported by the measurement of condensing and unraveling forces of DNA condensates by single molecular MT. PMID:27929107

  6. Effect of the Surface on Charge Reduction and Desorption Kinetics of Soft Landed Peptide Ions

    SciTech Connect

    Hadjar, Omar; Wang, Peng; Futrell, Jean H.; Laskin, Julia

    2009-06-01

    Charge reduction and desorption kinetics of ions and neutral molecules produced by soft-landing of mass-selected singly and doubly protonated Gramicidin S (GS) on different surfaces was studied using time dependant in situ secondary ion mass spectrometry (SIMS) integrated in a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) research instrument. Soft-landing targets utilized in this study included inert self-assembled monolayers (SAMs) of 1-dodecane thiol (HSAM) and its fluorinated analog (FSAM) on gold and hydrophilic carboxyl-terminated (COOH-SAM) and amine-terminated (NH2-SAM) SAM surfaces. We observed efficient neutralization of soft-landed ions on the COOH-SAM surface, partial retention of only one proton on the HSAM surface and efficient retention of two protons on the FSAM surface. Slow desorption rates measured experimentally indicate fairly strong binding between peptide molecules and SAM surfaces with the binding energy of 20-25 kcal/mol.

  7. Implications of lipid monolayer charge characteristics on their selective interactions with a short antimicrobial peptide.

    PubMed

    Ciumac, Daniela; Campbell, Richard A; Xu, Hai; Clifton, Luke A; Hughes, Arwel V; Webster, John R P; Lu, Jian R

    2017-02-01

    Many antimicrobial peptides (AMPs) target bacterial membranes and they kill bacteria by causing structural disruptions. One of the fundamental issues however lies in the selective responses of AMPs to different cell membranes as a lack of selectivity can elicit toxic side effects to mammalian host cells. A key difference between the outer surfaces of bacterial and mammalian cells is the charge characteristics. We report a careful study of the binding of one of the representative AMPs, with the general sequence G(IIKK)4I-NH2 (G4), to the spread lipid monolayers of DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (sodium salt)) mimicking the charge difference between them, using the combined measurements from Langmuir trough, Brewster angle microscopy (BAM) and neutron reflection (NR). The difference in pressure rise upon peptide addition into the subphase clearly demonstrated the different interactions arising from different lipid charge features. Morphological changes from the BAM imaging confirmed the association of the peptide into the lipid monolayers, but there was little difference between them. However, NR studies revealed that the peptide bound 4 times more onto the DPPG monolayer than onto the DPPC monolayer. Importantly, whilst the peptide could only be associated with the head groups of DPPC it was well penetrated into the entire DPPG monolayer, showing that the electrostatic interaction strengthened the hydrophobic interaction and that the combined molecular interactive processes increased the power of G4 in disrupting the charged membranes. The results are discussed in the context of general antibacterial actions as observed from other AMPs and membrane lytic actions.

  8. Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy.

    PubMed

    Sun, Shiyu; Zhao, Guangxu; Huang, Yibing; Cai, Mingjun; Shan, Yuping; Wang, Hongda; Chen, Yuxin

    2016-07-01

    In this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers.

  9. Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy

    PubMed Central

    Sun, Shiyu; Zhao, Guangxu; Huang, Yibing; Cai, Mingjun; Shan, Yuping; Wang, Hongda; Chen, Yuxin

    2016-01-01

    In this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers. PMID:27363513

  10. Peptide Nanoparticle Delivery of Charge-Neutral Splice-Switching Morpholino Oligonucleotides

    PubMed Central

    Järver, Peter; Zaghloul, Eman M.; Arzumanov, Andrey A.; Saleh, Amer F.; McClorey, Graham; Hammond, Suzan M.; Hällbrink, Mattias; Langel, Ülo; Smith, C.I. Edvard; Wood, Matthew J.A.; Gait, Michael J.

    2015-01-01

    Oligonucleotide analogs have provided novel therapeutics targeting various disorders. However, their poor cellular uptake remains a major obstacle for their clinical development. Negatively charged oligonucleotides, such as 2′-O-Methyl RNA and locked nucleic acids have in recent years been delivered successfully into cells through complex formation with cationic polymers, peptides, liposomes, or similar nanoparticle delivery systems. However, due to the lack of electrostatic interactions, this promising delivery method has been unsuccessful to date using charge-neutral oligonucleotide analogs. We show here that lipid-functionalized cell-penetrating peptides can be efficiently exploited for cellular transfection of the charge-neutral oligonucleotide analog phosphorodiamidate morpholino. The lipopeptides form complexes with splice-switching phosphorodiamidate morpholino oligonucleotide and can be delivered into clinically relevant cell lines that are otherwise difficult to transfect while retaining biological activity. To our knowledge, this is the first study to show delivery through complex formation of biologically active charge-neutral oligonucleotides by cationic peptides. PMID:25594433

  11. All-atom molecular dynamics study of EAK16 peptide: the effect of pH on single-chain conformation, dimerization and self-assembly behavior.

    PubMed

    Emamyari, Soheila; Fazli, Hossein

    2014-05-01

    Single-chain equilibrium conformation and dimerization of the three types of ionic EAK16 peptide are studied under three pH conditions using all-atom molecular dynamics simulations. It is found that both the single-chain conformation and the dimerization process of EAK16-IV are considerably different from those of the two other types, EAK16-I and EAK16-II. The value of pH is found to have a stronger effect on the single-chain conformation and dimerization of EAK16-IV. It is shown that in addition to the charge pattern on the peptide chains, the size of the side chains of the charged amino acids plays role in the conformation of the peptide chains and their dimerization. The results shed light on the pH-dependent self-assembly behavior of EAK16 peptide in the bulk solution, which has been reported in the literature.

  12. Action growth of charged black holes with a single horizon

    NASA Astrophysics Data System (ADS)

    Cai, Rong-Gen; Sasaki, Misao; Wang, Shao-Jiang

    2017-06-01

    According to the conjecture "complexity equals action," the complexity of a holographic state is equal to the action of a Wheeler-DeWitt (WDW) patch of black holes in anti-de Sitter space. In this paper we calculate the action growth of charged black holes with a single horizon, paying attention to the contribution from a spacelike singularity inside the horizon. We consider two kinds of such charged black holes: one is a charged dilaton black hole, and the other is a Born-Infeld black hole with β2Q2<1 /4 . In both cases, although an electric charge appears in the black hole solutions, the inner horizon is absent; instead a spacelike singularity appears inside the horizon. We find that the action growth of the WDW patch of the charged black hole is finite and satisfies the Lloyd bound. As a check, we also calculate the action growth of a charged black hole with a phantom Maxwell field. In this case, although the contributions from the bulk integral and the spacelike singularity are individually divergent, these two divergences just cancel each other and a finite action growth is obtained. But in this case, the Lloyd bound is violated as expected.

  13. Biogenic and Synthetic Peptides with Oppositely Charged Amino Acids as Binding Sites for Mineralization

    PubMed Central

    Lemloh, Marie-Louise; Altintoprak, Klara; Wege, Christina; Weiss, Ingrid M.; Rothenstein, Dirk

    2017-01-01

    Proteins regulate diverse biological processes by the specific interaction with, e.g., nucleic acids, proteins and inorganic molecules. The generation of inorganic hybrid materials, such as shell formation in mollusks, is a protein-controlled mineralization process. Moreover, inorganic-binding peptides are attractive for the bioinspired mineralization of non-natural inorganic functional materials for technical applications. However, it is still challenging to identify mineral-binding peptide motifs from biological systems as well as for technical systems. Here, three complementary approaches were combined to analyze protein motifs consisting of alternating positively and negatively charged amino acids: (i) the screening of natural biomineralization proteins; (ii) the selection of inorganic-binding peptides derived from phage display; and (iii) the mineralization of tobacco mosaic virus (TMV)-based templates. A respective peptide motif displayed on the TMV surface had a major impact on the SiO2 mineralization. In addition, similar motifs were found in zinc oxide- and zirconia-binding peptides indicating a general binding feature. The comparative analysis presented here raises new questions regarding whether or not there is a common design principle based on acidic and basic amino acids for peptides interacting with minerals. PMID:28772478

  14. Effects of single amino acid substitution on the biophysical properties and biological activities of an amphipathic α-helical antibacterial peptide against Gram-negative bacteria.

    PubMed

    Tan, Juanjuan; Huang, Jinfeng; Huang, Yibing; Chen, Yuxin

    2014-07-24

    An antimicrobial peptide, known as V13K, was utilized as the framework to study the effects of charge, hydrophobicity and helicity on the biophysical properties and biological activities of α-helical peptides. Six amino acids (Lys, Glu, Gly, Ser, Ala, and Leu) were individually used to substitute the original hydrophobic valine at the selected sixteenth location on the non-polar face of V13K. The results showed that the single amino acid substitutions changed the hydrophobicity of peptide analogs as monitored by RP-HPLC, but did not cause significant changes on peptide secondary structures both in a benign buffer and in a hydrophobic environment. The biological activities of the analogs exhibited a hydrophobicity-dependent behavior. The mechanism of peptide interaction with the outer membrane and cytoplasmic membrane of Gram-negative bacteria was investigated. We demonstrated that this single amino acid substitution method has valuable potential for the rational design of antimicrobial peptides with enhanced activities.

  15. Optimization of Single-Sided Charge-Sharing Strip Detectors

    NASA Technical Reports Server (NTRS)

    Hamel, L.A.; Benoit, M.; Donmez, B.; Macri, J. R.; McConnell, M. L.; Ryan, J. M.; Narita, T.

    2006-01-01

    Simulation of the charge sharing properties of single-sided CZT strip detectors with small anode pads are presented. The effect of initial event size, carrier repulsion, diffusion, drift, trapping and detrapping are considered. These simulations indicate that such a detector with a 150 m pitch will provide good charge sharing between neighboring pads. This is supported by a comparison of simulations and measurements for a similar detector with a coarser pitch of 225 m that could not provide sufficient sharing. The performance of such a detector used as a gamma-ray imager is discussed.

  16. Dissecting a role of a charge and conformation of Tat2 peptide in allosteric regulation of 20S proteasome.

    PubMed

    Witkowska, Julia; Karpowicz, Przemysław; Gaczynska, Maria; Osmulski, Pawel A; Jankowska, Elżbieta

    2014-08-01

    Proteasome is a 'proteolytic factory' that constitutes an essential part of the ubiquitin-proteasome pathway. The involvement of proteasome in regulation of all major aspects of cellular physiology makes it an attractive drug target. So far, only inhibitors of the proteasome entered the clinic as anti-cancer drugs. However, proteasome regulators may also be useful for treatment of inflammatory and neurodegenerative diseases. We established in our previous studies that the peptide Tat2, comprising the basic domain of HIV-1 Tat protein: R(49) KKRRQRR(56) , supplemented with Q(66) DPI(69) fragment, inhibits the 20S proteasome in a noncompetitive manner. Mechanism of Tat2 likely involves allosteric regulation because it competes with the proteasome natural 11S activator for binding to the enzyme noncatalytic subunits. In this study, we performed alanine walking coupled with biological activity measurements and FTIR and CD spectroscopy to dissect contribution of a charge and conformation of Tat2 to its capability to influence peptidase activity of the proteasome. In solution, Tat2 and most of its analogs with a single Ala substitution preferentially adopted a conformation containing PPII/turn structural motifs. Replacing either Asp10 or two or more adjacent Arg/Lys residues induced a random coil conformation, probably by disrupting ionic interactions responsible for stabilization of the peptides ordered structure. The random coil Tat2 analogs lost their capability to activate the latent 20S proteasome. In contrast, inhibitory properties of the peptides more significantly depended on their positive charge. The data provide valuable clues for the future optimization of the Tat2-based proteasome regulators. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

  17. Charge transfer dissociation (CTD) mass spectrometry of peptide cations using kiloelectronvolt helium cations.

    PubMed

    Hoffmann, William D; Jackson, Glen P

    2014-11-01

    A kiloelectronvolt beam of helium ions is used to ionize and fragment precursor peptide ions starting in the 1+ charge state. The electron affinity of helium cations (24.6 eV) exceeds the ionization potential of protonated peptides and can therefore be used to abstract an electron from--or charge exchange with--the isolated precursor ions. Kiloelectronvolt energies are used, (1) to overcome the Coulombic repulsion barrier between the cationic reactants, (2) to overcome ion-defocussing effects in the ion trap, and (3) to provide additional activation energy. Charge transfer dissociation (CTD) of the [M+H](+) precursor of Substance P gives product ions such as [M+H](2+•) and a dominant series of a ions in both the 1+ and 2+ charge states. These observations, along with the less-abundant a + 1 ions, are consistent with ultraviolet photodissociation (UVPD) results of others and indicate that C-C(α) cleavages are possible through charge exchange with helium ions. Although the efficiencies and timescale of CTD are not yet suitable for on-line chromatography, this new approach to ion activation provides an additional potential tool for the interrogation of gas phase ions.

  18. Charge Transfer Dissociation (CTD) Mass Spectrometry of Peptide Cations: Study of Charge State Effects and Side-Chain Losses

    NASA Astrophysics Data System (ADS)

    Li, Pengfei; Jackson, Glen P.

    2017-01-01

    1+, 2+, and 3+ precursors of substance P and bradykinin were subjected to helium cation irradiation in a 3D ion trap mass spectrometer. Charge exchange with the helium cations produces a variety of fragment ions, the number and type of which are dependent on the charge state of the precursor ions. For 1+ peptide precursors, fragmentation is generally restricted to C-CO backbone bonds (a and x ions), whereas for 2+ and 3+ peptide precursors, all three backbone bonds (C-CO, C-N, and N-Cα) are cleaved. The type of backbone bond cleavage is indicative of possible dissociation channels involved in CTD process, including high-energy, kinetic-based, and ETD-like pathways. In addition to backbone cleavages, amino acid side-chain cleavages are observed in CTD, which are consistent with other high-energy and radical-mediated techniques. The unique dissociation pattern and supplementary information available from side-chain cleavages make CTD a potentially useful activation method for the structural study of gas-phase biomolecules.

  19. Charge Transfer Dissociation (CTD) Mass Spectrometry of Peptide Cations: Study of Charge State Effects and Side-Chain Losses

    NASA Astrophysics Data System (ADS)

    Li, Pengfei; Jackson, Glen P.

    2017-07-01

    1+, 2+, and 3+ precursors of substance P and bradykinin were subjected to helium cation irradiation in a 3D ion trap mass spectrometer. Charge exchange with the helium cations produces a variety of fragment ions, the number and type of which are dependent on the charge state of the precursor ions. For 1+ peptide precursors, fragmentation is generally restricted to C-CO backbone bonds ( a and x ions), whereas for 2+ and 3+ peptide precursors, all three backbone bonds (C-CO, C-N, and N-Cα) are cleaved. The type of backbone bond cleavage is indicative of possible dissociation channels involved in CTD process, including high-energy, kinetic-based, and ETD-like pathways. In addition to backbone cleavages, amino acid side-chain cleavages are observed in CTD, which are consistent with other high-energy and radical-mediated techniques. The unique dissociation pattern and supplementary information available from side-chain cleavages make CTD a potentially useful activation method for the structural study of gas-phase biomolecules.

  20. Charge Blinking Statistics of Semiconductor Nanocrystals Revealed by Carbon Nanotube Single Charge Sensors.

    PubMed

    Zbydniewska, Ewa; Duzynska, Anna; Popoff, Michka; Hourlier, Djamila; Lenfant, Stéphane; Judek, Jaroslaw; Zdrojek, Mariusz; Mélin, Thierry

    2015-10-14

    We demonstrate the relation between the optical blinking of colloidal semiconductor nanocrystals (NCs) and their electrical charge blinking for which we provide the first experimental observation of power-law statistics. To show this, we harness the performance of CdSe/ZnS NCs coupled with carbon nanotube field-effect transistors (CNTFETs), which act as single charge-sensitive electrometers with submillisecond time resolution, at room temperature. A random telegraph signal (RTS) associated with the NC single-trap charging is observed and exhibits power-law temporal statistics (τ(-α), with α in the range of ∼1-3), and a Lorentzian current noise power spectrum with a well-defined 1/f(2) corner. The spectroscopic analysis of the NC-CNTFET devices is consistent with the charging of NC defect states with a charging energy of Ec ≥ 200 meV. These results pave the way for a deeper understanding of the physics and technology of nanocrystal-based optoelectronic devices.

  1. Charging and defects in single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Nguyen, Khoi Thi

    2011-12-01

    Single-Walled Carbon Nanotubes (SWCNTs) have been one of the most intensively studied materials. Because of their single-atomic-layer structure, SWCNTs are extremely sensitive to environmental interactions, in which charge transfer and defect formation are the most notable effects. Among a number of microscopic and spectroscopic methods, Raman spectroscopy is a widely used technique to characterize physics and chemistry of CNTs. By utilizing simultaneous Raman and electron transport measurements along with polymer electrolyte gating, this dissertation focuses on studying charging and defects in SWCNTs at single nanotube level and in single layer graphene, the building block of SWCNTs. By controllably charging metallic SWCNTs (m-CNTs), the intrinsic nature of the broad and asymmetric Fano lineshape in Raman G band of m-CNTs was first time evidenced. The observation that Fano component is most broadened and downshifted when Fermi level is close to the Dirac point (DP) reveals its origin as the consequence of coupling of phonon to vertical electronic transitions. Furthermore, we have systematically introduced covalent defects to m-CNTs to study how phonon softening and electrical characteristics are affected by disorders. In addition to decreasing electrical conductance with increasing on/off current ratio eventually leading to semiconducting behavior, adding covalent defects reduces the degree of softening and broadening of longitudinal optical (LO) phonon mode but enhances the softening of transverse optical (TO) mode of the G-band near the DP. Charging and defect effects in semiconducting SWCNTs and single layer graphene, a closely related material to SWCNTs, have also been discussed.

  2. Photoinitated charge separation in a hybrid titanium dioxide metalloporphyrin peptide material

    NASA Astrophysics Data System (ADS)

    Fry, H. Christopher; Liu, Yuzi; Dimitrijevic, Nada M.; Rajh, Tijana

    2014-08-01

    In natural systems, electron flow is mediated by proteins that spatially organize donor and acceptor molecules with great precision. Achieving this guided, directional flow of information is a desirable feature in photovoltaic media. Here, we design self-assembled peptide materials that organize multiple electronic components capable of performing photoinduced charge separation. Two peptides, c16-AHL3K3-CO2H and c16-AHL3K9-CO2H, self-assemble into fibres and provide a scaffold capable of binding a metalloporphyrin via histidine axial ligation and mineralize titanium dioxide (TiO2) on the lysine-rich surface of the resulting fibrous structures. Electron paramagnetic resonance studies of this self-assembled material under continuous light excitation demonstrate charge separation induced by excitation of the metalloporphyrin and mediated by the peptide assembly structure. This approach to dye-sensitized semiconducting materials offers a means to spatially control the dye molecule with respect to the semiconducting material through careful, strategic peptide design.

  3. Charge inhomogeneity in a single and bilayer graphene

    NASA Astrophysics Data System (ADS)

    Dahal, Hari; Wehling, Tim; Bedell, Kevin; Zhu, Jian-Xin; Balatsky, Alexander

    2008-03-01

    We study the possibility of charge ordered state in both single and bilayer graphene using a real space tight binding model. We find that the single layer graphene always remains in a liquid phase; the reason being the higher kinetic energy compared to the potential energy. The bilayer graphene on the other hand can have an inhomogeneous distribution of the charge, namely the charge density wave (CDW) state. The CDW state is commensurate with the lattice. The charge ordered state is stabilized by the Coulomb interaction of the carriers of two layers. We also predicted a kinetic energy driven (KID) inhomogeneous phase. This phase can be stabilized by the inter layer hopping energy. The KID phase and the CDW phase compete with each other below the half filling whereas they cooperate above half filling. For the physical parameter of bilayer graphene CDW phase always wins over the KID phase. Hari P. Dahal, Tim O. Wehling, Kevin S. Bedell, Jian-Xin Zhu, Alexander V. Balatsky

  4. Charged-particle spectroscopy in organic semiconducting single crystals

    SciTech Connect

    Ciavatti, A.; Basiricò, L.; Fraboni, B.; Fraleoni-Morgera, A.

    2016-04-11

    The use of organic materials as radiation detectors has grown, due to the easy processability in liquid phase at room temperature and the possibility to cover large areas by means of low cost deposition techniques. Direct charged-particle detectors based on solution-grown Organic Semiconducting Single Crystals (OSSCs) are shown to be capable to detect charged particles in pulse mode, with very good peak discrimination. The direct charged-particle detection in OSSCs has been assessed both in the planar and in the vertical axes, and a digital pulse processing algorithm has been used to perform pulse height spectroscopy and to study the charge collection efficiency as a function of the applied bias voltage. Taking advantage of the charge spectroscopy and the good peak discrimination of pulse height spectra, an Hecht-like behavior of OSSCs radiation detectors is demonstrated. It has been possible to estimate the mobility-lifetime value in organic materials, a fundamental parameter for the characterization of radiation detectors, whose results are equal to μτ{sub coplanar} = (5 .5 ± 0.6 ) × 10{sup −6} cm{sup 2}/V and μτ{sub sandwich} = (1 .9 ± 0.2 ) × 10{sup −6} cm{sup 2}/V, values comparable to those of polycrystalline inorganic detectors. Moreover, alpha particles Time-of-Flight experiments have been carried out to estimate the drift mobility value. The results reported here indicate how charged-particle detectors based on OSSCs possess a great potential as low-cost, large area, solid-state direct detectors operating at room temperature. More interestingly, the good detection efficiency and peak discrimination observed for charged-particle detection in organic materials (hydrogen-rich molecules) are encouraging for their further exploitation in the detection of thermal and high-energy neutrons.

  5. Charged-particle spectroscopy in organic semiconducting single crystals

    NASA Astrophysics Data System (ADS)

    Ciavatti, A.; Sellin, P. J.; Basiricò, L.; Fraleoni-Morgera, A.; Fraboni, B.

    2016-04-01

    The use of organic materials as radiation detectors has grown, due to the easy processability in liquid phase at room temperature and the possibility to cover large areas by means of low cost deposition techniques. Direct charged-particle detectors based on solution-grown Organic Semiconducting Single Crystals (OSSCs) are shown to be capable to detect charged particles in pulse mode, with very good peak discrimination. The direct charged-particle detection in OSSCs has been assessed both in the planar and in the vertical axes, and a digital pulse processing algorithm has been used to perform pulse height spectroscopy and to study the charge collection efficiency as a function of the applied bias voltage. Taking advantage of the charge spectroscopy and the good peak discrimination of pulse height spectra, an Hecht-like behavior of OSSCs radiation detectors is demonstrated. It has been possible to estimate the mobility-lifetime value in organic materials, a fundamental parameter for the characterization of radiation detectors, whose results are equal to μτcoplanar = (5 .5 ± 0.6 ) × 10-6 cm2/V and μτsandwich = (1 .9 ± 0.2 ) × 10-6 cm2/V, values comparable to those of polycrystalline inorganic detectors. Moreover, alpha particles Time-of-Flight experiments have been carried out to estimate the drift mobility value. The results reported here indicate how charged-particle detectors based on OSSCs possess a great potential as low-cost, large area, solid-state direct detectors operating at room temperature. More interestingly, the good detection efficiency and peak discrimination observed for charged-particle detection in organic materials (hydrogen-rich molecules) are encouraging for their further exploitation in the detection of thermal and high-energy neutrons.

  6. Ion-Ion Reactions with Fixed-Charge Modified Proteins to Produce Ions in a Single, Very High Charge State

    PubMed Central

    Frey, Brian L.; Krusemark, Casey J.; Ledvina, Aaron R.; Coon, Joshua J.; Belshaw, Peter J.

    2008-01-01

    Electrospray ionization (ESI) of denatured proteins produces a mass spectrum with a broad distribution of multiply charged ions. Attaching fixed positive charges, specifically quaternary ammonium groups, to proteins at their carboxylic acid groups generates substantially higher charge states compared to the corresponding unmodified proteins in positive-mode ESI. Ion-ion reactions of these modified proteins with reagent anions leads to charge reduction by proton transfer. These proton transfer reactions cannot remove charge from the quaternary ammonium groups, which do not have a proton to transfer to the anion. Thus, one might expect charge reduction to stop at a single charge state equal to the number of fixed charges on the modified protein. However, ion-ion reactions yield charge states lower than this number of fixed charges due to anion attachment (adduction) to the proteins. Charge reduction via ion-molecule reactions involving gas-phase bases also give adducts on the modified protein ions in low charge states. Such adducts are avoided by keeping the ions in charge states well above the number of fixed charges. In the present work protein ions were selectively “parked” within an ion trap mass spectrometer in a high charge state by mild radiofrequency excitation that dramatically slows their ion-ion reaction rate—a technique termed “ion parking”. The combination of ion parking with the fixed-charge modified proteins permits generation of a large population of ions in a single, very high charge state. PMID:19802328

  7. Ion-Ion Reactions with Fixed-Charge Modified Proteins to Produce Ions in a Single, Very High Charge State.

    PubMed

    Frey, Brian L; Krusemark, Casey J; Ledvina, Aaron R; Coon, Joshua J; Belshaw, Peter J; Smith, Lloyd M

    2008-10-01

    Electrospray ionization (ESI) of denatured proteins produces a mass spectrum with a broad distribution of multiply charged ions. Attaching fixed positive charges, specifically quaternary ammonium groups, to proteins at their carboxylic acid groups generates substantially higher charge states compared to the corresponding unmodified proteins in positive-mode ESI. Ion-ion reactions of these modified proteins with reagent anions leads to charge reduction by proton transfer. These proton transfer reactions cannot remove charge from the quaternary ammonium groups, which do not have a proton to transfer to the anion. Thus, one might expect charge reduction to stop at a single charge state equal to the number of fixed charges on the modified protein. However, ion-ion reactions yield charge states lower than this number of fixed charges due to anion attachment (adduction) to the proteins. Charge reduction via ion-molecule reactions involving gas-phase bases also give adducts on the modified protein ions in low charge states. Such adducts are avoided by keeping the ions in charge states well above the number of fixed charges. In the present work protein ions were selectively "parked" within an ion trap mass spectrometer in a high charge state by mild radiofrequency excitation that dramatically slows their ion-ion reaction rate-a technique termed "ion parking". The combination of ion parking with the fixed-charge modified proteins permits generation of a large population of ions in a single, very high charge state.

  8. ``Hot spots'' growth on single nanowire controlled by electric charge

    NASA Astrophysics Data System (ADS)

    Xi, Shaobo; Liu, Xuehua; He, Ting; Tian, Lei; Wang, Wenhui; Sun, Rui; He, Weina; Zhang, Xuetong; Zhang, Jinping; Ni, Weihai; Zhou, Xiaochun

    2016-06-01

    ``Hot spots'' - a kind of highly active site, which are usually composed of some unique units, such as defects, interfaces, catalyst particles or special structures - can determine the performance of nanomaterials. In this paper, we study a model system, i.e. ``hot spots'' on a single Ag nanowire in the galvanic replacement reaction (GRR), by dark-field microscopy. The research reveals that electric charge can be released by the formation reaction of AgCl, and consequently the electrochemical potential on Ag nanowire drops. The electric charge could induce the reduction of Ag+ to form the ``hot spots'' on the nanowire during the GRR. The appearance probability of ``hot spots'' is almost even along the Ag nanowire, while it is slightly lower near the two ends. The spatial distance between adjacent ``hot spots'' is also controlled by the charge, and obeys a model based on Boltzmann distribution. In addition, the distance distribution here has an advantage in electron transfer and energy saving. Therefore, it's necessary to consider the functions of electric charge during the synthesis or application of nanomaterials.``Hot spots'' - a kind of highly active site, which are usually composed of some unique units, such as defects, interfaces, catalyst particles or special structures - can determine the performance of nanomaterials. In this paper, we study a model system, i.e. ``hot spots'' on a single Ag nanowire in the galvanic replacement reaction (GRR), by dark-field microscopy. The research reveals that electric charge can be released by the formation reaction of AgCl, and consequently the electrochemical potential on Ag nanowire drops. The electric charge could induce the reduction of Ag+ to form the ``hot spots'' on the nanowire during the GRR. The appearance probability of ``hot spots'' is almost even along the Ag nanowire, while it is slightly lower near the two ends. The spatial distance between adjacent ``hot spots'' is also controlled by the charge, and obeys a

  9. Charge State Coalescence During Electrospray Ionization Improves Peptide Identification by Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Meyer, Jesse G.; A. Komives, Elizabeth

    2012-08-01

    We report the effects of supercharging reagents dimethyl sulphoxide (DMSO) and m-nitrobenzyl alcohol ( m-NBA) applied to untargeted peptide identification, with special emphasis on non-tryptic peptides. Peptides generated from a mixture of five standard proteins digested with trypsin, elastase, or pepsin were separated with nanoflow liquid chromatography using mobile phases modified with either 5 % DMSO or 0.1 % m-NBA. Eluting peptides were ionized by online electrospray and sequenced by both CID and ETD using data-dependent MS/MS. Statistically significant improvements in peptide identifications were observed with DMSO co-solvent. In order to understand this observation, we assessed the effects of supercharging reagents on the chromatographic separation and the electrospray quality. The increase in identifications was not due to supercharging, which was greater for the 0.1 % m-NBA co-solvent and not observed for the 5.0 % DMSO co-solvent. The improved MS/MS efficiency using the DMSO modified mobile phase appeared to result from charge state coalescence.

  10. Generation of highly charged peptide and protein ions by atmospheric pressure matrix-assisted infrared laser desorption/ionization ion trap mass spectrometry.

    PubMed

    König, Simone; Kollas, Oliver; Dreisewerd, Klaus

    2007-07-15

    We show that highly charged ions can be generated if a pulsed infrared laser and a glycerol matrix are employed for atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry with a quadrupole ion trap. Already for small peptides like bradykinin, doubly protonated ions form the most abundant analyte signal in the mass spectra. The center of the charge-state distribution increases with the size of the analyte. For example, insulin is detected with a most abundant ion signal corresponding to a charge state of four, whereas for cytochrome c, the 10 times protonated ion species produces the most intense signal. Myoglobin is observed with up to 13 charges. The high m/z ratios allow us to use the Paul trap for the detection of MALDI-generated protein ions that are, owing to their high molecular weight, not amenable in their singly protonated charge state. Formation of multiple charges critically depends on the addition of diluted acid to the analyte-matrix solution. Tandem mass spectra generated by collision-induced dissociation of doubly charged peptides are also presented. The findings allow speculations about the involvement of electrospray ionization processes in these MALDI experiments.

  11. Gas-phase Structure and Fragmentation Pathways of Singly Protonated Peptides with N-terminal Arginine

    PubMed Central

    Bythell, Benjamin J.; Csonka, István P.; Suhai, Sándor; Barofsky, Douglas F.; Paizs, Béla

    2010-01-01

    The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b2 ions or facilely rearrange to form anhydrides from which both b2 and b2+H2O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b2 and b2+H2O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc., 2009, 131, 14057–14065.). In addition to these findings we also report on the mechanisms for the formation of the b1 ion, neutral loss (H2O, NH3, guanidine) fragment ions and the d3 ion. PMID:20973555

  12. Lipid dependence of membrane anchoring properties and snorkeling behavior of aromatic and charged residues in transmembrane peptides.

    PubMed

    Strandberg, Erik; Morein, Sven; Rijkers, Dirk T S; Liskamp, Rob M J; van der Wel, Patrick C A; Killian, J Antoinette

    2002-06-11

    31P NMR spectroscopy was used to investigate the effects of transmembrane alpha-helical peptides with different flanking residues on the phase behavior of phosphatidylethanolamine and phosphatidylethanolamine/phosphatidylglycerol (molar ratio 7:3) model membranes. It was found that tryptophan-flanked (WALP) peptides and lysine-flanked (KALP) peptides both promote formation of nonlamellar phases in these lipid systems in a mismatch-dependent manner. Based on this mismatch dependence, it was concluded that the effective hydrophobic length of KALP peptides is considerably shorter than that of the corresponding WALP peptides. Peptides with other positively charged residues showed very similar effects as KALP. The results suggest that the peptides have a well-defined effective hydrophobic length, which is different for charged and aromatic flanking residues, but which is independent of the precise chemical nature of the side chain. Strikingly, the effective length of KALP peptides in the lipid systems investigated here is much smaller than that previously found for the same peptides in phosphatidylcholine. This suggests that snorkeling of lysine side chains, as proposed to occur in phosphatidylcholine, does not occur in lipid systems that are prone to form nonlamellar phases by themselves. This suggestion was supported by using peptides with shortened lysine side chains and by investigating the effects of mixtures of WALP and KALP peptides. The lipid dependency of the snorkeling behavior is explained by considering the free energy cost of snorkeling in relation to the free energy cost of the formation of nonlamellar phases.

  13. Quantifying Polarization at Peptide-Gold Interfaces Due to Mirror Charges

    NASA Astrophysics Data System (ADS)

    Jha, Kshitij; Heinz, Hendrik

    2009-03-01

    The contribution of attractive polarization effects to interfacial interactions between even gold 111 and 100 surfaces with water, a neutral peptide (A3: AYSSGAPPMPPF), and a charged peptide (FlgNa3: DYKDDDDK with Na counter-ions) in aqueous solution is quantified as part of an investigation to understand binding and specific interactions between peptides and metal nanoparticles. We apply the simple concept of mirror charges (additional Coulomb energy) a posteriori to molecular dynamics trajectories for different locations of the mirror plane, using the Consistent Valence Force Field (CVFF) extended with accurate LJ parameters for fcc metals. The values of polarization energy show a relative trend A3 < Flg-Na3< H2O, and they are lower on 111 surfaces compared to 100 surfaces. On average, polarization energies amount to ˜140 mJ/m^2 when the image plane is located at the jellium edge and decrease to ˜5 mJ/m^2 when the image plane is located at the metal surface plane. Experiment and theory suggest a location close to the jellium edge, possibly inwards to the metal surface plane. Though absolute values are thus high, up to 2 kcal/mol per amino acid, they are <10% of the experimental value of 1400 mJ/m^2 for gold-water interfacial tensions and <10% compared to the strongest adsorbing amino acids (>20 kcal/mol).

  14. Consensus Prediction of Charged Single Alpha-Helices with CSAHserver.

    PubMed

    Dudola, Dániel; Tóth, Gábor; Nyitray, László; Gáspári, Zoltán

    2017-01-01

    Charged single alpha-helices (CSAHs) constitute a rare structural motif. CSAH is characterized by a high density of regularly alternating residues with positively and negatively charged side chains. Such segments exhibit unique structural properties; however, there are only a handful of proteins where its existence is experimentally verified. Therefore, establishing a pipeline that is capable of predicting the presence of CSAH segments with a low false positive rate is of considerable importance. Here we describe a consensus-based approach that relies on two conceptually different CSAH detection methods and a final filter based on the estimated helix-forming capabilities of the segments. This pipeline was shown to be capable of identifying previously uncharacterized CSAH segments that could be verified experimentally. The method is available as a web server at http://csahserver.itk.ppke.hu and also a downloadable standalone program suitable to scan larger sequence collections.

  15. A compact source for bunches of singly charged atomic ions

    NASA Astrophysics Data System (ADS)

    Murböck, T.; Schmidt, S.; Andelkovic, Z.; Birkl, G.; Nörtershäuser, W.; Vogel, M.

    2016-04-01

    We have built, operated, and characterized a compact ion source for low-energy bunches of singly charged atomic ions in a vacuum beam line. It is based on atomic evaporation from an electrically heated oven and ionization by electron impact from a heated filament inside a grid-based ionization volume. An adjacent electrode arrangement is used for ion extraction and focusing by applying positive high-voltage pulses to the grid. The method is particularly suited for experimental environments which require low electromagnetic noise. It has proven simple yet reliable and has been used to produce μs-bunches of up to 106 Mg+ ions at a repetition rate of 1 Hz. We present the concept, setup and characterizing measurements. The instrument has been operated in the framework of the SpecTrap experiment at the HITRAP facility at GSI/FAIR to provide Mg+ ions for sympathetic cooling of highly charged ions by laser-cooled 24Mg+.

  16. CD and NMR investigation of collagen peptides mimicking a pathological Gly-Ser mutation and a natural interruption in a similar highly charged sequence context.

    PubMed

    Sun, Xiuxia; Liu, Songqing; Yu, Wenyuan; Wang, Shaoru; Xiao, Jianxi

    2016-02-01

    Even a single Gly substitution in the triple helix domain of collagen leads to pathological conditions while natural interruptions are suggested to play important functional roles. Two peptides-one mimicking a pathological Gly-Ser substitution (ERSEQ) and the other one modeling a similar natural interruption sequence (DRSER)-are designed to facilitate the comparison for elucidating the molecular basis of their different biological roles. CD and NMR investigation of peptide ERSEQ indicates a reduction of the thermal stability and disruption of hydrogen bonding at the Ser mutation site, providing a structural basis of the OI disease resulting from the Gly-Ser mutation in the highly charged RGE environment. Both CD and NMR real-time folding results indicate that peptide ERSEQ displays a comparatively slower folding rate than peptide DRSER, suggesting that the Gly-Ser mutation may lead to a larger interference in folding than the natural interruption in a similar RSE context. Our studies suggest that unlike the rigid GPO environment, the abundant R(K)GE(D) motif may provide a more flexible sequence environment that better accommodates mutations as well as interruptions, while the electrostatic interactions contribute to its stability. These results shed insight into the molecular features of the highly charged motif and may aid the design of collagen biomimetic peptides containing important biological sites.

  17. Induced polymersome formation from a diblock PS-b-PAA polymer via encapsulation of positively charged proteins and peptides.

    PubMed

    Hvasanov, David; Wiedenmann, Jörg; Braet, Filip; Thordarson, Pall

    2011-06-14

    In contrast to simple salts or negatively charged macromolecules, positively charged proteins and peptides including cytochrome c (yeast) and poly-L-lysine are efficiently encapsulated while inducing the formation of polymersomes from polystyrene(140)-b-poly(acrylic acid)(48) (PS(140)-b-PAA(48)). This journal is © The Royal Society of Chemistry 2011

  18. Exploring the evaluation of net charge, hydrodynamic size and shape of peptides through experimental electrophoretic mobilities obtained from CZE.

    PubMed

    Piaggio, Maria V; Peirotti, Marta B; Deiber, Julio A

    2006-12-01

    This work explores the validity of simple CZE models to analyze the electrophoretic mobilities of 102 peptides reported in literature. These models are based mainly on fundamental physicochemical theories providing analytical expressions amenable to relatively simple numerical analysis. Thus, the Linderstrøm-Lang capillary electrophoresis model (LLCEM) and its perturbed version (PLLCEM), proposed and applied previously to the CZE of globular proteins, are adapted and used here for peptides. Also the effects of pK-shifts on net charge, hydration and hydrodynamic size and shape of peptides are analyzed and discussed. Emphasis is placed on the fact that these parameters are physically coupled, and thus a variation in the net charge may produce an appreciable change in the hydrodynamic size of peptides. Within the framework of CZE, peptides may be assumed as having a hydrodynamic volume associated with either spherical or spheroidal particles. The effects on peptide net charge and hydrodynamic size, of electrostatic interaction between a pair of charged groups in the chain and electrical permitivitty around the peptide domain are studied. The predictions of the PLLCEM and LLCEM are in good agreement with results reported previously in the literature. Several limitations concerning these models and some needs for further research are also described.

  19. Charge, Color, and Conformation: Spectroscopy on Isomer-Selected Peptide Ions.

    PubMed

    Choi, Chang Min; Simon, Anne-Laure; Chirot, Fabien; Kulesza, Alexander; Knight, Geoffrey; Daly, Steven; MacAleese, Luke; Antoine, Rodolphe; Dugourd, Philippe

    2016-02-04

    Monitoring the chromism induced by intramolecular hydrogen and charge transfers within proteins as well as the isomerization of both protein and cofactor is essential not only to understand photoactive signaling pathways but also to design targeted opto-switchable proteins. We used a dual-ion mobility drift tube coupled to a tunable picosecond laser to explore the optical and structural properties of a peptide chain bound to a chromophore-a prototype system allowing for a proton transfer coupled to conformational change. With the support of molecular dynamics and DFT calculations, we show how proton transfer between the peptide and its cofactor can dramatically modify the optical properties of the system and demonstrate that these changes can be triggered by collisional activation in the gas phase.

  20. Charge, Color, and Conformation: Spectroscopy on Isomer-Selected Peptide Ions

    PubMed Central

    2016-01-01

    Monitoring the chromism induced by intramolecular hydrogen and charge transfers within proteins as well as the isomerization of both protein and cofactor is essential not only to understand photoactive signaling pathways but also to design targeted opto-switchable proteins. We used a dual-ion mobility drift tube coupled to a tunable picosecond laser to explore the optical and structural properties of a peptide chain bound to a chromophore—a prototype system allowing for a proton transfer coupled to conformational change. With the support of molecular dynamics and DFT calculations, we show how proton transfer between the peptide and its cofactor can dramatically modify the optical properties of the system and demonstrate that these changes can be triggered by collisional activation in the gas phase. PMID:26756462

  1. Effects of electron-transfer coupled with collision-induced dissociation (ET/CID) on doubly charged peptides and phosphopeptides.

    PubMed

    Liu, Chih-Wei; Lai, Chien-Chen

    2011-01-01

    Electron-transfer dissociation (ETD) is a useful peptide fragmentation technique that can be applied to investigate post-translational modifications (PTMs), the sequencing of highly hydrophilic peptides, and the identification of large peptides and even intact proteins. In contrast to traditional fragmentation methods, such as collision-induced dissociation (CID), ETD produces c- and z(·)-type product ions by randomly cleaving the N-Cα bonds. The disappointing fragmentation efficiency of ETD for doubly charged peptides and phosphopeptide ions has been improved by ETcaD (supplemental activation). However, the ETD data derived from most database search algorithms yield low confidence scores due to the presence of unreacted precursors and charge-reduced ions within MS/MS spectra. In this work, we demonstrate that eight out of ten standard doubly charged peptides and phosphopeptides can be effortlessly identified by electron-transfer coupled with collision-induced dissociation (ET/CID) using the SEQUEST algorithm without further spectral processing. ET/CID was performed with the further dissociation of the charge-reduced ions isolated from ETD ion/ion reactions. ET/CID had high fragmentation efficiency, which elevated the confidence scores of doubly charged peptide and phosphospeptide sequencing. ET/CID was found to be an effective fragmentation strategy in "bottom-up" proteomic analysis.

  2. Effects of Electron-Transfer Coupled with Collision-Induced Dissociation (ET/CID) on Doubly Charged Peptides and Phosphopeptides

    NASA Astrophysics Data System (ADS)

    Liu, Chih-Wei; Lai, Chien-Chen

    2011-01-01

    Electron-transfer dissociation (ETD) is a useful peptide fragmentation technique that can be applied to investigate post-translational modifications (PTMs), the sequencing of highly hydrophilic peptides, and the identification of large peptides and even intact proteins. In contrast to traditional fragmentation methods, such as collision-induced dissociation (CID), ETD produces c- and z·-type product ions by randomly cleaving the N-Cα bonds. The disappointing fragmentation efficiency of ETD for doubly charged peptides and phosphopeptide ions has been improved by ETcaD (supplemental activation). However, the ETD data derived from most database search algorithms yield low confidence scores due to the presence of unreacted precursors and charge-reduced ions within MS/MS spectra. In this work, we demonstrate that eight out of ten standard doubly charged peptides and phosphopeptides can be effortlessly identified by electron-transfer coupled with collision-induced dissociation (ET/CID) using the SEQUEST algorithm without further spectral processing. ET/CID was performed with the further dissociation of the charge-reduced ions isolated from ETD ion/ion reactions. ET/CID had high fragmentation efficiency, which elevated the confidence scores of doubly charged peptide and phosphospeptide sequencing. ET/CID was found to be an effective fragmentation strategy in "bottom-up" proteomic analysis.

  3. Matrix-assisted laser desorption/ionization mass spectrometry method for selectively producing either singly or multiply charged molecular ions.

    PubMed

    Trimpin, Sarah; Inutan, Ellen D; Herath, Thushani N; McEwen, Charles N

    2010-01-01

    Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is noted for its ability to produce primarily singly charged ions. This is an attribute when using direct ionization for complex mixtures such as protein digests or synthetic polymers. However, the ability to produce multiply charged ions, as with electrospray ionization (ESI), has advantages such as extending the mass range on mass spectrometers with limited mass-to-charge (m/z) range and enhancing fragmentation for structural characterization. We designed and fabricated a novel field free transmission geometry atmopsheric pressure (AP) MALDI source mounted to a high-mass resolution Orbitrap Exactive mass spectrometer. We report the ability to produce at will either singly charged ions or highly charged ions using a MALDI process by simply changing the matrix or the matrix preparation conditions. Mass spectra with multiply charged ions very similar to those obtained with ESI of proteins such as cytochrome c and ubiquitin are obtained with low femtomole amounts applied to the MALDI target plate and for peptides such as angiotensin I and II with application of attomole amounts. Single scan acquisitions produce sufficient ion current even from proteins.

  4. Single phase dynamic CMOS PLA using charge sharing technique

    NASA Astrophysics Data System (ADS)

    Dhong, Y. B.; Tsang, C. P.

    A single phase dynamic CMOS NOR-NOR programmable logic array (PLA) using triggered decoders and charge sharing techniques for high speed and low power is presented. By using the triggered decoder technique, the ground switches are eliminated, thereby, making this new design much faster and lower power dissipation than conventional PLA's. By using the charge-sharing technique in a dynamic CMOS NOR structure, a cascading AND gate can be implemented. The proposed PLA's are presented with a delay-time of 15.95 and 18.05 nsec, respectively, which compare with a conventional single phase PLA with 35.5 nsec delay-time. For a typical example of PLA like the Signetics 82S100 with 16 inputs, 48 input minterms (m) and 8 output minterms (n), the 2-SOP PLA using the triggered 2-bit decoder is 2.23 times faster and has 2.1 times less power dissipation than the conventional PLA. These results are simulated using maximum drain current of 600 micro-A, gate length of 2.0 micron, V sub DD of 5 V, the capacitance of an input miniterm of 1600 fF, and the capacitance of an output minterm of 1500 fF.

  5. Single phase dynamic CMOS PLA using charge sharing technique

    NASA Technical Reports Server (NTRS)

    Dhong, Y. B.; Tsang, C. P.

    1991-01-01

    A single phase dynamic CMOS NOR-NOR programmable logic array (PLA) using triggered decoders and charge sharing techniques for high speed and low power is presented. By using the triggered decoder technique, the ground switches are eliminated, thereby, making this new design much faster and lower power dissipation than conventional PLA's. By using the charge-sharing technique in a dynamic CMOS NOR structure, a cascading AND gate can be implemented. The proposed PLA's are presented with a delay-time of 15.95 and 18.05 nsec, respectively, which compare with a conventional single phase PLA with 35.5 nsec delay-time. For a typical example of PLA like the Signetics 82S100 with 16 inputs, 48 input minterms (m) and 8 output minterms (n), the 2-SOP PLA using the triggered 2-bit decoder is 2.23 times faster and has 2.1 times less power dissipation than the conventional PLA. These results are simulated using maximum drain current of 600 micro-A, gate length of 2.0 micron, V sub DD of 5 V, the capacitance of an input miniterm of 1600 fF, and the capacitance of an output minterm of 1500 fF.

  6. Light-Induced Charge Transport within a Single Asymmetric Nanowire

    SciTech Connect

    Liu, Chong; Hwang, Yun Yeong; Jeong, Hoon Eui; Yang, Peidong

    2011-01-21

    Artificial photosynthetic systems using semiconductor materials have been explored for more than three decades in order to store solar energy in chemical fuels such as hydrogen. By mimicking biological photosynthesis with two light-absorbing centers that relay excited electrons in a nanoscopic space, a dual-band gap photoelectrochemical (PEC) system is expected to have higher theoretical energy conversion efficiency than a single band gap system. This work demonstrates the vectorial charge transport of photo-generated electrons and holes within a single asymmetric Si/TiO2 nanowire using Kelvin probe force microscopy (KPFM). Under UV illumination, higher surface potential was observed on the n-TiO₂ side, relative to the potential of the p-Si side, as a result of majority carriers’ recombination at the Si/TiO₂ interface. These results demonstrate a new approach to investigate charge separation and transport in a PEC system. This asymmetric nanowire heterostructure, with a dual band gap configuration and simultaneously exposed anode and cathode surfaces represents an ideal platform for the development of technologies for the generation of solar fuels, although better photoanode materials remain to be discovered.

  7. Cryogenic CMOS circuits for single charge digital readout.

    SciTech Connect

    Gurrieri, Thomas M.; Longoria, Erin Michelle; Eng, Kevin; Carroll, Malcolm S.; Hamlet, Jason R.; Young, Ralph Watson

    2010-03-01

    The readout of a solid state qubit often relies on single charge sensitive electrometry. However the combination of fast and accurate measurements is non trivial due to large RC time constants due to the electrometers resistance and shunt capacitance from wires between the cold stage and room temperature. Currently fast sensitive measurements are accomplished through rf reflectrometry. I will present an alternative single charge readout technique based on cryogenic CMOS circuits in hopes to improve speed, signal-to-noise, power consumption and simplicity in implementation. The readout circuit is based on a current comparator where changes in current from an electrometer will trigger a digital output. These circuits were fabricated using Sandia's 0.35 {micro}m CMOS foundry process. Initial measurements of comparators with an addition a current amplifier have displayed current sensitivities of < 1nA at 4.2K, switching speeds up to {approx}120ns, while consuming {approx}10 {micro}W. I will also discuss an investigation of noise characterization of our CMOS process in hopes to obtain a better understanding of the ultimate limit in signal to noise performance.

  8. Influence of the Charge State on the Structures and Interactions of Vancomycin Antibiotics with Cell-Wall Analogue Peptides: Experimental and Theoretical Studies

    SciTech Connect

    Yang, Zhibo; Vorpagel, Erich R.; Laskin, Julia

    2009-02-16

    In this study we examined the effect of the charge state on the energetics and dynamics of dissociation of the non-covalent complex between the vancomycin and the cell wall peptide analogue Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala (V-Ac2KDADA). The binding energies between the vancomycin and the peptide were obtained from the RRKM modeling of the time- and energy resolved surface-induced dissociation (SID) experiments. Our results demonstrate that the stability of the complex toward fragmentation increases in the order: [V+Ac2KDADA+H]+2 < [V+Ac2KDADA+H]+ < [V+Ac2KDADA-H]-. Dissociation of the singly protonated and singly deprotonated complex is characterized by very large entropy effects indicating substantial increase in the conformational flexibility of the resulting products. The experimental threshold energies of 1.75 eV and 1.34 eV obtained for the [V+Ac2KDADA-H]- and [V+Ac2KDADA+H]+ , respectively, are in excellent agreement with the results of density functional theory (DFT) calculations. The increased stability of the deprotonated complex observed experimentally is attributed to the presence of three charged sites in the deprotonated complex as compared to only one charged site in the singly protonated complex. The low binding energy of 0.93 eV obtained for the doubly protonated complex suggests that this ion is destabilized by Coulomb repulsion between the singly protonated vancomycin and the singly protonated peptide comprising the complex.

  9. Charge density wave transition in single-layer titanium diselenide

    SciTech Connect

    Chen, P.; Chan, Y. -H.; Fang, X. -Y.; Zhang, Y.; Chou, M. Y.; Mo, S. -K.; Hussain, Z.; Fedorov, A. -V.; Chiang, T. -C.

    2015-11-16

    A single molecular layer of titanium diselenide (TiSe2) is a promising material for advanced electronics beyond graphene--a strong focus of current research. Such molecular layers are at the quantum limit of device miniaturization and can show enhanced electronic effects not realizable in thick films. We show that single-layer TiSe2 exhibits a charge density wave (CDW) transition at critical temperature TC=232±5 K, which is higher than the bulk TC=200±5 K. Angle-resolved photoemission spectroscopy measurements reveal a small absolute bandgap at room temperature, which grows wider with decreasing temperature T below TC in conjunction with the emergence of (2 × 2) ordering. The results are rationalized in terms of first-principles calculations, symmetry breaking and phonon entropy effects. The behavior of the Bardeen-Cooper-Schrieffer (BCS) gap implies a mean-field CDW order in the single layer and an anisotropic CDW order in the bulk.

  10. Charge density wave transition in single-layer titanium diselenide

    DOE PAGES

    Chen, P.; Chan, Y. -H.; Fang, X. -Y.; ...

    2015-11-16

    A single molecular layer of titanium diselenide (TiSe2) is a promising material for advanced electronics beyond graphene--a strong focus of current research. Such molecular layers are at the quantum limit of device miniaturization and can show enhanced electronic effects not realizable in thick films. We show that single-layer TiSe2 exhibits a charge density wave (CDW) transition at critical temperature TC=232±5 K, which is higher than the bulk TC=200±5 K. Angle-resolved photoemission spectroscopy measurements reveal a small absolute bandgap at room temperature, which grows wider with decreasing temperature T below TC in conjunction with the emergence of (2 × 2) ordering.more » The results are rationalized in terms of first-principles calculations, symmetry breaking and phonon entropy effects. The behavior of the Bardeen-Cooper-Schrieffer (BCS) gap implies a mean-field CDW order in the single layer and an anisotropic CDW order in the bulk.« less

  11. Selective gas-phase cleavage at the peptide bond C-terminal to aspartic acid in fixed-charge derivatives of Asp-containing peptides.

    PubMed

    Gu, C; Tsaprailis, G; Breci, L; Wysocki, V H

    2000-12-01

    This study focuses on the molecular level interpretation of the selective gas-phase cleavage at aspartic acid residues (Asp) in protonated peptides. A phi3P+CH2C(=O)group (phi = 2,4,6-trimethoxyphenyl) is attached to the N-terminal nitrogen of the selected peptides LDIFSDF and LDIFSDFR, via solid-phase synthesis, to "mimic" the tightly held charge of a protonated arginine (Arg) residue. Collision-induced dissociation in a quadrupole ion trap instrument and surface-induced dissociation in a dual quadrupole instrument were performed for electrospray-generated ions of the fixed-charge peptide derivatives. Selective cleavages at Asp-Xxx are observed for those ions with charge provided only by the fixed charge or for those with a fixed charge and one Arg plus one added proton. This supports a previously proposed mechanism which suggests that the cleavages at Asp-Xxx, initiated by the acidic hydrogen of the Asp residue, become significant when ionizing protons are strongly bound by Arg in the protonated peptides. It is clear that the fixed charge is indeed serving as a "mimic" of protonated Arg and that a protonated Arg side chain is not required to interact with the Asp to induce cleavage at Asp-Xxx. When the number of protons exceeds the number of Arg in a peptide containing Arg and Asp, nonselective cleavages occur. The fragmentation efficiency of the peptides is consistent with the idea that these nonselective cleavages are promoted by a mobile proton. The peptide with a fixed charge and one added proton, [phi3P+CH2C(=O)-LDIFSDF + H]2+, fragments much more efficiently than the corresponding peptide with a fixed charge, an Arg and one added proton, [phi3P+CH2C(=O)-LDIFSDFR + H]2+; both of these fragment more efficiently than the peptide with a fixed charge and no added proton, phi3P+CH2C(=O)-LDIFSDF. MS/MS/MS (i.e., MS3) experimental results for bn ions formed at Asp-Xxx from phi3P+CH2C(=O)-LDIFSDF and its H/D exchange derivative, phi3P+CH2C(=O)-LDIFSDF-d11, are

  12. A compact source for bunches of singly charged atomic ions

    SciTech Connect

    Murböck, T.; Birkl, G.; Schmidt, S.; Nörtershäuser, W.; Andelkovic, Z.; Vogel, M.

    2016-04-15

    We have built, operated, and characterized a compact ion source for low-energy bunches of singly charged atomic ions in a vacuum beam line. It is based on atomic evaporation from an electrically heated oven and ionization by electron impact from a heated filament inside a grid-based ionization volume. An adjacent electrode arrangement is used for ion extraction and focusing by applying positive high-voltage pulses to the grid. The method is particularly suited for experimental environments which require low electromagnetic noise. It has proven simple yet reliable and has been used to produce μs-bunches of up to 10{sup 6} Mg{sup +} ions at a repetition rate of 1 Hz. We present the concept, setup and characterizing measurements. The instrument has been operated in the framework of the SpecTrap experiment at the HITRAP facility at GSI/FAIR to provide Mg{sup +} ions for sympathetic cooling of highly charged ions by laser-cooled {sup 24}Mg{sup +}.

  13. A compact source for bunches of singly charged atomic ions.

    PubMed

    Murböck, T; Schmidt, S; Andelkovic, Z; Birkl, G; Nörtershäuser, W; Vogel, M

    2016-04-01

    We have built, operated, and characterized a compact ion source for low-energy bunches of singly charged atomic ions in a vacuum beam line. It is based on atomic evaporation from an electrically heated oven and ionization by electron impact from a heated filament inside a grid-based ionization volume. An adjacent electrode arrangement is used for ion extraction and focusing by applying positive high-voltage pulses to the grid. The method is particularly suited for experimental environments which require low electromagnetic noise. It has proven simple yet reliable and has been used to produce μs-bunches of up to 10(6) Mg(+) ions at a repetition rate of 1 Hz. We present the concept, setup and characterizing measurements. The instrument has been operated in the framework of the SpecTrap experiment at the HITRAP facility at GSI/FAIR to provide Mg(+) ions for sympathetic cooling of highly charged ions by laser-cooled (24)Mg(+).

  14. Charge transport in single CuO nanowires

    SciTech Connect

    Wu, Junnan; Yin, Bo; Wu, Fei; Myung, Yoon; Banerjee, Parag

    2014-11-03

    Charge transport in single crystal, p-type cupric oxide (CuO) nanowire (NW) was studied through temperature based (120 K–400 K) current-voltage measurements. CuO NW with a diameter of 85 nm was attached to Au electrodes 2.25 μm apart, using dielectrophoresis. At low electrical field (<0.89 × 10{sup 3 }V/cm), an ohmic conduction is observed with an activation energy of 272 meV. The injected electrons fill traps with an average energy, E{sub T} = 26.6 meV and trap density, N{sub T} = 3.4 × 10{sup 15 }cm{sup −3}. After the traps are saturated, space charge limited current mechanism becomes dominant. For 120 K ≤ T ≤ 210 K phonon scattering limits mobility. For T ≥ 220 K, a thermally activated mobility is observed and is attributed to small polaron hopping with an activation energy of 44 meV. This mechanism yields a hole mobility of 0.0015 cm{sup 2}/V s and an effective hole concentration of 4 × 10{sup 18 }cm{sup −3} at 250 K.

  15. Inclusive photoproduction of single charged particles at high p T

    NASA Astrophysics Data System (ADS)

    Apsimon, R. J.; Atkinson, M.; Baake, M.; Bagdasarian, L. S.; Barberis, D.; Brodbeck, T. J.; Brook, N.; Charity, T.; Clegg, A. B.; Coyle, P.; Danaher, S.; Danagulian, S.; Davenport, M.; Dickinson, B.; Diekmann, B.; Donnachie, A.; Doyle, A. T.; Eades, J.; Ellison, R. J.; Flower, P. S.; Foster, J. M.; Galbraith, W.; Galumian, P. I.; Gapp, C.; Gebert, F.; Hallewell, G.; Heinloth, K.; Henderson, R. C. W.; Hickman, M. T.; Hoeger, C.; Holzkamp, S.; Hughes-Jones, R. E.; Ibbotson, M.; Jakob, H. P.; Joseph, D.; Keemer, N. R.; Kingler, J.; Koersgen, G.; Kolya, S. D.; Lafferty, G. D.; McCann, H.; McClatchey, R.; McManus, C.; Mercer, D.; Morris, J. A. G.; Morris, J. V.; Newton, D.; O'Connor, A.; Oedingen, R.; Oganesian, A. G.; Ottewell, P. J.; Paterson, C. N.; Paul, E.; Reid, D.; Rotscheidt, H.; Sharp, P. H.; Soeldner-Rembold, S.; Thacker, N. A.; Thompson, L.; Thompson, R. J.; Voigtlaender-Tetzner, A.; Waterhouse, J.; Weigend, A. S.; Wilson, G. W.

    1989-03-01

    Single charged-particle inclusive cross sections for photon, pion and kaon beams on hydrogen at the CERN-SPS are presented as functions of p T and x F . Data cover the range 0.0< p T <5.0 GeV/c and 0.0< x F <1.0 at incident momenta from 70 to 170 GeV/c. The comparison between photon- and hadron-induced data indicates a relative excess of particles with p T >1.6 GeV/c for the photon-induced data. Using the hadron-induced data to estimate the hadronic behaviour of the photon, the difference distributions and ratios of cross sections are a measure of the contribution of the point-like photon interactions. The data are compared with QCD calculations and show broadly similar features.

  16. Cleaning of raw peptide MS/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise.

    PubMed

    Mujezinovic, Nedim; Raidl, Günther; Hutchins, James R A; Peters, Jan-Michael; Mechtler, Karl; Eisenhaber, Frank

    2006-10-01

    The dominant ions in MS/MS spectra of peptides, which have been fragmented by low-energy CID, are often b-, y-ions and their derivatives resulting from the cleavage of the peptide bonds. However, MS/MS spectra typically contain many more peaks. These can result not only from isotope variants and multiply charged replicates of the peptide fragmentation products but also from unknown fragmentation pathways, sample-specific or systematic chemical contaminations or from noise generated by the electronic detection system. The presence of this background complicates spectrum interpretation. Besides dramatically prolonged computation time, it can lead to incorrect protein identification, especially in the case of de novo sequencing algorithms. Here, we present an algorithm for detection and transformation of multiply charged peaks into singly charged monoisotopic peaks, removal of heavy isotope replicates, and random noise. A quantitative criterion for the recognition of some noninterpretable spectra has been derived as a byproduct. The approach is based on numerical spectral analysis and signal detection methods. The algorithm has been implemented in a stand-alone computer program called MS Cleaner that can be obtained from the authors upon request.

  17. Note: Charge transfer in a hydrated peptide group is determined mainly by its intrinsic hydrogen-bond energetics

    SciTech Connect

    Mirkin, Noemi G.; Krimm, Samuel

    2014-01-28

    Charge transfer in a hydrogen-bonded N-methylacetamide(H{sub 2}O){sub 3} system is obtained from ωB97X-D/6-31++G** and CHelpG atomic charge calculations of individual peptide-water interactions as well as that of the entire complex. In the latter, the electron transfer to water is 0.19 e, influenced primarily by the hydrogen bonds to the C=O group. The values of such charge transfer are paralleled by the corresponding intrinsic hydrogen-bond energies. These results support the desirability of incorporating charge transfer in molecular mechanics energy functions.

  18. Charge cluster distribution in nanosites traversed by a single ionizing particle An experimental approach

    NASA Astrophysics Data System (ADS)

    Pszona, S.; Bantsar, A.; Kula, J.

    2008-11-01

    A method for modeling charge cluster formation by a single ionizing particle in nanoelectronic structures of few nanometres size is presented. The method is based on experimental modeling of charge formation in the equivalent gaseous nanosites irradiated by single charged particles and the subsequent scaling procedure to a needed medium. Propane irradiated by alpha particles is presented as an example.

  19. Comparison of CID, ETD and metastable atom-activated dissociation (MAD) of doubly and triply charged phosphorylated tau peptides.

    PubMed

    Cook, Shannon L; Zimmermann, Carolyn M; Singer, David; Fedorova, Maria; Hoffmann, Ralf; Jackson, Glen P

    2012-06-01

    The fragmentation behavior of the 2+ and 3+ charge states of eleven different phosphorylated tau peptides was studied using collision-induced dissociation (CID), electron transfer dissociation (ETD) and metastable atom-activated dissociation (MAD). The synthetic peptides studied contain up to two known phosphorylation sites on serine or threonine residues, at least two basic residues, and between four and eight potential sites of phosphorylation. CID produced mainly b-/y-type ions with abundant neutral losses of the phosphorylation modification. ETD produced c-/z-type ions in highest abundance but also showed numerous y-type ions at a frequency about 50% that of the z-type ions. The major peaks observed in the ETD spectra correspond to the charge-reduced product ions and small neutral losses from the charge-reduced peaks. ETD of the 2+ charge state of each peptide generally produced fewer backbone cleavages than the 3+ charge state, consistent with previous reports. Regardless of charge state, MAD achieved more extensive backbone cleavage than CID or ETD, while retaining the modification(s) in most cases. In all but one case, unambiguous modification site determination was achieved with MAD. MAD produced 15-20% better sequence coverage than CID and ETD for both the 2+ and 3+ charge states and very different fragmentation products indicating that the mechanism of fragmentation in MAD is unique and complementary to CID and ETD.

  20. The negatively charged regions of lactoferrin binding protein B, an adaptation against anti-microbial peptides.

    PubMed

    Morgenthau, Ari; Beddek, Amanda; Schryvers, Anthony B

    2014-01-01

    Lactoferrin binding protein B (LbpB) is a bi-lobed membrane bound lipoprotein that is part of the lactoferrin receptor complex in a variety of Gram-negative pathogens. Despite high sequence diversity among LbpBs from various strains and species, a cluster of negatively charged amino acids is invariably present in the protein's C-terminal lobe in all species except Moraxella bovis. The function of LbpB in iron acquisition has yet to be experimentally demonstrated, whereas in vitro studies have shown that LbpB confers protection against lactoferricin, a short cationic antimicrobial peptide released from the N- terminus of lactoferrin. In this study we demonstrate that the negatively charged regions can be removed from the Neisseria meningitidis LbpB without compromising stability, and this results in the inability of LbpB to protect against the bactericidal effects of lactoferricin. The release of LbpB from the cell surface by the autotransporter NalP reduces the protection against lactoferricin in the in vitro killing assay, attributed to removal of LbpB during washing steps, but is unlikely to have a similar impact in vivo. The protective effect of the negatively charged polysaccharide capsule in the killing assay was less than the protection conferred by LbpB, suggesting that LbpB plays a major role in protection against cationic antimicrobial peptides in vivo. The selective release of LbpB by NalP has been proposed to be a mechanism for evading the adaptive immune response, by reducing the antibody binding to the cell surface, but may also provide insights into the primary function of LbpB in vivo. Although TbpB and LbpB have been shown to be major targets of the human immune response, the selective release of LbpB suggests that unlike TbpB, LbpB may not be essential for iron acquisition, but important for protection against cationic antimicrobial peptides.

  1. The Negatively Charged Regions of Lactoferrin Binding Protein B, an Adaptation against Anti-Microbial Peptides

    PubMed Central

    Morgenthau, Ari; Beddek, Amanda; Schryvers, Anthony B.

    2014-01-01

    Lactoferrin binding protein B (LbpB) is a bi-lobed membrane bound lipoprotein that is part of the lactoferrin receptor complex in a variety of Gram-negative pathogens. Despite high sequence diversity among LbpBs from various strains and species, a cluster of negatively charged amino acids is invariably present in the protein’s C-terminal lobe in all species except Moraxella bovis. The function of LbpB in iron acquisition has yet to be experimentally demonstrated, whereas in vitro studies have shown that LbpB confers protection against lactoferricin, a short cationic antimicrobial peptide released from the N- terminus of lactoferrin. In this study we demonstrate that the negatively charged regions can be removed from the Neisseria meningitidis LbpB without compromising stability, and this results in the inability of LbpB to protect against the bactericidal effects of lactoferricin. The release of LbpB from the cell surface by the autotransporter NalP reduces the protection against lactoferricin in the in vitro killing assay, attributed to removal of LbpB during washing steps, but is unlikely to have a similar impact in vivo. The protective effect of the negatively charged polysaccharide capsule in the killing assay was less than the protection conferred by LbpB, suggesting that LbpB plays a major role in protection against cationic antimicrobial peptides in vivo. The selective release of LbpB by NalP has been proposed to be a mechanism for evading the adaptive immune response, by reducing the antibody binding to the cell surface, but may also provide insights into the primary function of LbpB in vivo. Although TbpB and LbpB have been shown to be major targets of the human immune response, the selective release of LbpB suggests that unlike TbpB, LbpB may not be essential for iron acquisition, but important for protection against cationic antimicrobial peptides. PMID:24465982

  2. Intrinsic Charge Carrier Mobility in Single-Layer Black Phosphorus.

    PubMed

    Rudenko, A N; Brener, S; Katsnelson, M I

    2016-06-17

    We present a theory for single- and two-phonon charge carrier scattering in anisotropic two-dimensional semiconductors applied to single-layer black phosphorus (BP). We show that in contrast to graphene, where two-phonon processes due to the scattering by flexural phonons dominate at any practically relevant temperatures and are independent of the carrier concentration n, two-phonon scattering in BP is less important and can be considered negligible at n≳10^{13}  cm^{-2}. At smaller n, however, phonons enter in the essentially anharmonic regime. Compared to the hole mobility, which does not exhibit strong anisotropy between the principal directions of BP (μ_{xx}/μ_{yy}∼1.4 at n=10^{13} cm^{-2} and T=300  K), the electron mobility is found to be significantly more anisotropic (μ_{xx}/μ_{yy}∼6.2). Absolute values of μ_{xx} do not exceed 250 (700)  cm^{2} V^{-1} s^{-1} for holes (electrons), which can be considered as an upper limit for the mobility in BP at room temperature.

  3. Single-Molecule Motions of MHC Class II Rely on Bound Peptides

    PubMed Central

    Kozono, Haruo; Matsushita, Yufuku; Ogawa, Naoki; Kozono, Yuko; Miyabe, Toshihiro; Sekiguchi, Hiroshi; Ichiyanagi, Kouhei; Okimoto, Noriaki; Taiji, Makoto; Kanagawa, Osami; Sasaki, Yuji C.

    2015-01-01

    The major histocompatibility complex (MHC) class II protein can bind peptides of different lengths in the region outside the peptide-binding groove. Peptide-flanking residues (PFRs) contribute to the binding affinity of the peptide for MHC and change the immunogenicity of the peptide/MHC complex with regard to T cell receptor (TCR). The mechanisms underlying these phenomena are currently unknown. The molecular flexibility of the peptide/MHC complex may be an important determinant of the structures recognized by certain T cells. We used single-molecule x-ray analysis (diffracted x-ray tracking (DXT)) and fluorescence anisotropy to investigate these mechanisms. DXT enabled us to monitor the real-time Brownian motion of the peptide/MHC complex and revealed that peptides without PFRs undergo larger rotational motions than peptides with PFRs. Fluorescence anisotropy further revealed that peptides without PFRs exhibit slightly larger motions on the nanosecond timescale. These results demonstrate that peptides without PFRs undergo dynamic motions in the groove of MHC and consequently are able to assume diverse structures that can be recognized by T cells. PMID:25606683

  4. Nature of the Charged-Group Effect on the Stability of the C-Peptide Helix

    NASA Astrophysics Data System (ADS)

    Shoemaker, Kevin R.; Kim, Peter S.; Brems, David N.; Marqusee, Susan; York, Eunice J.; Chaiken, Irwin M.; Stewart, John M.; Baldwin, Robert L.

    1985-04-01

    The residues responsible for the pH-dependent stability of the helix formed by the isolated C-peptide (residues 1-13 of ribonuclease A) have been identified by chemical synthesis of analogues and measurement of their helix-forming properties. Each of the residues ionizing between pH 2 and pH 8 has been replaced separately by an uncharged residue. Protonation of Glu-2- is responsible for the sharp decrease in helix stability between pH 5 and pH 2, and deprotonation of His-12+ causes a similar decrease between pH 5 and pH 8. Glu-9- is not needed for helix stability. The results cannot be explained by the Zimm-Bragg model and host-guest data for α -helix formation, which predict that the stability of the C-peptide helix should increase when Glu-2- is protonated or when His-12+ is deprotonated. Moreover, histidine+ is a strong helix-breaker in host-guest studies. In proteins, acidic and basic residues tend to occur at opposite ends of α -helices: acidic residues occur preferentially near the NH2-terminal end and basic residues near the COOH-terminal end. A possible explanation, based on a helix dipole model, has been given [Blagdon, D. E. & Goodman, M. (1975) Biopolymers 14, 241-245]. Our results are consistent with the helix dipole model and they support the suggestion that the distribution of charged residues in protein helices reflects the helix-stabilizing propensity of those residues. Because Glu-9 is not needed for helix stability, a possible Glu-9-\\cdots His-12+ salt bridge does not contribute significantly to helix stability. The role of a possible Glu-2-\\cdots Arg-10+ salt bridge has not yet been evaluated. A charged-group effect on α -helix stability in water has also been observed in a different peptide system [Ihara, S., Ooi, T. & Takahashi, S. (1982) Biopolymers 21, 131-145]: block copolymers containing (Ala)20 and (Glu)20 show partial helix formation at low temperatures, pH 7.5, where the glutamic acid residues are ionized. (Glu)20(Ala)20Phe forms a

  5. Ferromagnetism in Silicon Single Crystals with Positively Charged Vacancy Clusters

    NASA Astrophysics Data System (ADS)

    Liu, Yu; Zhang, Xinghong; Yuan, Quan; Han, Jiecai; Zhou, Shengqiang; Song, Bo

    Defect-induced ferromagnetism provides an alternative for organic and semiconductor spintronics. Here, we investigated the magnetism in Silicon after neutron irradiation and try to correlate the observed magnetism to particular defects in Si. Commercially available p-type Si single crystal wafer is cut into pieces for performing neutron irradiations. The magnetic impurities are ruled out as they can not be detected by secondary ion mass spectroscopy. With positron annihilation lifetime spectroscopy, the positron trapping center corresponding to lifetime 375 ps is assigned to a kind of stable vacancy clusters of hexagonal rings (V6) and its concentration is enhanced by increasing neutron doses. After irradiation, the samples still show strong diamagnetism. The weak ferromagnetic signal in Si after irradiation enhances and then weakens with increasing irradiation doses. The saturation magnetization at room temperature is almost the same as that at 5 K. The X-ray magnetic circular dichroism further provides the direct evidence that Silicon is the origin of this ferromagnetism. Using first-principles calculations, it is found that positively charged V6 brings the spin polarization and the defects have coupling with each other. The work is financially supported by the Helmholtz Postdoc Programme (Initiative and Networking Fund, PD-146).

  6. Electronic Structure, Dielectric Response, and Surface Charge Distribution of RGD (1FUV) Peptide

    NASA Astrophysics Data System (ADS)

    Adhikari, Puja; Wen, Amy M.; French, Roger H.; Parsegian, V. Adrian; Steinmetz, Nicole F.; Podgornik, Rudolf; Ching, Wai-Yim

    2014-07-01

    Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

  7. Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

    PubMed

    Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim

    2014-07-08

    Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

  8. Amplification of single molecule translocation signal using β-strand peptide functionalized nanopores.

    PubMed

    Liebes-Peer, Yael; Rapaport, Hanna; Ashkenasy, Nurit

    2014-07-22

    Changes in ionic current flowing through nanopores due to binding or translocation of single biopolymer molecules enable their detection and characterization. It is, however, much more challenging to detect small molecules due to their rapid and small signal signature. Here we demonstrate the use of de novo designed peptides for functionalization of nanopores that enable the detection of a small analytes at the single molecule level. The detection relies on cooperative peptide conformational change that is induced by the binding of the small molecule to a receptor domain on the peptide. This change results in alteration of the nanopore effective diameter and hence induces current perturbation signal. On the basis of this approach, we demonstrate here the detection of diethyl 4-nitrophenyl phosphate (paraoxon), a poisonous organophosphate molecule. Paraoxon binding is induced by the incorporation of the catalytic triad of acetylcholine esterase in the hydrophilic domain of a short amphiphilic peptide and promotes β-sheet assembly of the peptide both in solution and for peptide molecules immobilized on solid surfaces. Nanopores coated with this peptide allowed the detection of paraoxon at the single molecule level revealing two binding arrangements. This unique approach, hence, provides the ability to study interactions of small molecules with the corresponding engineered receptors at the single molecule level. Furthermore, the suggested versatile platform may be used for the development of highly sensitive small analytes sensors.

  9. Single tryptophan and tyrosine comparisons in the N-terminal and C-terminal interface regions of transmembrane GWALP peptides.

    PubMed

    Gleason, Nicholas J; Greathouse, Denise V; Grant, Christopher V; Opella, Stanley J; Koeppe, Roger E

    2013-11-07

    Hydrophobic membrane-spanning helices often are flanked by interfacial aromatic or charged residues. In this paper, we compare the consequences of single Trp → Tyr substitutions at each interface for the properties of a defined transmembrane helix in the absence of charged residues. The choice of molecular framework is critical for these single-residue experiments because the presence of "too many" aromatic residues (more than one at either membrane-water interface) introduces excess dynamic averaging of solid state NMR observables. To this end, we compare the outcomes when changing W(5) or W(19), or both of them, to tyrosine in the well-characterized transmembrane peptide acetyl-GGALW(5)(LA)6LW(19)LAGA-amide ("GWALP23"). By means of solid-state (2)H and (15)N NMR experiments, we find that Y(19)GW(5)ALP23 displays similar magnitudes of peptide helix tilt as Y(5)GW(19)ALP23 and responds similarly to changes in bilayer thickness, from DLPC to DMPC to DOPC. The presence of Y(19) changes the azimuthal rotation angle ρ (about the helix axis) to a similar extent as Y(5), but in the opposite direction. When tyrosines are substituted for both tryptophans to yield GY(5,19)ALP23, the helix tilt angle is again of comparable magnitude, and furthermore, the preferred azimuthal rotation angle ρ is relatively unchanged from that of GW(5,19)ALP23. The extent of dynamic averaging increases marginally when Tyr replaces Trp. Yet, importantly, all members of the peptide family having single Tyr or Trp residues near each interface exhibit only moderate and not highly extensive dynamic averaging. The results provide important benchmarks for evaluating conformational and dynamic control of membrane protein function.

  10. Comparative simulation studies of native and single-site mutant human beta-defensin-1 peptides.

    PubMed

    Toubar, Rabab A; Zhmurov, Artem; Barsegov, Valeri; Marx, Kenneth A

    2013-01-01

    Human defensins play important roles in a broad range of biological functions, such as microbial defense and immunity. Yet, little is known about their molecular properties, i.e. secondary structure stability, structural variability, important side chain interactions, surface charge distribution, and resistance to thermal fluctuations, and how these properties are related to their functions. To assess these factors, we studied the native human β-defensin-1 monomer and dimer as well as several single-site mutants using molecular dynamics simulations. The results showed that disulfide bonds are important determinants in maintaining the defensins' structural integrity, as no structural transitions were observed at 300 K and only minor structural unfolding was detected upon heating to 500 K. The α-helix was less thermally stable than the core β-sheet structure held together by hydrogen bonds and hydrophobic interactions. The monomer α-helix stability was directly correlated, whereas the end-to-end distance was inversely correlated to the experimentally measured β-defensin-1 chemotactic activity, in the order: mutant 2 (Gln24Glu) > mutant 3 (Lys31Ala) = wild type > mutant 1 (Asn4Ala). The structural stability of the β-defensin-1 dimer species exhibited an inverse correlation to their chemotactic activity. In dimers formed by mutants 2 and 3, we observed sliding of one monomer upon the surface of the other in the absence of unbinding. This dynamic sliding feature may enhance the molecular oligomerization of β-defensin-1 peptides contributing to their antibacterial activity. It could also help these peptides orient correctly in the CC chemokine receptor 6 binding site, thereby initiating their chemotactic activity. In agreement with this notion, the remarkable sliding behavior was observed only for the mutants with the highest chemotactic activity.

  11. A single autoimmune T cell receptor recognizes more than a million different peptides.

    PubMed

    Wooldridge, Linda; Ekeruche-Makinde, Julia; van den Berg, Hugo A; Skowera, Anna; Miles, John J; Tan, Mai Ping; Dolton, Garry; Clement, Mathew; Llewellyn-Lacey, Sian; Price, David A; Peakman, Mark; Sewell, Andrew K

    2012-01-06

    The T cell receptor (TCR) orchestrates immune responses by binding to foreign peptides presented at the cell surface in the context of major histocompatibility complex (MHC) molecules. Effective immunity requires that all possible foreign peptide-MHC molecules are recognized or risks leaving holes in immune coverage that pathogens could quickly evolve to exploit. It is unclear how a limited pool of <10(8) human TCRs can successfully provide immunity to the vast array of possible different peptides that could be produced from 20 proteogenic amino acids and presented by self-MHC molecules (>10(15) distinct peptide-MHCs). One possibility is that T cell immunity incorporates an extremely high level of receptor degeneracy, enabling each TCR to recognize multiple peptides. However, the extent of such TCR degeneracy has never been fully quantified. Here, we perform a comprehensive experimental and mathematical analysis to reveal that a single patient-derived autoimmune CD8(+) T cell clone of pathogenic relevance in human type I diabetes recognizes >one million distinct decamer peptides in the context of a single MHC class I molecule. A large number of peptides that acted as substantially better agonists than the wild-type "index" preproinsulin-derived peptide (ALWGPDPAAA) were identified. The RQFGPDFPTI peptide (sampled from >10(8) peptides) was >100-fold more potent than the index peptide despite differing from this sequence at 7 of 10 positions. Quantification of this previously unappreciated high level of CD8(+) T cell cross-reactivity represents an important step toward understanding the system requirements for adaptive immunity and highlights the enormous potential of TCR degeneracy to be the causative factor in autoimmune disease.

  12. Modifying the electronic properties of single-walled carbon nanotubes using designed surfactant peptides

    NASA Astrophysics Data System (ADS)

    Samarajeewa, Dinushi R.; Dieckmann, Gregg R.; Nielsen, Steven O.; Musselman, Inga H.

    2012-07-01

    The electronic properties of carbon nanotubes can be altered significantly by modifying the nanotube surface. In this study, single-walled carbon nanotubes (SWCNTs) were functionalized noncovalently using designed surfactant peptides, and the resultant SWCNT electronic properties were investigated. These peptides have a common amino acid sequence of X(Valine)5(Lysine)2, where X indicates an aromatic amino acid containing either an electron-donating or electron-withdrawing functional group (i.e. p-amino-phenylalanine or p-cyano-phenylalanine). Circular dichroism spectra showed that the surfactant peptides primarily have random coil structures in an aqueous medium, both alone and in the presence of SWCNTs, simplifying analysis of the peptide/SWCNT interaction. The ability of the surfactant peptides to disperse individual SWCNTs in solution was verified using atomic force microscopy and ultraviolet-visible-near-infrared spectroscopy. The electronic properties of the surfactant peptide/SWCNT composites were examined using the observed nanotube Raman tangential band shifts and the observed additional features near the Fermi level in the scanning tunneling spectroscopy dI/dV spectra. The results revealed that SWCNTs functionalized with surfactant peptides containing electron-donor or electron-acceptor functional groups showed n-doped or p-doped altered electronic properties, respectively. This work unveils a facile and versatile approach to modify the intrinsic electronic properties of SWCNTs using a simple peptide structure, which is easily adaptable to obtain peptide/SWCNT composites for the design of tunable nanoscale electronic devices.The electronic properties of carbon nanotubes can be altered significantly by modifying the nanotube surface. In this study, single-walled carbon nanotubes (SWCNTs) were functionalized noncovalently using designed surfactant peptides, and the resultant SWCNT electronic properties were investigated. These peptides have a common amino

  13. Determining the chirality of Yukawa couplings via single charged Higgs boson production in polarized photon collisions.

    PubMed

    He, Hong-Jian; Kanemura, Shinya; Yuan, C-P

    2002-09-02

    When the charged Higgs boson is too heavy to be produced in pairs, the predominant production mechanism at linear colliders is via the single charged Higgs boson production processes, such as e(-)e(+)-->bcH+,taunuH+ and gammagamma-->bcH+,taunuH+. We show that the yield of a heavy charged Higgs boson at a gammagamma collider is typically 1 or 2 orders of magnitude larger than that at an e(-)e(+) collider. Furthermore, a polarized gammagamma collider can determine the chirality of the Yukawa couplings of fermions with charged Higgs boson via single charged Higgs boson production and, thus, discriminate models of new physics.

  14. Short Peptides Enhance Single Cell Adhesion and Viability onMicroarrays

    SciTech Connect

    Veiseh, Mandana; Veiseh, Omid; Martin, Michael C.; Asphahani,Fareid; Zhang, Miqin

    2007-01-19

    Single cell patterning holds important implications forbiology, biochemistry, biotechnology, medicine, and bioinformatics. Thechallenge for single cell patterning is to produce small islands hostingonly single cells and retaining their viability for a prolonged period oftime. This study demonstrated a surface engineering approach that uses acovalently bound short peptide as a mediator to pattern cells withimproved single cell adhesion and prolonged cellular viabilityon goldpatterned SiO2 substrates. The underlying hypothesis is that celladhesion is regulated bythe type, availability, and stability ofeffective cell adhesion peptides, and thus covalently bound shortpeptides would promote cell spreading and, thus, single cell adhesion andviability. The effectiveness of this approach and the underlyingmechanism for the increased probability of single cell adhesion andprolonged cell viability by short peptides were studied by comparingcellular behavior of human umbilical cord vein endothelial cells on threemodelsurfaces whose gold electrodes were immobilized with fibronectin,physically adsorbed Arg-Glu-Asp-Val-Tyr, and covalently boundLys-Arg-Glu-Asp-Val-Tyr, respectively. The surface chemistry and bindingproperties were characterized by reflectance Fourier transform infraredspectroscopy. Both short peptides were superior to fibronectin inproducing adhesion of only single cells, whereas the covalently boundpeptide also reduced apoptosis and necrosisof adhered cells. Controllingcell spreading by peptide binding domains to regulate apoptosis andviability represents a fundamental mechanism in cell-materialsinteraction and provides an effective strategy in engineering arrays ofsingle cells.

  15. Positively charged polymer brush-functionalized filter paper for DNA sequence determination following Dot blot hybridization employing a pyrrolidinyl peptide nucleic acid probe.

    PubMed

    Laopa, Praethong S; Vilaivan, Tirayut; Hoven, Voravee P

    2013-01-07

    As inspired by the Dot blot analysis, a well known technique in molecular biology and genetics for detecting biomolecules, a new paper-based platform for colorimetric detection of specific DNA sequences employing peptide nucleic acid (PNA) as a probe has been developed. In this particular study, a pyrrolidinyl PNA bearing a conformationally rigid d-prolyl-2-aminocyclopentanecarboxylic acid backbone (acpcPNA) was used as a probe. The filter paper was modified to be positively charged with grafted polymer brushes of quaternized poly(dimethylamino)ethyl methacrylate (QPDMAEMA) prepared by surface-initiated polymerization of 2-(dimethylamino)ethyl methacrylate from the filter paper via ARGET ATRP followed by quaternization with methyl iodide. Following the Dot blot format, a DNA target was first immobilized via electrostatic interactions between the positive charges of the QPDMAEMA brushes and negative charges of the phosphate backbone of DNA. Upon hybridization with the biotinylated pyrrolidinyl peptide nucleic acid (b-PNA) probe, the immobilized DNA can be detected by naked eye observation of the yellow product generated by the enzymatic reaction employing HRP-labeled streptavidin. It has been demonstrated that this newly developed assay was capable of discriminating between complementary and single base mismatch targets at a detection limit of at least 10 fmol. In addition, the QPDMAEMA-grafted filter paper exhibited a superior performance to the commercial membranes, namely Nylon 66 and nitrocellulose.

  16. Spontaneous Mass and Charge Losses from Single Multi-Megadalton Ions Studied by Charge Detection Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Keifer, David Z.; Alexander, Andrew W.; Jarrold, Martin F.

    2017-01-01

    Spontaneous mass and charge losses from individual multi-megadalton ions have been observed with charge detection mass spectrometry (CDMS) by trapping single hepatitis B virus (HBV) capsids for 3 s. Gradual increases in the oscillation frequency of single ions in the ion trap are attributed mainly to mass loss (probably solvent, water, and/or salt). The total mass lost during the 3 s trapping period peaks at around 20 kDa for 4 MDa HBV T = 4 capsids. Discrete frequency drops punctuate the gradual increases in the oscillation frequencies. The drops are attributed to a sudden loss of charge. In most cases a single positive charge is lost along with some mass (on average around 1000 Da). Charge loss occurs for over 40% of the trapped ions. It usually occurs near the beginning of the trapping event, and it occurs preferentially in regions of the trap with strong electric fields, indicating that external electric fields promote charge loss. This process may contribute to the decrease in m/z resolution that often occurs with megadalton ions.

  17. Spontaneous Mass and Charge Losses from Single Multi-Megadalton Ions Studied by Charge Detection Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Keifer, David Z.; Alexander, Andrew W.; Jarrold, Martin F.

    2017-03-01

    Spontaneous mass and charge losses from individual multi-megadalton ions have been observed with charge detection mass spectrometry (CDMS) by trapping single hepatitis B virus (HBV) capsids for 3 s. Gradual increases in the oscillation frequency of single ions in the ion trap are attributed mainly to mass loss (probably solvent, water, and/or salt). The total mass lost during the 3 s trapping period peaks at around 20 kDa for 4 MDa HBV T = 4 capsids. Discrete frequency drops punctuate the gradual increases in the oscillation frequencies. The drops are attributed to a sudden loss of charge. In most cases a single positive charge is lost along with some mass (on average around 1000 Da). Charge loss occurs for over 40% of the trapped ions. It usually occurs near the beginning of the trapping event, and it occurs preferentially in regions of the trap with strong electric fields, indicating that external electric fields promote charge loss. This process may contribute to the decrease in m/ z resolution that often occurs with megadalton ions.

  18. Charge-reversal lipids, peptide-based lipids, and nucleoside-based lipids for gene delivery.

    PubMed

    LaManna, Caroline M; Lusic, Hrvoje; Camplo, Michel; McIntosh, Thomas J; Barthélémy, Philippe; Grinstaff, Mark W

    2012-07-17

    Twenty years after gene therapy was introduced in the clinic, advances in the technique continue to garner headlines as successes pique the interest of clinicians, researchers, and the public. Gene therapy's appeal stems from its potential to revolutionize modern medical therapeutics by offering solutions to myriad diseases through treatments tailored to a specific individual's genetic code. Both viral and non-viral vectors have been used in the clinic, but the low transfection efficiencies when non-viral vectors are used have lead to an increased focus on engineering new gene delivery vectors. To address the challenges facing non-viral or synthetic vectors, specifically lipid-based carriers, we have focused on three main themes throughout our research: (1) The release of the nucleic acid from the carrier will increase gene transfection. (2) The use of biologically inspired designs, such as DNA binding proteins, to create lipids with peptide-based headgroups will improve delivery. (3) Mimicking the natural binding patterns observed within DNA, by using lipids having a nucleoside headgroup, will produce unique supramolecular assembles with high transfection efficiencies. The results presented in this Account demonstrate that engineering the chemical components of the lipid vectors to enhance nucleic acid binding and release kinetics can improve the cellular uptake and transfection efficacy of nucleic acids. Specifically, our research has shown that the incorporation of a charge-reversal moiety to initiate a shift of the lipid from positive to negative net charge improves transfection. In addition, by varying the composition of the spacer (rigid, flexible, short, long, or aromatic) between the cationic headgroup and the hydrophobic chains, we can tailor lipids to interact with different nucleic acids (DNA, RNA, siRNA) and accordingly affect delivery, uptake outcomes, and transfection efficiency. The introduction of a peptide headgroup into the lipid provides a

  19. Charge-reversal Lipids, Peptide-based Lipids, and Nucleoside-based Lipids for Gene Delivery

    PubMed Central

    LaManna, Caroline M.; Lusic, Hrvoje; Camplo, Michel; McIntosh, Thomas J.; Barthélémy, Philippe; Grinstaff, Mark W.

    2013-01-01

    Conspectus Twenty years after gene therapy was introduced in the clinic, advances in the technique continue to garner headlines as successes pique the interest of clinicians, researchers, and the public. Gene therapy’s appeal stems from its potential to revolutionize modern medical therapeutics by offering solutions to a myriad of diseases by tailoring the treatment to a specific individual’s genetic code. Both viral and non-viral vectors have been used in the clinic, but the low transfection efficiencies when utilizing non-viral vectors have lead to an increased focus on engineering new gene delivery vectors. To address the challenges facing non-viral or synthetic vectors, specifically lipid-based carriers, we have focused on three main themes throughout our research: 1) that releasing the nucleic acid from the carrier will increase gene transfection; 2) that utilizing biologically inspired designs, such as DNA binding proteins, to create lipids with peptide-based headgroups will improve delivery; and 3) that mimicking the natural binding patterns observed within DNA, by using lipids having a nucleoside headgroup, will give unique supramolecular assembles with high transfection efficiency. The results presented in this Account demonstrate that cellular uptake and transfection efficacy can be improved by engineering the chemical components of the lipid vectors to enhance nucleic acid binding and release kinetics. Specifically, our research has shown that the incorporation of a charge-reversal moiety to initiate change of the lipid from positive to negative net charge during the transfection process improves transfection. In addition, by varying the composition of the spacer (rigid, flexible, short, long, and aromatic) between the cationic headgroup and the hydrophobic chains, lipids can be tailored to interact with different nucleic acids (DNA, RNA, siRNA) and accordingly affect delivery, uptake outcomes, and transfection efficiency. Introduction of a peptide

  20. Charge Effects on the Fibril-Forming Peptide KTVIIE: A Two-Dimensional Replica Exchange Simulation Study

    PubMed Central

    Jeon, Joohyun; Shell, M. Scott

    2012-01-01

    The assembly of peptides into ordered nanostructures is increasingly recognized as both a bioengineering tool for generating new materials and a critical aspect of aggregation processes that underlie neurological diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease. There is a major problem in understanding how extremely subtle sequence changes can lead to profound and often unexpected differences in self-assembly behavior. To better delineate the complex interplay of different microscopic driving forces in such cases, we develop a methodology to quantify and compare the propensity of different peptide sequences to form small oligomers during early self-assembly stages. This umbrella-sampling replica exchange molecular dynamics method performs a replica exchange molecular dynamics simulation along peptide association reaction coordinates using umbrella restraints. With this method, we study a set of sequence-similar peptides that differ in net charge: K+TVIIE−, K+TVIIE, and +K+TVIIE. Interestingly, experiments show that only the monovalent peptide, K+TVIIE, forms fibrils, whereas the others do not. We examine dimer, trimer, and tetramer formation processes of these peptides, and compute high-accuracy potential of mean force association curves. The potential of mean forces recapitulate a higher stability and equilibrium constant of the fibril-forming peptide, similar to experiment, but reveal that entropic contributions to association free energies can play a surprisingly significant role. The simulations also show behavior reminiscent of experimental aggregate polymorphism, revealed in multiple stable conformational states and association pathways. Our results suggest that sequence changes can have significant effects on self-assembly through not only direct peptide-peptide interactions but conformational entropies and degeneracies as well. PMID:22768952

  1. Contactless measurements of charge migration within single molecules

    SciTech Connect

    Nagaya, Kiyonobu; Iwayama, Hiroshi; Sugishima, Akinori; Ohmasa, Yoshinori; Yao, Makoto

    2010-06-07

    Contactless measurements of charge migration were carried out for three pi-conjugated molecules in each of which a bromine atom and an oxygen atom are located on the opposite sides of the aromatic ring. A core hole was generated selectively in the Br atom by x-ray absorption, followed by the Auger cascade, and the subsequent charge migration within the molecule was examined by detecting an O{sup +} ion by means of the coincidence momentum imaging measurements.

  2. Adsorption of peptide nucleic acid and DNA decamers at electrically charged surfaces.

    PubMed Central

    Fojta, M; Vetterl, V; Tomschik, M; Jelen, F; Nielsen, P; Wang, J; Palecek, E

    1997-01-01

    Adsorption behavior of peptide nucleic acid (PNA) and DNA decamers (GTAGATCACT and the complementary sequence) on a mercury surface was studied by means of AC impedance measurements at a hanging mercury drop electrode. The nucleic acid was first attached to the electrode by adsorption from a 5-microliter drop of PNA (or DNA) solution, and the electrode with the adsorbed nucleic acid layer was then washed and immersed in the blank background electrolyte where the differential capacity C of the electrode double layer was measured as a function of the applied potential E. It was found that the adsorption behavior of the PNA with an electrically neutral backbone differs greatly from that of the DNA (with a negatively charged backbone), whereas the DNA-PNA hybrid shows intermediate behavior. At higher surface coverage PNA molecules associate at the surface, and the minimum value of C is shifted to negative potentials because of intermolecular interactions of PNA at the surface. Prolonged exposure of PNA to highly negative potentials does not result in PNA desorption, whereas almost all of the DNA is removed from the surface at these potentials. Adsorption of PNA decreases with increasing NaCl concentration in the range from 0 to 50 mM NaCl, in contrast to DNA, the adsorption of which increases under the same conditions. PMID:9129832

  3. Improving Software Performance for Peptide Electron Transfer Dissociation Data Analysis by Implementation of Charge State- and Sequence-Dependent Scoring*

    PubMed Central

    Baker, Peter R.; Medzihradszky, Katalin F.; Chalkley, Robert J.

    2010-01-01

    The use of electron transfer dissociation (ETD) fragmentation for analysis of peptides eluting in liquid chromatography tandem mass spectrometry experiments is increasingly common and can allow identification of many peptides and proteins in complex mixtures. Peptide identification is performed through the use of search engines that attempt to match spectra to peptides from proteins in a database. However, software for the analysis of ETD fragmentation data is currently less developed than equivalent algorithms for the analysis of the more ubiquitous collision-induced dissociation fragmentation spectra. In this study, a new scoring system was developed for analysis of peptide ETD fragmentation data that varies the ion type weighting depending on the precursor ion charge state and peptide sequence. This new scoring regime was applied to the analysis of data from previously published results where four search engines (Mascot, Open Mass Spectrometry Search Algorithm (OMSSA), Spectrum Mill, and X!Tandem) were compared (Kandasamy, K., Pandey, A., and Molina, H. (2009) Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Anal. Chem. 81, 7170–7180). Protein Prospector identified 80% more spectra at a 1% false discovery rate than the most successful alternative searching engine in this previous publication. These results suggest that other search engines would benefit from the application of similar rules. PMID:20513802

  4. Peptide-induced Asymmetric Distribution of Charged Lipids in a Vesicle Bilayer Revealed by Small-Angle Neutron Scattering

    NASA Astrophysics Data System (ADS)

    Heller, William; Qian, Shuo

    2012-02-01

    Cellular membranes are complex mixtures of lipids, proteins and other small molecules that provide functional, dynamic barriers between the cell and its environment, as well as between environments within the cell. The lipid composition of the membrane is highly specific and controlled in terms of both content and lipid localization. Here, small-angle neutron scattering and selective deuterium labeling were used to probe the impact of the membrane-active peptides melittin and alamethicin on the structure of lipid bilayers composed of a mixture of the lipids dimyristoyl phosphatidylglycerol (DMPG) and chain-perdeuterated dimyristoyl phosphatidylcholine (DMPC). We found that both peptides enriched the outer leaflet of the bilayer with the negatively charged DMPG, creating an asymmetric distribution of lipids. The level of enrichment is peptide concentration-dependent and is stronger for melittin than alamethicin. The enrichment between the inner and outer bilayer leaflets occurs at very low peptide concentrations, and increases with peptide concentration, including when the peptide adopts a membrane-spanning, pore-forming state.

  5. Responses of peptide-specific T cells to stimulation with polystyrene beads carrying HLA class I molecules loaded with single peptides.

    PubMed

    Chersi, Alberto; Galati, Rossella; Accapezzato, Daniele; Francavilla, Vittorio; Barnaba, Vincenzo; Butler, Richard H; Tanigaki, Nobuyuki

    2004-08-01

    Cell-sized microbeads carrying single peptide-loaded HLA class I molecules were prepared for HLA-A2 and HLA-B7 by a simple procedure which transfers single peptide-loaded HLA class I molecules from cultured cells to polystyrene beads using anti-peptide antibodies directed to an intracellular segment of HLA-A alpha chains. The surface density of peptide-loaded HLA class I molecules on beads was comparable to that on the peptide-loaded cells. HLA-A2 beads loaded with an HCV peptide HCV1073 were tested for stimulation activity on an HCV1073-specific CD8+ T cell clone NS3-1. A substantial level of gamma-IFN production was induced. The stimulation was peptide-specific. The efficiency was dependent on the bead concentration and the surface HLA class I density on beads and enhanced significantly by co-coupling of anti-CD28 to peptide-loaded beads. The peptide-loading efficiency on HLA class I molecules and the transfer efficiency of HLA class I molecules to polystyrene beads were reasonably high for HLA-A2 and HLA-B7. Thus, polystyrene beads carrying these single peptide-loaded HLA class I molecules are potentially useful in further analysis of the co-stimulatory or inhibitory factors involved in CD8+ T cell responses and eventually in detection of cytotoxic T cells in PBLs.

  6. Charge-carrier screening in single-layer graphene.

    PubMed

    Siegel, David A; Regan, William; Fedorov, Alexei V; Zettl, A; Lanzara, Alessandra

    2013-04-05

    The effect of charge-carrier screening on the transport properties of a neutral graphene sheet is studied by directly probing its electronic structure. We find that the Fermi velocity, Dirac point velocity, and overall distortion of the Dirac cone are renormalized due to the screening of the electron-electron interaction in an unusual way. We also observe an increase of the electron mean free path due to the screening of charged impurities. These observations help us to understand the basis for the transport properties of graphene, as well as the fundamental physics of these interesting electron-electron interactions at the Dirac point crossing.

  7. Study on the dispersion of charged single-wall carbon nanotube bundles by first principles calculation.

    PubMed

    Liu, Wenshuo; Luo, Guangfu; Li, Hong; Wang, Lu; Lu, Jing; Zhou, Jing; Qin, Rui; Gao, Zhengxiang; Lai, Lin

    2009-09-01

    We have investigated the dispersion of charged single-wall carbon nanotube bundles by using density functional theory. We obtained the variation of equilibrium spacing between tubes as a function of charge density for the (4, 4) and (7, 0) tubes with different charge signs and the minimum charge density to cause separation. We also calculated the cohesive energies between two charged tubes as a function of interwall spacing and found that extra energy supply can promote separation of nanotube bundle. Our results are in good agreement with the experimental values.

  8. Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA2 in AOT Reverse Micelles

    PubMed Central

    2015-01-01

    The propensity of peptides to form α-helices has been intensely studied using theory, computation, and experiment. Important model peptides for the study of the coil-to-helix transition have been alanine–lysine (AKA) peptides in which the lysine residues are placed on opposite sides of the helix avoiding charge repulsion while enhancing solubility. In this study, the effects of capped versus zwitterionic peptide termini on the secondary structure of alanine-rich peptides in reverse micelles are explored. The reverse micelles are found to undergo substantial shape fluctuations, a property observed in previous studies of AOT reverse micelles in the absence of solvated peptide. The peptides are observed to interact with water, as well as the AOT surfactant, including interactions between the nonpolar residues and the aliphatic surfactant tails. Computation of IR spectra for the amide I band of the peptide allows for direct comparison with experimental spectra. The results demonstrate that capped AKA2 peptides form more stable α helices than zwitterionic AKA2 peptides in reverse micelles. The rotational anisotropy decay of water is found to be distinctly different in the presence or absence of peptide within the reverse micelle, suggesting that the introduction of peptide significantly alters the number of free waters within the reverse micelle nanopool. However, neither the nature of the peptide termini (capped or charged) nor the degree of peptide helicity is found to significantly alter the balance of interactions between the peptides and the environment. Observed changes in the degree of helicity in AKA2 peptides in bulk solution and in reverse micelle environments result from changes in peptide confinement and hydration as well as direct nonpolar and polar interactions with the water–surfactant interface. PMID:25337983

  9. From Peptides to Proteins: Systematic Control of Net Molecular Charge and Hydrophilicity on the Kinetics of Calcite Growth

    NASA Astrophysics Data System (ADS)

    Elhadj, S.; de Yoreo, J. J.; Hoyer, J. J.; Dove, P. M.

    2006-12-01

    The compartment-specific compositions of biologic molecules isolated from biominerals suggest that control of mineral growth may be linked to biochemical features. Here we define a systematic relationship between the ability of biomolecules in solution to promote the growth of calcite (CaCO3) and their net negative molecular charge and hydrophilicity. The degree of enhancement is dependent on peptide composition, but not on peptide sequence. Data analysis shows that this rate enhancement arises from an increase in the kinetic coefficient. We interpret the mechanism of growth enhancement to be a catalytic process whereby biomolecules reduce the magnitude of the diffusive barrier, Ek, by perturbations that displace water molecules- a water shell destruction mechanism. The result is a decrease in the repulsive barrier for attachment of solutes to the solid phase. This previously unrecognized relationship also rationalizes recently reported data showing acceleration of calcite growth rates over rates measured in the pure system by nanomolar levels of abalone nacre proteins. These findings show that the growth-modifying properties of small model peptides may be scaled up to analyze mineralization processes that are mediated by more complex proteins. We suggest that enhancement of calcite growth may now be estimated a priori from the composition of peptide sequences and the calculated values of hydrophilicity and net molecular charge without need for detailed tests for each biomolecule. This insight may contribute to an improved understanding of mineralization in diverse systems of biomineralization.

  10. Enhancement of charge remote fragmentation in protonated peptides by high-energy CID MALDI-TOF-MS using "cold" matrices

    NASA Astrophysics Data System (ADS)

    Stimson, E.; Truong, O.; Richter, W. J.; Waterfield, M. D.; Burlingame, A. L.

    1997-12-01

    Delayed extraction matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (DE-MALDI-TOF-MS) is employed to evaluate its potential for peptide sequencing using both post-source decay (PSD) and high-energy collision-induced dissociation (CID). This work provides evidence that complete amino-acid sequences may be obtained employing a dual approach including PSD of [M + H]+ ions using a "hot" matrix ([alpha]-cyano-4-hydroxycinnamic acid, CHCA), followed by high-energy CID using "cold" matrices (2,5-dihydroxybenzoic acid, DHB; 2,6-dihydroxyacetophenone/di-ammonium hydrogen citrate, DHAP/DAHC). This strategy ensures that PSD results in a rich variety of product ions derived from charge-driven processes that provide gross structural information. High-energy CID (20 keV collision energy range) of low internal energy [M + H]+ ions is then employed to reveal complementary side-chain detail (i.e. Leu/Ile distinction) in a manner highly selective for charge remote fragmentation (CRF), because PSD is largely reduced. As expected from the known behaviour of protonated peptides at 10 keV collision energies, charge fixation at basic sites required for CRF is more pronounced in CID than in PSD. We have obtained spectra for a synthetic peptide that approximate the results and performance of MALDI high-energy CID obtained on sector-based instrumentation (EBE-oa-TOF).

  11. Microscopic rates of peptide-phospholipid bilayer interactions from single-molecule residence times.

    PubMed

    Myers, Grant A; Gacek, Daniel A; Peterson, Eric M; Fox, Christopher B; Harris, Joel M

    2012-12-05

    The binding of glucagon-like peptide-1 (GLP-1) to a planar phospholipid bilayer is measured using single-molecule total internal reflection fluorescence microscopy. From several reports in the literature, GLP-1 has been shown to be a random coil in free solution, adopting a folded, α-helix conformation when intercalated into membrane environments. Single-molecule fluorescence measurements of GLP-1 binding to supported lipid bilayers show evidence of two populations of membrane-associated molecules having different residence times, suggesting weakly adsorbed peptides and strongly bound peptides in the lipid bilayer. The path to and from a strongly bound (folded, intercalated) state would likely include an adsorbed state as an intermediate, so that the resulting kinetics would correspond to a consecutive first-order reversible three-state model. In this work, the relationships between measured single-molecule residence times and the microscopic rates in a three-state kinetic model are derived and used to interpret the binding of GLP-1 to a supported lipid bilayer. The system of differential equations associated with the proposed consecutive-three state kinetics scheme is solved, and the solution is applied to interpret histograms of single-molecule, GLP-1 residence times in terms of the microscopic rates in the sequential two-step model. These microscopic rates are used to estimate the free energy barrier to adsorption, the fraction of peptides adsorbing to the membrane surface that successfully intercalate in the bilayer, the lifetime of inserted peptides in the membrane, and the free energy change of insertion into the lipid bilayer from the adsorbed state. The transition from a random coil in solution to a folded state in a membrane has been recognized as a common motif for insertion of membrane active peptides. Therefore, the relationships developed here could have wide application to the kinetic analysis of peptide-membrane interactions.

  12. Speed improvements of peptide-spectrum matching using single-instruction multiple-data instructions.

    PubMed

    Zhang, Jian; McQuillan, Ian; Wu, Fang-Xiang

    2011-10-01

    Peptide-spectrum matching is one of the most time-consuming portion of the database search method for assignment of tandem mass spectra to peptides. In this study, we develop a parallel algorithm for peptide-spectrum matching using Single-Instruction Multiple Data (SIMD) instructions. Unlike other parallel algorithms in peptide-spectrum matching, our algorithm parallelizes the computation of matches between a single spectrum and a given peptide sequence from the database. It also significantly reduces the number of comparison operations. Extra improvements are obtained by using SIMD instructions to avoid conditional branches and unnecessary memory access within the algorithm. The implementation of the developed algorithm is based on the Streaming SIMD Extensions technology that is embedded in most Intel microprocessors. Similar technology also exists in other modern microprocessors. A simulation shows that the developed algorithm achieves an 18-fold speedup over the previous version of Real-Time Peptide-Spectrum Matching algorithm [F. X. Wu et al., Rapid Commun. Mass Sepctrom. 2006, 20, 1199-1208]. Therefore, the developed algorithm can be employed to develop real-time control methods for MS/MS.

  13. Bioassisted multi-nanoparticle patterning using single-layer peptide templates

    NASA Astrophysics Data System (ADS)

    Nochomovitz, Ravit; Amit, Moran; Matmor, Maayan; Ashkenasy, Nurit

    2010-04-01

    Patterning of nanoparticles on solid substrates is one of the main challenges of current nanotechnology applications. The use of organic molecules as templates for the deposition of the nanoparticles makes it possible to utilize simple soft lithography techniques for patterning. Peptides appear to be powerful candidates for this job due to their versatility and design flexibility. In this work, we demonstrate the use of dual-affinity peptides, which bind both to the substrate and to the deposited nanoparticles, as single-layer linkers for the creation of multi-component nanoparticle patterns via microcontact printing processes. Controlled deposition and patterning of gold colloids or carbon nanotubes (CNTs) on silicon oxide surfaces and that of silicon oxide nanoparticles on gold surfaces have been achieved by the use of the corresponding dual-affinity peptides. Furthermore, patterning of both gold colloids and CNTs on a single substrate on predefined locations has been achieved. The suggested generic approach offers great flexibility by allowing binding of any material to a substrate of choice, provided that a peptide binding segment has been engineered for each of the inorganic components. Furthermore, the diversity of possible peptide sequences allows the formation of multi-component patterns, paving the way to fabricating complex functional structures based on peptide templates.

  14. Bioassisted multi-nanoparticle patterning using single-layer peptide templates.

    PubMed

    Nochomovitz, Ravit; Amit, Moran; Matmor, Maayan; Ashkenasy, Nurit

    2010-04-09

    Patterning of nanoparticles on solid substrates is one of the main challenges of current nanotechnology applications. The use of organic molecules as templates for the deposition of the nanoparticles makes it possible to utilize simple soft lithography techniques for patterning. Peptides appear to be powerful candidates for this job due to their versatility and design flexibility. In this work, we demonstrate the use of dual-affinity peptides, which bind both to the substrate and to the deposited nanoparticles, as single-layer linkers for the creation of multi-component nanoparticle patterns via microcontact printing processes. Controlled deposition and patterning of gold colloids or carbon nanotubes (CNTs) on silicon oxide surfaces and that of silicon oxide nanoparticles on gold surfaces have been achieved by the use of the corresponding dual-affinity peptides. Furthermore, patterning of both gold colloids and CNTs on a single substrate on predefined locations has been achieved. The suggested generic approach offers great flexibility by allowing binding of any material to a substrate of choice, provided that a peptide binding segment has been engineered for each of the inorganic components. Furthermore, the diversity of possible peptide sequences allows the formation of multi-component patterns, paving the way to fabricating complex functional structures based on peptide templates.

  15. Estimation of acidity constants, ionic mobilities and charges of antimicrobial peptides by capillary electrophoresis.

    PubMed

    Tůmová, Tereza; Monincová, Lenka; Čeřovský, Václav; Kašička, Václav

    2016-12-01

    Capillary electrophoresis (CE) was employed for the determination of thermodynamic acidity constants (pKa ) and actual ionic mobilities of polycationic antimicrobial peptides (AMPs). The effective electrophoretic mobilities of AMPs were measured by CE in a series of the background electrolytes within a wide pH range (2.00-12.25), at constant ionic strength (25 mM) and ambient temperature, using polybrene coated fused silica capillaries to suppress sorption of cationic AMPs to the capillary wall. Eventually, Haarhoff-Van der Linde peak fitting function was used for the determination of correct migration times of some AMPs peaks that were distorted by electromigration dispersion. The measured effective mobilities were corrected to 25°C. Mixed acidity constants, pKa,i mix , and actual ionic mobilities, mi , of AMPs were determined by the nonlinear regression analysis of pH dependence of their effective mobilities. The pKa,i mix values were recalculated to thermodynamic pKa s using the Debye-Hückel theory. Thermodynamic pKa of imidazolium group of histidine residues was found to be in the range 3.72-4.98, pKa of α-NH3(+) group was in the range 6.14-6.93, and pKa of ε-NH3(+) group of lysine spanned the interval 7.26-9.84, depending on the particular amino acid sequence of the AMPs. Actual ionic mobilities of AMPs with positive charges from one to six elementary units achieved values (9.8 - 36.5) × 10(-9) m(2) V(-1) s(-1) . © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Structural transformation of peptide amphiphile self-assembly induced by headgroup charge and size regulation

    NASA Astrophysics Data System (ADS)

    Gao, Changrui; Bedzyk, Michael; Olvera, Monica; Kewalramani, Sumit; Palmer, Liam

    The ability to control the nano and the meso-scale architecture of molecular assemblies is one of the major challenges in nanoscience. Significantly, structural transformations of amphiphilic aggregates induced by variations in environmental conditions have attracted attention due to their biotechnological relevance. Here, we study the assembly in aqueous solution for a modular series of peptide amphiphiles with 3, 2 or 1 lysine groups conjugated to a C16 carbon tail (C16K3, C16K2 and C16K1) . This system design allow us to probe how the equilibrium structure of the self-assembly can be tuned by controlling the coupling between steric (via choice of headgroup: K3, K2, or K1) and electrostatic (via solution pH) interactions. Solution small- and wide-angle X-ray scattering (SAXS/WAXS) and transmission electron microscopy (TEM) studies reveal that depending on pH and number of lysines in the lipid headgroup, amphiphiles can assemble into a range of structures: spherical micelles, bilayer ribbons and vesicles. We also perform detailed phase space mapping of pH-and headgroup size dependency of the structures of assembly over 0.1-100 nm length scales via SAXS/WAXS. The experimental results in conjunction with molecular dynamics (MD) simulations deduce quantitative relations between pH-dependent molecular charges, steric constraints and self-assembly morphologies, which is significant for developing experimental routes to obtain assembly structures with specific nano- and meso-scale features through controlled external stimuli.

  17. The two-step assemblies of basic-amino-Acid-rich Peptide with a highly charged polyoxometalate.

    PubMed

    Zhang, Teng; Li, Hong-Wei; Wu, Yuqing; Wang, Yizhan; Wu, Lixin

    2015-06-15

    Two-step assembly of a peptide from HPV16 L1 with a highly charged europium-substituted polyoxometalate (POM) cluster, accompanying a great luminescence enhancement of the inorganic polyanions, is reported. The mechanism is discussed in detail by analyzing the thermodynamic parameters from isothermal titration calorimetry (ITC), time-resolved fluorescent and NMR spectra. By comparing the actions of the peptide analogues, a binding process and model are proposed accordingly. The driving forces in each binding step are clarified, and the initial POM aggregation, basic-sequence and hydrophobic C termini of peptide are revealed to contribute essentially to the two-step assembly. The present study demonstrates both a meaningful preparation for bioinorganic materials and a strategy using POMs to modulate the assembly of peptides and even proteins, which could be extended to other proteins and/or viruses by using peptides and POMs with similar properties. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Electrical detection of the biological interaction of a charged peptide via gallium arsenide junction-field-effect transistors

    PubMed Central

    Lee, Kangho; Nair, Pradeep R.; Alam, Muhammad A.; Janes, David B.; Wampler, Heeyeon P.; Zemlyanov, Dmitry Y.; Ivanisevic, Albena

    2008-01-01

    GaAs junction-field-effect transistors (JFETs) are utilized to achieve label-free detection of biological interaction between a probe transactivating transcriptional activator (TAT) peptide and the target trans-activation-responsive (TAR) RNA. The TAT peptide is a short sequence derived from the human immunodeficiency virus-type 1 TAT protein. The GaAs JFETs are modified with a mixed adlayer of 1-octadecanethiol (ODT) and TAT peptide, with the ODT passivating the GaAs surface from polar ions in physiological solutions and the TAT peptide providing selective binding sites for TAR RNA. The devices modified with the mixed adlayer exhibit a negative pinch-off voltage (VP) shift, which is attributed to the fixed positive charges from the arginine-rich regions in the TAT peptide. Immersing the modified devices into a TAR RNA solution results in a large positive VP shift (>1 V) and a steeper subthreshold slope (∼80 mV∕decade), whereas “dummy” RNA induced a small positive VP shift (∼0.3 V) without a significant change in subthreshold slopes (∼330 mV∕decade). The observed modulation of device characteristics is analyzed with analytical modeling and two-dimensional numerical device simulations to investigate the electronic interactions between the GaAs JFETs and biological molecules. PMID:19484151

  19. Electrical detection of the biological interaction of a charged peptide via gallium arsenide junction-field-effect transistors

    NASA Astrophysics Data System (ADS)

    Lee, Kangho; Nair, Pradeep R.; Alam, Muhammad A.; Janes, David B.; Wampler, Heeyeon P.; Zemlyanov, Dmitry Y.; Ivanisevic, Albena

    2008-06-01

    GaAs junction-field-effect transistors (JFETs) are utilized to achieve label-free detection of biological interaction between a probe transactivating transcriptional activator (TAT) peptide and the target trans-activation-responsive (TAR) RNA. The TAT peptide is a short sequence derived from the human immunodeficiency virus-type 1 TAT protein. The GaAs JFETs are modified with a mixed adlayer of 1-octadecanethiol (ODT) and TAT peptide, with the ODT passivating the GaAs surface from polar ions in physiological solutions and the TAT peptide providing selective binding sites for TAR RNA. The devices modified with the mixed adlayer exhibit a negative pinch-off voltage (VP) shift, which is attributed to the fixed positive charges from the arginine-rich regions in the TAT peptide. Immersing the modified devices into a TAR RNA solution results in a large positive VP shift (>1 V) and a steeper subthreshold slope (˜80 mV/decade), whereas "dummy" RNA induced a small positive VP shift (˜0.3 V) without a significant change in subthreshold slopes (˜330 mV/decade). The observed modulation of device characteristics is analyzed with analytical modeling and two-dimensional numerical device simulations to investigate the electronic interactions between the GaAs JFETs and biological molecules.

  20. Electrical detection of the biological interaction of a charged peptide via gallium arsenide junction-field-effect transistors.

    PubMed

    Lee, Kangho; Nair, Pradeep R; Alam, Muhammad A; Janes, David B; Wampler, Heeyeon P; Zemlyanov, Dmitry Y; Ivanisevic, Albena

    2008-06-01

    GaAs junction-field-effect transistors (JFETs) are utilized to achieve label-free detection of biological interaction between a probe transactivating transcriptional activator (TAT) peptide and the target trans-activation-responsive (TAR) RNA. The TAT peptide is a short sequence derived from the human immunodeficiency virus-type 1 TAT protein. The GaAs JFETs are modified with a mixed adlayer of 1-octadecanethiol (ODT) and TAT peptide, with the ODT passivating the GaAs surface from polar ions in physiological solutions and the TAT peptide providing selective binding sites for TAR RNA. The devices modified with the mixed adlayer exhibit a negative pinch-off voltage (V(P)) shift, which is attributed to the fixed positive charges from the arginine-rich regions in the TAT peptide. Immersing the modified devices into a TAR RNA solution results in a large positive V(P) shift (>1 V) and a steeper subthreshold slope ( approximately 80 mVdecade), whereas "dummy" RNA induced a small positive V(P) shift ( approximately 0.3 V) without a significant change in subthreshold slopes ( approximately 330 mVdecade). The observed modulation of device characteristics is analyzed with analytical modeling and two-dimensional numerical device simulations to investigate the electronic interactions between the GaAs JFETs and biological molecules.

  1. Charge collection measurements with p-type Magnetic Czochralski silicon single pad detectors

    NASA Astrophysics Data System (ADS)

    Tosi, C.; Bruzzi, M.; Macchiolo, A.; Scaringella, M.; Petterson, M. K.; Sadrozinski, H. F.-W.; Betancourt, C.; Manna, N.; Creanza, D.; Boscardin, M.; Piemonte, C.; Zorzi, N.; Borrello, L.; Messineo, A.

    2007-09-01

    The charge collected from beta source particles in single pad detectors produced on p-type Magnetic Czochralski (MCz) silicon wafers has been measured before and after irradiation with 26 MeV protons. After a 1 MeV neutron equivalent fluence of 1×1015 cm-2 the collected charge is reduced to 77% at bias voltages below 900 V. This result is compared with previous results from charge collection measurements.

  2. Single electron charge sensitivity of liquid-gated carbon nanotube transistors.

    PubMed

    Sharf, Tal; Wang, Neng-Ping; Kevek, Joshua W; Brown, Morgan A; Wilson, Heather; Heinze, Stefan; Minot, Ethan D

    2014-09-10

    Random telegraph signals corresponding to activated charge traps were observed with liquid-gated CNT FETs. The high signal-to-noise ratio that we observe demonstrates that single electron charge sensing is possible with CNT FETs in liquids at room temperature. We have characterized the gate-voltage dependence of the random telegraph signals and compared to theoretical predictions. The gate-voltage dependence clearly identifies the sign of the activated trapped charge.

  3. Using blocking peptides to control and analyze the mechanical properties of single fibrin fibers

    NASA Astrophysics Data System (ADS)

    Maddi, Pranav; O'Brien, E. Tim, III; Gorkun, Oleg; Falvo, Michael R.

    2011-10-01

    Fibrin is the main structural protein involved in blood clotting, and exhibits high strength and elasticity. Fibrin study traditionally focuses on fully formed clots, whereas we employ new AFM nanoManipulation techniques to study single fibrin fiber mechanics. We used 4 and 10 residue peptides to interfere with the knob-hole and αC interactions involved in fibrin polymerization to evaluate the contribution of each interaction to the fiber's mechanical properties. We varied the concentration of each peptide present during polymerization to find the concentration that inhibited polymerization by half. The presence of either peptide during fibrin polymerization did not affect single fiber breaking strain (δLL0). The breaking force of all treated fibers reduced from 10-50nN to 2-10nN, suggesting treated fibers are thinner or are the same diameter with some inhibition of interactions. Fibers polymerized with the knob-hole targeting peptide visibly lost elasticity after 100% strain, while fibers polymerized with the αC targeting peptide lost elasticity after reaching 150% strain, suggesting that the knob-hole interactions control single fiber elasticity.

  4. Charge division using carbon filaments for obtaining coordinate information from detection of single electrons

    SciTech Connect

    Bird, F.; Shapiro, S.; Ashford, V.; McShurley, D.; Reif, R.; Lirth, D.W.G.S.; Williams, S.

    1985-09-01

    Seven micron diameter Carbon filaments forming the anode of a multiwire proportional chamber have been used to detect single electrons. Charge division techniques applied to the 5 cm long wire resulted in a position resolution of sigma/L < 2% for a collected signal charge of 30 fC.

  5. Bioelectronic interfaces by spontaneously organized peptides on 2D atomic single layer materials

    NASA Astrophysics Data System (ADS)

    Hayamizu, Yuhei; So, Christopher R.; Dag, Sefa; Page, Tamon S.; Starkebaum, David; Sarikaya, Mehmet

    2016-09-01

    Self-assembly of biological molecules on solid materials is central to the “bottom-up” approach to directly integrate biology with electronics. Inspired by biology, exquisite biomolecular nanoarchitectures have been formed on solid surfaces. We demonstrate that a combinatorially-selected dodecapeptide and its variants self-assemble into peptide nanowires on two-dimensional nanosheets, single-layer graphene and MoS2. The abrupt boundaries of nanowires create electronic junctions via spatial biomolecular doping of graphene and manifest themselves as a self-assembled electronic network. Furthermore, designed peptides form nanowires on single-layer MoS2 modifying both its electric conductivity and photoluminescence. The biomolecular doping of nanosheets defined by peptide nanostructures may represent the crucial first step in integrating biology with nano-electronics towards realizing fully self-assembled bionanoelectronic devices.

  6. Bioelectronic interfaces by spontaneously organized peptides on 2D atomic single layer materials.

    PubMed

    Hayamizu, Yuhei; So, Christopher R; Dag, Sefa; Page, Tamon S; Starkebaum, David; Sarikaya, Mehmet

    2016-09-22

    Self-assembly of biological molecules on solid materials is central to the "bottom-up" approach to directly integrate biology with electronics. Inspired by biology, exquisite biomolecular nanoarchitectures have been formed on solid surfaces. We demonstrate that a combinatorially-selected dodecapeptide and its variants self-assemble into peptide nanowires on two-dimensional nanosheets, single-layer graphene and MoS2. The abrupt boundaries of nanowires create electronic junctions via spatial biomolecular doping of graphene and manifest themselves as a self-assembled electronic network. Furthermore, designed peptides form nanowires on single-layer MoS2 modifying both its electric conductivity and photoluminescence. The biomolecular doping of nanosheets defined by peptide nanostructures may represent the crucial first step in integrating biology with nano-electronics towards realizing fully self-assembled bionanoelectronic devices.

  7. Bioelectronic interfaces by spontaneously organized peptides on 2D atomic single layer materials

    PubMed Central

    Hayamizu, Yuhei; So, Christopher R.; Dag, Sefa; Page, Tamon S.; Starkebaum, David; Sarikaya, Mehmet

    2016-01-01

    Self-assembly of biological molecules on solid materials is central to the “bottom-up” approach to directly integrate biology with electronics. Inspired by biology, exquisite biomolecular nanoarchitectures have been formed on solid surfaces. We demonstrate that a combinatorially-selected dodecapeptide and its variants self-assemble into peptide nanowires on two-dimensional nanosheets, single-layer graphene and MoS2. The abrupt boundaries of nanowires create electronic junctions via spatial biomolecular doping of graphene and manifest themselves as a self-assembled electronic network. Furthermore, designed peptides form nanowires on single-layer MoS2 modifying both its electric conductivity and photoluminescence. The biomolecular doping of nanosheets defined by peptide nanostructures may represent the crucial first step in integrating biology with nano-electronics towards realizing fully self-assembled bionanoelectronic devices. PMID:27653460

  8. A singly charged ion source for radioactive 11C ion acceleration

    NASA Astrophysics Data System (ADS)

    Katagiri, K.; Noda, A.; Nagatsu, K.; Nakao, M.; Hojo, S.; Muramatsu, M.; Suzuki, K.; Wakui, T.; Noda, K.

    2016-02-01

    A new singly charged ion source using electron impact ionization has been developed to realize an isotope separation on-line system for simultaneous positron emission tomography imaging and heavy-ion cancer therapy using radioactive 11C ion beams. Low-energy electron beams are used in the electron impact ion source to produce singly charged ions. Ionization efficiency was calculated in order to decide the geometric parameters of the ion source and to determine the required electron emission current for obtaining high ionization efficiency. Based on these considerations, the singly charged ion source was designed and fabricated. In testing, the fabricated ion source was found to have favorable performance as a singly charged ion source.

  9. A singly charged ion source for radioactive {sup 11}C ion acceleration

    SciTech Connect

    Katagiri, K.; Noda, A.; Nagatsu, K.; Nakao, M.; Hojo, S.; Muramatsu, M.; Suzuki, K.; Wakui, T.; Noda, K.

    2016-02-15

    A new singly charged ion source using electron impact ionization has been developed to realize an isotope separation on-line system for simultaneous positron emission tomography imaging and heavy-ion cancer therapy using radioactive {sup 11}C ion beams. Low-energy electron beams are used in the electron impact ion source to produce singly charged ions. Ionization efficiency was calculated in order to decide the geometric parameters of the ion source and to determine the required electron emission current for obtaining high ionization efficiency. Based on these considerations, the singly charged ion source was designed and fabricated. In testing, the fabricated ion source was found to have favorable performance as a singly charged ion source.

  10. Binding affinities of amino acid analogues at the charged aqueous titania interface: implications for titania-binding peptides.

    PubMed

    Sultan, Anas M; Hughes, Zak E; Walsh, Tiffany R

    2014-11-11

    Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and interactions at the aqueous titania interface remain far from being fully understood. Here, atomistic molecular dynamics simulations, in partnership with metadynamics, are used to calculate the free energy of adsorption of different amino acid side chain analogues at the negatively-charged aqueous rutile TiO2 (110) interface, under conditions corresponding with neutral pH. Our calculations predict that charged amino acid analogues have a relatively high affinity to the titania surface, with the arginine analogue predicted to be the strongest binder. Interactions between uncharged amino acid analogues and titania are found to be repulsive or weak at best. All of the residues that bound to the negatively-charged interface show a relatively stronger adsorption compared with the charge-neutral interface, including the negatively-charged analogue. Of the analogues that are found to bind to the titania surface, the rank ordering of the binding affinities is predicted to be "arginine" > "lysine" ≈ aspartic acid > "serine". This is the same ordering as was found previously for the charge-neutral aqueous titania interface. Our results show very good agreement with available experimental data and can provide a baseline for the interpretation of peptide-TiO2 adsorption data.

  11. Time-resolved single dopant charge dynamics in silicon

    NASA Astrophysics Data System (ADS)

    Rashidi, Mohammad; Burgess, Jacob A. J.; Taucer, Marco; Achal, Roshan; Pitters, Jason L.; Loth, Sebastian; Wolkow, Robert A.

    2016-10-01

    As the ultimate miniaturization of semiconductor devices approaches, it is imperative that the effects of single dopants be clarified. Beyond providing insight into functions and limitations of conventional devices, such information enables identification of new device concepts. Investigating single dopants requires sub-nanometre spatial resolution, making scanning tunnelling microscopy an ideal tool. However, dopant dynamics involve processes occurring at nanosecond timescales, posing a significant challenge to experiment. Here we use time-resolved scanning tunnelling microscopy and spectroscopy to probe and study transport through a dangling bond on silicon before the system relaxes or adjusts to accommodate an applied electric field. Atomically resolved, electronic pump-probe scanning tunnelling microscopy permits unprecedented, quantitative measurement of time-resolved single dopant ionization dynamics. Tunnelling through the surface dangling bond makes measurement of a signal that would otherwise be too weak to detect feasible. Distinct ionization and neutralization rates of a single dopant are measured and the physical process controlling those are identified.

  12. Molecular dynamics simulation of non-covalent single-walled carbon nanotube functionalization with surfactant peptides.

    PubMed

    Barzegar, Abolfazl; Mansouri, Alireza; Azamat, Jafar

    2016-03-01

    Non-covalent functionalized single-walled carbon nanotubes (SWCNTs) with improved solubility and biocompatibility can successfully transfer drugs, DNA, RNA, and proteins into the target cells. Theoretical studies such as molecular docking and molecular dynamics simulations in fully atomistic scale were used to investigate the hydrophobic and aromatic π-π-stacking interaction of designing four novel surfactant peptides for non-covalent functionalization of SWCNTs. The results indicated that the designed peptides have binding affinity towards SWCNT with constant interactions during MD simulation times, and it can even be improved by increasing the number of tryptophan residues. The aromatic content of the peptides plays a significant role in their adsorption in SWCNT wall. The data suggest that π-π stacking interaction between the aromatic rings of tryptophan and π electrons of SWCNTs is more important than hydrophobic effects for dispersing carbon nanotubes; nevertheless SWCNTs are strongly hydrophobic in front of smooth surfaces. The usage of aromatic content of peptides for forming SWCNT/peptide complex was proved successfully, providing new insight into peptide design strategies for future nano-biomedical applications. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. De novo generation of antimicrobial LK peptides with a single tryptophan at the critical amphipathic interface.

    PubMed

    Kang, Su-Jin; Won, Hyung-Sik; Choi, Wahn-Soo; Lee, Bong-Jin

    2009-09-01

    De novo design of amphipathic model peptides has been successful for generating many antimicrobial peptides with various lengths and amino acid compositions. Here, we suggest a very simple strategy to design antimicrobial peptides with a short length and a simple amino acid composition. Amphipathic helical properties were conferred by using only leucines and lysines and a single tryptophan was positioned at the critical amphipathic interface between the hydrophilic ending side and the hydrophobic starting side, in the helical wheel projection. According to this rule, the model peptides with 7 to 13 residues exhibited antimicrobial activity. Among them, the most potent activity against both Gram-positive and Gram-negative bacteria, covering all of the nine bacterial strains tested in this study, was found for the 11-mer sequences having a 1:1 (L(5)K(5)W(6)) or a 3:2 (L(6)K(4)W(6)) ratio of leucines to lysines. In particular, the former peptide L(5)K(5)W(6) could be evaluated as the most useful agent, as it showed no significant hemolytic activity with a broad-spectrum of antimicrobial activity. Copyright 2009 European Peptide Society and John Wiley & Sons, Ltd.

  14. Superconducting and charge density wave transition in single crystalline LaPt2Si2

    NASA Astrophysics Data System (ADS)

    Gupta, Ritu; Dhar, S. K.; Thamizhavel, A.; Rajeev, K. P.; Hossain, Z.

    2017-06-01

    We present results of our comprehensive studies on single crystalline LaPt2Si2. Pronounced anomaly in electrical resistivity and heat capacity confirms the bulk nature of superconductivity (SC) and charge density wave (CDW) transition in the single crystals. While the charge density wave transition temperature is lower, the superconducting transition temperature is higher in single crystal compared to the polycrystalline sample. This result confirms the competing nature of CDW and SC. Another important finding is the anomalous temperature dependence of upper critical field H C2(T). We also report the anisotropy in the transport and magnetic measurements of the single crystal.

  15. Development of a Single-Chain Peptide Agonist of the Relaxin-3 Receptor Using Hydrocarbon Stapling.

    PubMed

    Hojo, Keiko; Hossain, Mohammed Akhter; Tailhades, Julien; Shabanpoor, Fazel; Wong, Lilian L L; Ong-Pålsson, Emma E K; Kastman, Hanna E; Ma, Sherie; Gundlach, Andrew L; Rosengren, K Johan; Wade, John D; Bathgate, Ross A D

    2016-08-25

    Structure-activity studies of the insulin superfamily member, relaxin-3, have shown that its G protein-coupled receptor (RXFP3) binding site is contained within its central B-chain α-helix and this helical structure is essential for receptor activation. We sought to develop a single B-chain mimetic that retained agonist activity. This was achieved by use of solid phase peptide synthesis together with on-resin ruthenium-catalyzed ring closure metathesis of a pair of judiciously placed i,i+4 α-methyl, α-alkenyl amino acids. The resulting hydrocarbon stapled peptide was shown by solution NMR spectroscopy to mimic the native helical conformation of relaxin-3 and to possess potent RXFP3 receptor binding and activation. Alternative stapling procedures were unsuccessful, highlighting the critical need to carefully consider both the peptide sequence and stapling methodology for optimal outcomes. Our result is the first successful minimization of an insulin-like peptide to a single-chain α-helical peptide agonist which will facilitate study of the function of relaxin-3.

  16. Single channel conductance modeling of the peptide alamethicin in synthetically formed bilayers

    NASA Astrophysics Data System (ADS)

    Creasy, M. Austin; Leo, Donald J.

    2011-04-01

    Bilayers are synthetically made cell membranes that are used to study cell membrane properties and make functional devices that incorporate inherent properties of the cell membranes. Lipids and proteins are two of the main components of a cell membrane. Lipids provide the structure of the membrane in the form of two leaflets or layers that are held together by the amphiphilic interaction between the lipids and water. Proteins are made from a combination of amino acids and the properties of these proteins are dependent on the amino acid sequence. Some proteins are antibiotics and can easily self insert into the membrane of a cell or into a synthetically formed bilayer. The peptide alamethicin is one such antibiotic that easily inserts into a bilayer and changes the conductance properties of the bilayer. Analytical models of the conductance change with respect to the potential and other variables across the bilayer follows the nonlinear conductance changes seen with the incorporation of the peptide in a bilayer. The individual channels formed by the peptide have been studied and the peptide has several discrete conductance levels. These discrete levels have been shown to be dependent on the potential across the bilayer and several other variables including the lipid variety. The conductance level for a single channel can change with time in a probabilistic fashion. This paper will model these discrete conductance levels of the peptide alamethicin and the model of the single channel conductance will be used to model the cumulative effect of multiple channels within a bilayer.

  17. Antitumor potential of a synthetic interferon-alpha/PLGF-2 positive charge peptide hybrid molecule in pancreatic cancer cells

    PubMed Central

    Yin, Hongmei; Chen, Naifei; Guo, Rui; Wang, Hong; Li, Wei; Wang, Guanjun; Cui, Jiuwei; Jin, Haofan; Hu, Ji-Fan

    2015-01-01

    Pancreatic cancer is the most aggressive malignant disease, ranking as the fourth leading cause of cancer-related death among men and women in the United States. Interferon alpha (IFNα) has been used to treat pancreatic cancer, but its clinical application has been significantly hindered due to the low antitumor activity. We used a “cDNA in-frame fragment library” screening approach to identify short peptides that potentiate the antitumor activity of interferons. A short positively charged peptide derived from the C-terminus of placental growth factor-2 (PLGF-2) was selected to enhance the activity of IFNα. For this, we constructed a synthetic interferon hybrid molecule (SIFα) by fusing the positively charged PLGF-2 peptide to the C-terminus of the human IFNα. Using human pancreatic cell lines (ASPC and CFPAC1) as a model system, we found that SIFα exhibited a significantly higher activity than did the wild-type IFNα in inhibiting the tumor cell growth. The enhanced activity of the synthetic SIFα was associated with the activation of interferon pathway target genes and the increased binding of cell membrane receptor. This study demonstrates the potential of a synthetic SIFα as a novel antitumor agent. PMID:26584517

  18. Switching of the fluorescence emission of single molecules between the locally excited and charge transfer states

    NASA Astrophysics Data System (ADS)

    Angeles Izquierdo, M.; Bell, Toby D. M.; Habuchi, Satoshi; Fron, Eduard; Pilot, Roberto; Vosch, Tom; De Feyter, Steven; Verhoeven, Jan; Jacob, Josemon; Müllen, Klaus; Hofkens, Johan; De Schryver, Frans C.

    2005-01-01

    A novel perylene imide and oligo-pentaphenyl bisfluorene containing molecule is shown to undergo electron transfer to form an emissive charge transfer state in di-benzyl ether and THF. At the single molecule level in a PMMA film, fluorescence spectra characteristic of both emissive states (locally excited and charge transfer) are observed with 44% of the molecules studied showing switching between the two states. These results demonstrate that charge transfer fluorescence from single molecules can be used to report on the properties and dynamics of a molecule's immediate surroundings or nano-environment.

  19. Temperature dependence of charge transport in conjugated single molecule junctions

    NASA Astrophysics Data System (ADS)

    Huisman, Eek; Kamenetska, Masha; Venkataraman, Latha

    2011-03-01

    Over the last decade, the break junction technique using a scanning tunneling microscope geometry has proven to be an important tool to understand electron transport through single molecule junctions. Here, we use this technique to probe transport through junctions at temperatures ranging from 5K to 300K. We study three amine-terminated (-NH2) conjugated molecules: a benzene, a biphenyl and a terphenyl derivative. We find that amine groups bind selectively to undercoordinate gold atoms gold all the way down to 5K, yielding single molecule junctions with well-defined conductances. Furthermore, we find that the conductance of a single molecule junction increases with temperature and we present a mechanism for this temperature dependent transport result. Funded by a Rubicon Grant from The Netherlands Organisation for Scientific Research (NWO) and the NSEC program of NSF under grant # CHE-0641523.

  20. Detection of charged particles with a methylammonium lead tribromide perovskite single crystal

    NASA Astrophysics Data System (ADS)

    Xu, Qiang; Wei, Haotong; Wei, Wei; Chuirazzi, William; DeSantis, Dylan; Huang, Jinsong; Cao, Lei

    2017-03-01

    Methylammonium lead tribromide (MAPbBr3) perovskite crystals have attracted significant attention due to their attractive performance in various optoelectronic applications such as solar cells, light-emitting devices, photodetectors, and recently in X-ray detectors. In this study, we demonstrate a possible use of perovskite-based devices for detection of charged particles (which can be applied in basic scientific research, health physics, and environmental analysis) and investigate the mechanism of fundamental charge transport inside perovskite crystals. It was found that inexpensive MAPbBr3 single crystals could be used for measuring the energy spectrum of charged particles through direct collection of the produced charge. After fitting the plot of the centroid peak position versus voltage with the Hecht equation for single-polarity charge transport, the obtained hole mobility-lifetime product was in the range of (0.4-1.6)×10-3 cm2/V.

  1. Single-electron charging effects. Technical progress report

    SciTech Connect

    Ruggiero, S.T.

    1991-12-15

    The status of our project on single-electron tunneling is, again, excellent. As outlined in our original proposal, a key goal for this project has been the development of a scanning tunneling instrument for the purpose of imaging individual particles and tunneling into these particles at high magnetic fields. Further progress is discussed in this report.

  2. Time-resolved single dopant charge dynamics in silicon

    PubMed Central

    Rashidi, Mohammad; Burgess, Jacob A. J.; Taucer, Marco; Achal, Roshan; Pitters, Jason L.; Loth, Sebastian; Wolkow, Robert A.

    2016-01-01

    As the ultimate miniaturization of semiconductor devices approaches, it is imperative that the effects of single dopants be clarified. Beyond providing insight into functions and limitations of conventional devices, such information enables identification of new device concepts. Investigating single dopants requires sub-nanometre spatial resolution, making scanning tunnelling microscopy an ideal tool. However, dopant dynamics involve processes occurring at nanosecond timescales, posing a significant challenge to experiment. Here we use time-resolved scanning tunnelling microscopy and spectroscopy to probe and study transport through a dangling bond on silicon before the system relaxes or adjusts to accommodate an applied electric field. Atomically resolved, electronic pump-probe scanning tunnelling microscopy permits unprecedented, quantitative measurement of time-resolved single dopant ionization dynamics. Tunnelling through the surface dangling bond makes measurement of a signal that would otherwise be too weak to detect feasible. Distinct ionization and neutralization rates of a single dopant are measured and the physical process controlling those are identified. PMID:27782125

  3. Visualizing Cyclic Peptide Hydration at the Single-Molecule Level

    NASA Astrophysics Data System (ADS)

    Chen, Yumin; Deng, Ke; Qiu, Xiaohui; Wang, Chen

    2013-08-01

    The role of water molecules in the selective transport of potassium ions across cell membranes is important. Experimental investigations of valinomycin-water interactions remain huge challenge due to the poor solubility of valinomycin in water. Herein, we removed this experimental obstacle by introducing gaseous water and valinomycin onto a Cu(111) surface to investigate the hydration of valinomycin. By combining scanning tunneling microscopy (STM) with density functional theory (DFT) calculations, we revealed that water could affect the adsorption structure of valinomycin. Hydrogen bond interactions occurred primarily at the carbonyl oxygen of valinomycin and resulted in the formation of valinomycin hydrates. The single-molecule perspective revealed in our investigation could provide new insight into the role of water on the conformation transition of valinomycin, which might provide a new molecular basis for the ion transport mechanism at the water/membrane interface.

  4. A Study of Charged Current Single Charged Pion Productions on Carbon in a Few-GeV Neutrino Beam

    SciTech Connect

    Hiraide, Katsuki

    2009-01-01

    Understanding single charged pion production via neutrino-nucleus charged current interaction in the neutrino energy region of a few GeV is essential for future neutrino oscillation experiments since this process is a dominant background for vμ → vx oscillation measurements. There are two contributions to this process: single pion production via baryonic resonance (vμN → μ-+) and coherent pion production interacting with the entire nucleus (vμA → μ-+), where N is nucleon in the nucleus and A is the nucleus. The purpose of the study presented in this thesis is a precise measurement of charged current single charged pion productions, resonant and coherent pion productions, with a good final state separation in the neutrino energy region of a few GeV. In this thesis, we focus on the study of charged current coherent pion production from muon neutrinos scattering on carbon, vμ 12C → μ-12+, in the SciBooNE experiment. This is motivated by the fact that without measuring this component first, the precise determination of resonant pion production cross section can not be achieved since the contribution of coherent pion production in the region of small muon scattering angle is not small. Furthermore, the coherent process is particularly interesting because it is deeply rooted in fundamental physics via Adler's partially conserved axial-vector current theorem. We took data from June 2007 until August 2008, in both the neutrino and antineutrino beam. In total, 2.52 x 1020 protons on target were collected. We have performed a search for charged current coherent pion production by using SciBooNE's full neutrino data set, corresponding to 0.99 x 1020 protons on target. No evidence for coherent pion production is observed. We set 90% confidence level upper limits on the cross section ratio of charged

  5. Quantitative analysis of the T cell repertoire selected by a single peptide-major histocompatibility complex.

    PubMed

    Gapin, L; Fukui, Y; Kanellopoulos, J; Sano, T; Casrouge, A; Malier, V; Beaudoing, E; Gautheret, D; Claverie, J M; Sasazuki, T; Kourilsky, P

    1998-06-01

    The positive selection of CD4+ T cells requires the expression of major histocompatibility complex (MHC) class II molecules in the thymus, but the role of self-peptides complexed to class II molecules is still a matter of debate. Recently, it was observed that transgenic mice expressing a single peptide-MHC class II complex positively select significant numbers of diverse CD4+ T cells in the thymus. However, the number of selected T cell specificities has not been evaluated so far. Here, we have sequenced 700 junctional complementarity determining regions 3 (CDR3) from T cell receptors (TCRs) carrying Vbeta11-Jbeta1.1 or Vbeta12-Jbeta1.1 rearrangements. We found that a single peptide-MHC class II complex positively selects at least 10(5) different Vbeta rearrangements. Our data yield a first evaluation of the size of the T cell repertoire. In addition, they provide evidence that the single Ealpha52-68-I-Ab complex skews the amino acid frequency in the TCR CDR3 loop of positively selected T cells. A detailed analysis of CDR3 sequences indicates that a fraction of the beta chain repertoire bears the imprint of the selecting self-peptide.

  6. The 4-pyridylmethyl ester as a protecting group for glutamic and aspartic acids: 'flipping' peptide charge states for characterization by positive ion mode ESI-MS.

    PubMed

    Garapati, Sriramya; Burns, Colin S

    2014-03-01

    Use of the 4-pyridylmethyl ester group for side-chain protection of glutamic acid residues in solid-phase peptide synthesis enables switching of the charge state of a peptide from negative to positive, thus making detection by positive ion mode ESI-MS possible. The pyridylmethyl ester moiety is readily removed from peptides in high yield by hydrogenation. Combining the 4-pyridylmethyl ester protecting group with benzyl ester protection reduces the number of the former needed to produce a net positive charge and allows for purification by RP HPLC. This protecting group is useful in the synthesis of highly acidic peptide sequences, which are often beset by problems with purification by standard RP HPLC and characterization by ESI-MS. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

  7. Piezoelectric peptide-based nanogenerator enhanced by single-electrode triboelectric nanogenerator

    NASA Astrophysics Data System (ADS)

    Nguyen, Vu; Kelly, Steve; Yang, Rusen

    2017-07-01

    Peptide has recently been demonstrated as a sustainable and smart material for piezoelectric energy conversion. Although the power output was improved compared to other biomaterials, the use of a piezoelectric device alone can only capture the energy from the minute deformation in materials. In comparison, the triboelectric effect can convert mechanical energy from large motion. Consequently, utilizing both piezoelectric and triboelectric effects is of significant research interest due to their complementary energy conversion mechanisms. Here we demonstrated a hybrid nanogenerator that combined a peptide-based piezoelectric nanogenerator with a single-electrode triboelectric nanogenerator. Our device structure enabled the voltage and current outputs of each individual type of nanogenerator to be superposed in the hybrid nanogenerator, producing overall constructive outputs. The design of our device also enabled a simplified configuration of hybrid nanogenerator. This study is important not only for the enhancement of peptide-based piezoelectric device but also for the future design of hybrid piezoelectric and triboelectric nanogenerators.

  8. High-Sensitivity Charge Detection with a Single-Lead Quantum Dot for Scalable Quantum Computation

    NASA Astrophysics Data System (ADS)

    House, M. G.; Bartlett, I.; Pakkiam, P.; Koch, M.; Peretz, E.; van der Heijden, J.; Kobayashi, T.; Rogge, S.; Simmons, M. Y.

    2016-10-01

    We report the development of a high-sensitivity semiconductor charge sensor based on a quantum dot coupled to a single lead designed to minimize the geometric requirements of a charge sensor for scalable quantum-computing architectures. The quantum dot is fabricated in Si:P using atomic precision lithography, and its charge transitions are measured with rf reflectometry. A second quantum dot with two leads placed 42 nm away serves as both a charge for the sensor to measure and as a conventional rf single-electron transistor (rf SET) with which to make a comparison of the charge-detection sensitivity. We demonstrate sensitivity equivalent to an integration time of 550 ns to detect a single charge with a signal-to-noise ratio of 1 compared with an integration time of 55 ns for the rf SET. This level of sensitivity is suitable for fast (<15 μ s ) single-spin readout in quantum-information applications, with a significantly reduced geometric footprint compared to the rf SET.

  9. Single-file diffusion of macroscopic charged particles.

    PubMed

    Coste, C; Delfau, J-B; Even, C; Saint Jean, M

    2010-05-01

    In this paper, we study a macroscopic system of electrically interacting metallic beads organized as a sequence along an annulus. A random mechanical shaking mimics the thermal excitation. We exhibit non-Fickian diffusion (single-file diffusion) at large time. We measure the mobility of the particles and compare it to theoretical expectations. We show that our system cannot be accurately described by theories assuming only hard-sphere interactions. Its behavior is qualitatively described by a theory extended to more realistic potentials [M. Kollmann, Phys. Rev. Lett. 90, 180602 (2003)]. A correct quantitative agreement is shown and we interpret the discrepancies by the violation of the assumption of overdamped dynamics, which is a key point in the theory. We recast previous results on colloids with known interaction potentials and compare them quantitatively to the theory. Focusing on the transition between ordinary and single-file diffusions, we exhibit a dimensionless crossover time that is of order 1 both for colloids and our system, although the time and length scales differ by several orders of magnitude.

  10. Bridging adhesion of mussel-inspired peptides: role of charge, chain length, and surface type.

    PubMed

    Wei, Wei; Yu, Jing; Gebbie, Matthew A; Tan, Yerpeng; Martinez Rodriguez, Nadine R; Israelachvili, Jacob N; Waite, J Herbert

    2015-01-27

    The 3,4-dihydroxyphenylalanine (Dopa)-containing proteins of marine mussels provide attractive design paradigms for engineering synthetic polymers that can serve as high performance wet adhesives and coatings. Although the role of Dopa in promoting adhesion between mussels and various substrates has been carefully studied, the context by which Dopa mediates a bridging or nonbridging macromolecular adhesion to surfaces is not understood. The distinction is an important one both for a mechanistic appreciation of bioadhesion and for an intelligent translation of bioadhesive concepts to engineered systems. On the basis of mussel foot protein-5 (Mfp-5; length 75 res), we designed three short, simplified peptides (15-17 res) and one relatively long peptide (30 res) into which Dopa was enzymatically incorporated. Peptide adhesion was tested using a surface forces apparatus. Our results show that the short peptides are capable of weak bridging adhesion between two mica surfaces, but this adhesion contrasts with that of full length Mfp-5, in that (1) while still dependent on Dopa, electrostatic contributions are much more prominent, and (2) whereas Dopa surface density remains similar in both, peptide adhesion is an order of magnitude weaker (adhesion energy E(ad) ∼ -0.5 mJ/m(2)) than full length Mfp-5 adhesion. Between two mica surfaces, the magnitude of bridging adhesion was approximately doubled (E(ad) ∼ -1 mJ/m(2)) upon doubling the peptide length. Notably, the short peptides mediate much stronger adhesion (E(ad) ∼ -3.0 mJ/m(2)) between mica and gold surfaces, indicating that a long chain length is less important when different interactions are involved on each of the two surfaces.

  11. Bridging Adhesion of Mussel-Inspired Peptides: Role of Charge, Chain Length, and Surface Type

    PubMed Central

    2015-01-01

    The 3,4-dihydroxyphenylalanine (Dopa)-containing proteins of marine mussels provide attractive design paradigms for engineering synthetic polymers that can serve as high performance wet adhesives and coatings. Although the role of Dopa in promoting adhesion between mussels and various substrates has been carefully studied, the context by which Dopa mediates a bridging or nonbridging macromolecular adhesion to surfaces is not understood. The distinction is an important one both for a mechanistic appreciation of bioadhesion and for an intelligent translation of bioadhesive concepts to engineered systems. On the basis of mussel foot protein-5 (Mfp-5; length 75 res), we designed three short, simplified peptides (15–17 res) and one relatively long peptide (30 res) into which Dopa was enzymatically incorporated. Peptide adhesion was tested using a surface forces apparatus. Our results show that the short peptides are capable of weak bridging adhesion between two mica surfaces, but this adhesion contrasts with that of full length Mfp-5, in that (1) while still dependent on Dopa, electrostatic contributions are much more prominent, and (2) whereas Dopa surface density remains similar in both, peptide adhesion is an order of magnitude weaker (adhesion energy Ead ∼ −0.5 mJ/m2) than full length Mfp-5 adhesion. Between two mica surfaces, the magnitude of bridging adhesion was approximately doubled (Ead ∼ −1 mJ/m2) upon doubling the peptide length. Notably, the short peptides mediate much stronger adhesion (Ead ∼ −3.0 mJ/m2) between mica and gold surfaces, indicating that a long chain length is less important when different interactions are involved on each of the two surfaces. PMID:25540823

  12. Comment on ‘The effect of single-particle charge limits on charge distributions in dusty plasmas’

    NASA Astrophysics Data System (ADS)

    Heijmans, L. C. J.; van de Wetering, F. M. J. H.; Nijdam, S.

    2016-09-01

    It was recently suggested that the electron affinity may pose an additional upper limit on the charge of a single particle in a plasma, in addition to the electron field emission limit. Here we will, however, show that these two limits both rely on the same physical process and that the limit is only relevant for small particles, because it relies on electron tunneling. Plasma-produced particles of only several nanometres (≲ 10~\\text{nm} ) in size are actively studied, for example in the application of quantum dots and the implications of the proposed charge limit are certainly significant there. However, care must be taken to extend the results to larger particles, which are also actively studied in the field of dusty plasma physics, where typically the limit can be neglected, as we will also show.

  13. Single molecule detection using charge-coupled device array technology. Technical progress report

    SciTech Connect

    Denton, M.B.

    1992-07-29

    A technique for the detection of single fluorescent chromophores in a flowing stream is under development. This capability is an integral facet of a rapid DNA sequencing scheme currently being developed by Los Alamos National Laboratory. In previous investigations, the detection sensitivity was limited by the background Raman emission from the water solvent. A detection scheme based on a novel mode of operating a Charge-Coupled Device (CCD) is being developed which should greatly enhance the discrimination between fluorescence from a single molecule and the background Raman scattering from the solvent. Register shifts between rows in the CCD are synchronized with the sample flow velocity so that fluorescence from a single molecule is collected in a single moving charge packet occupying an area approaching that of a single pixel while the background is spread evenly among a large number of pixels. Feasibility calculations indicate that single molecule detection should be achieved with an excellent signal-to-noise ratio.

  14. Sequential enrichment of singly- and multiply-phosphorylated peptides with zwitterionic hydrophilic interaction chromatography material.

    PubMed

    Sheng, Qianying; Yang, Kaiya; Xue, Xingya; Li, Xiuling; Guo, Zhimou; Shen, Aijin; Ke, Yanxiong; Lan, Minbo; Liang, Xinmiao

    2015-09-25

    An interesting and novel method for the selective and sequential enrichment of singly- and multiply-phosphorylated peptides with a zwitterionic material "Click TE-Cys" is presented. Retention mechanisms between phosphopeptides and Click TE-Cys are systematically investigated by checking the influence of acetonitrile content, pH value, and buffer concentration on the retention of phosphopeptides. Both hydrophilic interaction and electrostatic interaction are involved in retention between phosphopeptides and Click TE-Cys. Based on these results, an optimized method is established for selective enrichment of phosphopeptides using Click TE-Cys. This method not only exhibits high selectivity for phosphopeptides, but also fractionates singly- and multiply-phosphorylated peptides into two fractions. This method was evaluated using relatively complex samples, including peptide mixtures of α-casein and bovine serum albumin (BSA) at a molar ratio of 1:10 and skim milk. This efficient and optimized protocol has great potential for enriching multiply-phosphorylated peptides and could be a valuable tool for specific enrichment of phosphopeptides in phosphoproteome analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Conformational Transitions and Stop-and-Go Nanopore Transport of Single Stranded DNA on Charged Graphene

    PubMed Central

    Shankla, Manish; Aksimentiev, Aleksei

    2014-01-01

    Control over interactions with biomolecules holds the key to applications of graphene in biotechnology. One such application is nanopore sequencing, where a DNA molecule is electrophoretically driven through a graphene nanopore. Here, we investigate how interactions of single-stranded DNA and a graphene membrane can be controlled by electrically biasing the membrane. The results of our molecular dynamics simulations suggest that electric charge on graphene can force a DNA homopolymer to adopt a range of strikingly different conformations. The conformational response is sensitive to even very subtle nucleotide modifications, such as DNA methylation. The speed of DNA motion through a graphene nanopore is strongly affected by the graphene charge: a positive charge accelerates the motion whereas a negative charge arrests it. As a possible application of the effect, we demonstrate stop-and-go transport of DNA controlled by the charge of graphene. Such on-demand transport of DNA is essential for realizing nanopore sequencing. PMID:25296960

  16. A 2.45 GHz Singly-charged ECR Ion Source for RIB Production

    SciTech Connect

    Zhao, H.Y.; Zhang, X.Z.; Zhao, H.W.; Zhang, Z.M.; Sun, L.T.; Wang, H.; Ma, B.H.

    2005-03-15

    The stripping mode for production of multi-charged radioactive ion beams is discussed, and its advantages are also discussed. A 2.45 GHz ECRIS serving as the primary ion source was designed for production of singly charged radioactive ion beams. This source is compact, reliable, and economical. The magnetic field of the source provided by two permanent magnet rings has been calculated with POISSON code. Additionally, the structure of the source is presented.

  17. Consecutive Charging of a Molecule-on-Insulator Ensemble Using Single Electron Tunnelling Methods.

    PubMed

    Rahe, Philipp; Steele, Ryan P; Williams, Clayton C

    2016-02-10

    We present the local charge state modification at room temperature of small insulator-supported molecular ensembles formed by 1,1'-ferrocenedicarboxylic acid on calcite. Single electron tunnelling between the conducting tip of a noncontact atomic force microscope (NC-AFM) and the molecular islands is observed. By joining NC-AFM with Kelvin probe force microscopy, successive charge build-up in the sample is observed from consecutive experiments. Charge transfer within the islands and structural relaxation of the adsorbate/surface system is suggested by the experimental data.

  18. Strong thermo-induced single and two-photon green luminescence in self-organized peptide microtubes.

    PubMed

    Semin, S; van Etteger, A; Cattaneo, L; Amdursky, N; Kulyuk, L; Lavrov, S; Sigov, A; Mishina, E; Rosenman, G; Rasing, Th

    2015-03-01

    Diphenylalanine peptide nano- and microtubes formed by self-assembly demonstrate strongly enhanced and tunable single-photon and two-photon luminescence in the visible range, which appears after heat- or laser treatment of these self-organized peptide microtubes. This process significantly extends the functionality of these microstructures and can trigger a new interest in the optical properties of structures based on short peptides.

  19. Intermolecular charge flux as the origin of infrared intensity enhancement upon halogen-bond formation of the peptide group

    NASA Astrophysics Data System (ADS)

    Torii, Hajime

    2010-07-01

    The changes in the vibrational properties of the peptide group upon formation of O⋯X and N⋯X halogen bonds are studied theoretically. Calculations are carried out for complexes of N-methylacetamide (NMA), a well known model molecule of the peptide group, with halogen-containing molecules. For comparison, calculations are also carried out for some NMA-water hydrogen-bonding complexes. It is shown that the infrared (IR) intensity of the amide I mode of the peptide group is enhanced significantly (up to about 520 km mol-1 or 2.6 times) upon CO⋯X halogen-bond formation, in spite of rather modest magnitudes of the intermolecular electric field and of the changes in the CO bond length and in the amide I vibrational frequency as compared with the cases of the CO⋯H(D) hydrogen bonding. From the analysis of the changes in the dipole derivative and in the electronic structure, it is shown that this IR intensity enhancement arises from the intermolecular charge flux. For the N⋯X halogen bonding complexes, some characteristic changes in the vibrational properties are seen, among which the IR intensity enhancement of the ND out-of-plane wagging mode is most notable. The reason why such large IR intensity enhancements are seen for these particular vibrational modes is examined.

  20. Intermolecular charge flux as the origin of infrared intensity enhancement upon halogen-bond formation of the peptide group.

    PubMed

    Torii, Hajime

    2010-07-21

    The changes in the vibrational properties of the peptide group upon formation of O...X and N...X halogen bonds are studied theoretically. Calculations are carried out for complexes of N-methylacetamide (NMA), a well known model molecule of the peptide group, with halogen-containing molecules. For comparison, calculations are also carried out for some NMA-water hydrogen-bonding complexes. It is shown that the infrared (IR) intensity of the amide I mode of the peptide group is enhanced significantly (up to about 520 km mol(-1) or 2.6 times) upon C=O...X halogen-bond formation, in spite of rather modest magnitudes of the intermolecular electric field and of the changes in the C=O bond length and in the amide I vibrational frequency as compared with the cases of the C=O...H(D) hydrogen bonding. From the analysis of the changes in the dipole derivative and in the electronic structure, it is shown that this IR intensity enhancement arises from the intermolecular charge flux. For the N...X halogen bonding complexes, some characteristic changes in the vibrational properties are seen, among which the IR intensity enhancement of the ND out-of-plane wagging mode is most notable. The reason why such large IR intensity enhancements are seen for these particular vibrational modes is examined.

  1. Targeting EphA2-Sam and Its Interactome: Design and Evaluation of Helical Peptides Enriched in Charged Residues.

    PubMed

    Mercurio, Flavia A; Marasco, Daniela; Di Natale, Concetta; Pirone, Luciano; Costantini, Susan; Pedone, Emilia M; Leone, Marilisa

    2016-11-17

    The EphA2 receptor controls diverse physiological and pathological conditions and its levels are often upregulated in cancer. Targeting receptor overexpression, through modulation of endocytosis and consequent degradation, appears to be an appealing strategy for attacking tumor malignancy. In this scenario, the Sam domain of EphA2 plays a pivotal role because it is the site where protein regulators of endocytosis and stability are recruited by means of heterotypic Sam-Sam interactions. Because EphA2-Sam heterotypic complexes are largely based on electrostatic contacts, we have investigated the possibility of attacking these interactions with helical peptides enriched in charged residues. Several peptide sequences with high predicted helical propensities were designed, and detailed conformational analyses were conducted by diverse techniques including NMR, CD, and molecular dynamics (MD) simulations. Interaction studies were also performed by NMR, surface plasmon resonance (SPR), and microscale thermophoresis (MST) and led to the identification of two peptides capable of binding to the first Sam domain of Odin. These molecules represent early candidates for the generation of efficient Sam domain binders and antagonists of Sam-Sam interactions involving EphA2.

  2. High-sensitivity single NV magnetometry by spin-to-charge state mapping

    NASA Astrophysics Data System (ADS)

    Jaskula, Jean-Christophe; Shields, Brendan; Bauch, Erik; Lukin, Mikhail; Walsworth, Ronald; Trifonov, Alexei

    2015-05-01

    Nitrogen-Vacancy (NV) centers in diamond are atom-like quantum system in a solid state matrix whom its structure allows optical readout of the electronic spin. However, the optimal duration of optical readout is limited by a singlet state lifetime making single shot spin readout out of reach. On the other side, the NV center charge state readout can be extremely efficient (up to 99% fidelity) by using excitation at 594 nm. We will present a new method of spin readout utilizing a spin-depending photoionization process to map the electronic spin state of the NV onto the its charge state. Moreover, pre-selection on the charged state allows to minimize data acquisition time. This scheme improves single NV AC magnetometry by a factor of 5 and will benefit other single NV center experiments as well.

  3. Pion single charge exchange in three body nuclei at intermediate energies

    SciTech Connect

    Dowell, Marla L.

    1994-01-01

    The purpose of this thesis is to present new experimental information about modifications to the pion-nucleon single charge exchange interaction, π+n → π0 p or π- p → π0n, due to the presence of other nucleons. The results of two experimental studies of pion single charge exchange in the three nucleon system near the Δ-resonance are presented. Both of these experiments were performed at the Clinton P. Anderson Meson Physics Facility (LAMPF), a division of the Los Alamos National Laboratory. Each explored different aspects of pion single charge exchange in three body nuclei--3He and 3H. Since the nuclear wavefunctions of the three nucleon systems are believed to be well understood, it should be possible to perform theoretical calculations of pion interactions with this system and compare their predictions with the experimental results.

  4. Organization of model helical peptides in lipid bilayers: insight into the behavior of single-span protein transmembrane domains.

    PubMed Central

    Sharpe, Simon; Barber, Kathryn R; Grant, Chris W M; Goodyear, David; Morrow, Michael R

    2002-01-01

    Selectively deuterated transmembrane peptides comprising alternating leucine-alanine subunits were examined in fluid bilayer membranes by solid-state nuclear magnetic resonance (NMR) spectroscopy in an effort to gain insight into the behavior of membrane proteins. Two groups of peptides were studied: 21-mers having a 17-amino-acid hydrophobic domain calculated to be close in length to the hydrophobic thickness of 1-palmitoyl-2-oleoyl phosphatidylcholine and 26-mers having a 22-amino-acid hydrophobic domain calculated to exceed the membrane hydrophobic thickness. (2)H NMR spectral features similar to ones observed for transmembrane peptides from single-span receptors of higher animal cells were identified which apparently correspond to effectively monomeric peptide. Spectral observations suggested significant distortion of the transmembrane alpha-helix, and/or potential for restriction of rotation about the tilted helix long axis for even simple peptides. Quadrupole splittings arising from the 26-mer were consistent with greater peptide "tilt" than were those of the analogous 21-mer. Quadrupole splittings associated with monomeric peptide were relatively insensitive to concentration and temperature over the range studied, indicating stable average conformations, and a well-ordered rotation axis. At high peptide concentration (6 mol% relative to phospholipid) it appeared that the peptide predicted to be longer than the membrane thickness had a particular tendency toward reversible peptide-peptide interactions occurring on a timescale comparable with or faster than approximately 10(-5) s. This interaction may be direct or lipid-mediated and was manifest as line broadening. Peptide rotational diffusion rates within the membrane, calculated from quadrupolar relaxation times, T(2e), were consistent with such interactions. In the case of the peptide predicted to be equal to the membrane thickness, at low peptide concentration spectral lineshape indicated the additional

  5. Introducing charge transfer functionality into prebiotically relevant β-sheet peptide fibrils.

    PubMed

    Ivnitski, Denis; Amit, Moran; Rubinov, Boris; Cohen-Luria, Rivka; Ashkenasy, Nurit; Ashkenasy, Gonen

    2014-06-28

    Incorporation of naphthalene diimide moieties as side chains of short amphiphilic peptide results in the formation of fibrils that exhibit substantial intermolecular π-stacking interactions. These interactions can be manipulated without affecting the structure. The new system is suggested as a first step towards functional self-synthesizing materials.

  6. Current quantization due to single-electron transfer in Si-wire charge-coupled devices

    NASA Astrophysics Data System (ADS)

    Fujiwara, Akira; Zimmerman, Neil M.; Ono, Yukinori; Takahashi, Yasuo

    2004-02-01

    We observe a quantized current due to single-electron transfer in a small charge-coupled device, which consists of a narrow Si-wire channel with fine gates; the gate is used to form a tunable barrier potential. By modulating two barrier potentials under the fine gates with phase-shifted pulse voltages, quantized numbers of electrons are injected into and extracted from the charge island sandwiched by the two barriers. Current plateaus due to single-electron transfer are clearly observed at 20 K with frequencies up to 100 MHz and a current level of 16 pA.

  7. Single-molecule peptide-lipid affinity assay reveals interplay between solution structure and partitioning.

    PubMed

    Matin, Tina R; Sigdel, Krishna P; Utjesanovic, Milica; Marsh, Brendan P; Gallazzi, Fabio; Smith, Virginia F; Kosztin, Ioan; King, Gavin M

    2017-03-27

    Interactions between short protein segments and phospholipid bilayers dictate fundamental aspects of cellular activity and have important applications in biotechnology. Yet, a lack of suitable methodology for directly probing these interactions has hindered mechanistic understanding. We developed a precision atomic force microscope (AFM)-based single-molecule force spectroscopy assay and probed partitioning into lipid bilayers by measuring the mechanical force experienced by a peptide. Protein segments were constructed from the peripheral membrane protein SecA, a key ATPase in bacterial secretion. We focused on the first 10 amino-terminal residues of SecA (SecA2-11) which are known to be lipophilic. In addition to the core SecA2-11 sequence, constructs with nearly identical chemical composition but with differing geometry were used: two copies of SecA2-11 linked in series, and two copies in parallel. Lipid bilayer partitioning interactions of peptides with differing structures were distinguished. To model the energetic landscape, a theory of diffusive barrier crossing was extended to incorporate a superposition of potential barriers with variable weights. Analysis revealed two dissociation pathways for the core SecA2-11 sequence with well-separated intrinsic dissociation rates. Molecular dynamics simulations showed that the three peptides had significant conformational differences in solution that correlated well with measured variations in the propensity to partition into the bilayer. The methodology is generalizable and can be applied to other peptide and lipid species.

  8. Identification of peptide mimotopes of gp96 using single-chain antibody library.

    PubMed

    Shanmugam, Arulkumaran; Suriano, Robert; Goswami, Neha; Chaudhuri, Devyani; Ashok, Badithe T; Rajoria, Shilpi; George, Andrea L; Mittelman, Abraham; Tiwari, Raj K

    2011-03-01

    Heat shock proteins such as gp96 are immunogenic and are widely used as vaccines in immunotherapy of cancers. The present study focuses on the use of peptide mimotopes as immunotherapeutic vaccines for prostate cancer. To this end, we developed a 15-mer gp96 peptide mimotope specifically reactive to MAT-LyLu gp96-peptide complex using combinatorial single-chain antibody and peptide phage display library. The immunogenicity of the synthesized gp96 mimotope was analyzed initially in normal BALB/c mice in combination with various adjuvants such as complete Freund's adjuvant (CFA), aluminum salts (ALUM), granulocyte-macrophage colony-stimulating factor (GM-CSF), and liposome, of which CFA served as a positive control. The antibody response was determined and found that the gp96 mimotope with ALUM showed a significant increase in antibody titer, followed by GM-CSF and liposomes. Further, the T cell (CD4(+) and CD8(+)) populations from splenocytes, as well as IgG isotypes, interleukin-4, and interleukin-5 of gp96 mimotope with ALUM-immunized animals, were analyzed. The results suggest that the gp96 mimotope may elicit a potent and effective antitumor antibody response. Further, the study identifies ALUM and GM-CSF as adjuvant options to drive an appropriate protective immune response as these adjuvants have prior use in humans.

  9. Charge-dependent transport switching of single molecular ions in a weak polyelectrolyte multilayer.

    PubMed

    Tauzin, Lawrence J; Shuang, Bo; Kisley, Lydia; Mansur, Andrea P; Chen, Jixin; de Leon, Al; Advincula, Rigoberto C; Landes, Christy F

    2014-07-22

    The tunable nature of weak polyelectrolyte multilayers makes them ideal candidates for drug loading and delivery, water filtration, and separations, yet the lateral transport of charged molecules in these systems remains largely unexplored at the single molecule level. We report the direct measurement of the charge-dependent, pH-tunable, multimodal interaction of single charged molecules with a weak polyelectrolyte multilayer thin film, a 10 bilayer film of poly(acrylic acid) and poly(allylamine hydrochloride) PAA/PAH. Using fluorescence microscopy and single-molecule tracking, two modes of interaction were detected: (1) adsorption, characterized by the molecule remaining immobilized in a subresolution region and (2) diffusion trajectories characteristic of hopping (D ∼ 10(-9) cm(2)/s). Radius of gyration evolution analysis and comparison with simulated trajectories confirmed the coexistence of the two transport modes in the same single molecule trajectories. A mechanistic explanation for the probe and condition mediated dynamics is proposed based on a combination of electrostatics and a reversible, pH-induced alteration of the nanoscopic structure of the film. Our results are in good agreement with ensemble studies conducted on similar films, confirm a previously-unobserved hopping mechanism for charged molecules in polyelectrolyte multilayers, and demonstrate that single molecule spectroscopy can offer mechanistic insight into the role of electrostatics and nanoscale tunability of transport in weak polyelectrolyte multilayers.

  10. Large tunable image-charge effects in single-molecule junctions.

    PubMed

    Perrin, Mickael L; Verzijl, Christopher J O; Martin, Christian A; Shaikh, Ahson J; Eelkema, Rienk; van Esch, Jan H; van Ruitenbeek, Jan M; Thijssen, Joseph M; van der Zant, Herre S J; Dulić, Diana

    2013-04-01

    Metal/organic interfaces critically determine the characteristics of molecular electronic devices, because they influence the arrangement of the orbital levels that participate in charge transport. Studies on self-assembled monolayers show molecule-dependent energy-level shifts as well as transport-gap renormalization, two effects that suggest that electric-field polarization in the metal substrate induced by the formation of image charges plays a key role in the alignment of the molecular energy levels with respect to the metal's Fermi energy. Here, we provide direct experimental evidence for an electrode-induced gap renormalization in single-molecule junctions. We study charge transport through single porphyrin-type molecules using electrically gateable break junctions. In this set-up, the position of the occupied and unoccupied molecular energy levels can be followed in situ under simultaneous mechanical control. When increasing the electrode separation by just a few ångströms, we observe a substantial increase in the transport gap and level shifts as high as several hundreds of meV. Analysis of this large and tunable gap renormalization based on atomic charges obtained from density functional theory confirms and clarifies the dominant role of image-charge effects in single-molecule junctions.

  11. Nanojunctions in conducting polypyrrole single nanowire made by focused electron beam: Charge transport characteristics

    SciTech Connect

    Koo, Min Ho; Hong, Young Ki; Park, Dong Hyuk; Jo, Seong Gi; Joo, Jinsoo

    2011-07-15

    A focused electron (E)-beam with various doses was irradiated on the intended positions of conducting polypyrrole (PPy) single nanowire (NW) to fabricate nanojunctions. The current-voltage characteristics and their temperature dependence of the PPy single NW with nanojunctions were measured and analyzed. By increasing the E-beam dose and the number of nanojunctions, the current level of the single NW was dramatically decreased, and the conductance gap became more severe as the temperature decreased. The charge transport behavior varied from three-dimensional variable range hopping to fluctuation induced tunneling models, depending on the dose of focused E-beam. From micro-Raman spectra, the focused E-beam irradiation induced the de-doped states and conformational modification of polymer chains in the nanojunctions. The results suggest that the nanojunctions made by focused E-beam acted as a quasi-potential barrier for charge conduction in the conducting PPy single NW.

  12. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes.

    PubMed

    Dell, Emma J; Capozzi, Brian; Xia, Jianlong; Venkataraman, Latha; Campos, Luis M

    2015-03-01

    To develop advanced materials for electronic devices, it is of utmost importance to design organic building blocks with tunable functionality and to study their properties at the molecular level. For organic electronic and photovoltaic applications, the ability to vary the nature of charge carriers and so create either electron donors or acceptors is critical. Here we demonstrate that charge carriers in single-molecule junctions can be tuned within a family of molecules that contain electron-deficient thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed to increase electron affinity and maintain delocalized frontier orbitals while significantly decreasing the transport gap. Through thermopower measurements we show that the dominant charge carriers change from holes to electrons as the number of TDO units is increased. This results in a unique system in which the charge carrier depends on the backbone length, and provides a new means to tune p- and n-type transport in organic materials.

  13. MONO1001: A source for singly charged ions applied to the production of multicharged fullerene beams

    NASA Astrophysics Data System (ADS)

    Maunoury, L.; Andersen, J. U.; Cederquist, H.; Huber, B. A.; Hvelplund, P.; Leroy, R.; Manil, B.; Pacquet, J. Y.; Pedersen, U. V.; Rangamma, J.; Tomita, S.

    2004-05-01

    The present article reports on a recent study of the production of multiply charged fullerene beams based on an electron cyclotron resonance (ECR) ion source (ECRIS). As collision studies in fundamental physics are demanding intense beams of multiply charged ions of small molecules, clusters, and particularly of fullerenes, we have further developed the ion source ECRIS MONO1000 [P. Jardin et al., Rev. Sci. Instrum. 73, 789 (2002)], originally devoted to produce singly charged ions, towards the production of multiply charged fullerene beams. In this article, the test measurements performed at the Electrostatic Ion Storage Ring Århus rf power (ELISA) facility will be described. Typical mass spectra (from pure C60 and C70 powder) will be shown and the influence of several source parameters (rf power, support gas, gas pressure,…) will be discussed specifying the conditions necessary for an optimum ion source operation.

  14. Sequential elution of multiply and singly phosphorylated peptides with polar-copolymerized mixed-mode RP18/SCX material.

    PubMed

    Li, Xiuling; Guo, Zhimou; Sheng, Qianying; Xue, Xingya; Liang, Xinmiao

    2012-06-21

    Novel polar-copolymerized mixed-mode RP18/SCX material was developed for feasible phosphopeptide enrichment, in which multiply and singly phosphorylated peptides could be sequentially eluted and separated with high selectivity.

  15. Ionic Strength, Surface Charge, and Packing Density Effects on the Properties of Peptide Self-Assembled Monolayers.

    PubMed

    Leo, Norman; Liu, Juan; Archbold, Ian; Tang, Yongan; Zeng, Xiangqun

    2017-02-28

    The various environmental parameters of packing density, ionic strength, and solution charge were examined for their effects on the properties of the immobilized peptide mimotope CH19 (CGSGSGSQLGPYELWELSH) that binds with the therapeutic antibody Trastuzumab (Herceptin) on a gold substrate. The immobilization of CH19 onto gold was examined with a quartz crystal microbalance (QCM). The QCM data showed the presence of intermolecular interactions resulting in the increase of viscoelastic properties of the peptide self-assembled monolayer (SAM). The CH19 SAM was diluted with CS7 (CGSGSGS) to decrease the packing density as CH19/CS7. The packing density and ionic strength parameters were evaluated by atomic force microscopy (AFM), ellipsometry, and QCM. AFM and ellipsometry showed a distinct conformational difference between CH19 and CH19/CS7, indicating a relationship between packing density and conformational state of the immobilized peptide. The CH19 SAM thickness was 40 Å with a rough topology, while the CH19/CS7 SAM thickness was 20 Å with a smooth topology. The affinity studies showed that the affinity of CH19 and CH19/CS7 to Trastuzumab were both on the order of 10(7) M(-1) in undiluted PBS buffer, while the dilution of the buffer by 1000× increased both SAMs affinities to Trastuzumab to the order of 10(15) M(-2) and changed the binding behavior from noncooperative to cooperative binding. This indicated that ionic strength had a more pronounced effect on binding properties of the CH19 SAM than packing density. Electrochemical impedance spectroscopy (EIS) was conducted on the CH19/CS7 SAM, which showed an increase in impedance after each EIS measurement cycle. Cyclic voltammetry on the CH19/CS7 SAM decreased impedance to near initial values. The impact of the packing density, buffer ionic strength, and local charge perturbation of the peptide SAM properties was interpreted based on the titratable sites in CH19 that could participate in the proton transfer and

  16. Measuring the size and charge of single nanoscale objects in solution using an electrostatic fluidic trap

    NASA Astrophysics Data System (ADS)

    Mojarad, Nassiredin; Krishnan, Madhavi

    2012-07-01

    Measuring the size and charge of objects suspended in solution, such as dispersions of colloids or macromolecules, is a significant challenge. Measurements based on light scattering are inherently biased to larger entities, such as aggregates in the sample, because the intensity of light scattered by a small object scales as the sixth power of its size. Techniques that rely on the collective migration of species in response to external fields (electric or hydrodynamic, for example) are beset with difficulties including low accuracy and dispersion-limited resolution. Here, we show that the size and charge of single nanoscale objects can be directly measured with high throughput by analysing their thermal motion in an array of electrostatic traps. The approach, which is analogous to Millikan's oil drop experiment, could in future be used to detect molecular binding events with high sensitivity or carry out dynamic single-charge resolved measurements at the solid/liquid interface.

  17. Measuring the size and charge of single nanoscale objects in solution using an electrostatic fluidic trap.

    PubMed

    Mojarad, Nassiredin; Krishnan, Madhavi

    2012-06-24

    Measuring the size and charge of objects suspended in solution, such as dispersions of colloids or macromolecules, is a significant challenge. Measurements based on light scattering are inherently biased to larger entities, such as aggregates in the sample, because the intensity of light scattered by a small object scales as the sixth power of its size. Techniques that rely on the collective migration of species in response to external fields (electric or hydrodynamic, for example) are beset with difficulties including low accuracy and dispersion-limited resolution. Here, we show that the size and charge of single nanoscale objects can be directly measured with high throughput by analysing their thermal motion in an array of electrostatic traps. The approach, which is analogous to Millikan's oil drop experiment, could in future be used to detect molecular binding events with high sensitivity or carry out dynamic single-charge resolved measurements at the solid/liquid interface.

  18. Charge transport and photoresponses in a single-stranded DNA/single-walled carbon nanotube composite film

    NASA Astrophysics Data System (ADS)

    Hong, Wonseon; Lee, Eunmo; Kue Park, Jun; Eui Lee, Cheol

    2013-06-01

    Electrical conductivity and photoresponse measurements have been carried out on a single-stranded DNA (ssDNA)/single-walled carbon nanotube (SWNT) composite film in comparison to those of a SWNT film. While the temperature-dependent electrical conductivity of the pristine SWNT film was described well by the combined mechanism of a three-dimensional variable-range hopping and hopping conduction, that of the ssDNA/SWNT composite film followed a fluctuation-induced tunneling model. Besides, competition of photoexcited charge carrier generation and oxygen adsorption/photodesorption in the photoresponses of the films was observed and discussed in view of the role of the DNA wrapping. Thus, the biopolymer coating of the SWNTs is shown to play a significant role in modifying the charge dynamics of the composite system.

  19. Quantitative Analysis of Single Amino Acid Variant Peptides Associated with Pancreatic Cancer in Serum by an Isobaric Labeling Quantitative Method

    PubMed Central

    2015-01-01

    Single amino acid variations are highly associated with many human diseases. The direct detection of peptides containing single amino acid variants (SAAVs) derived from nonsynonymous single nucleotide polymorphisms (SNPs) in serum can provide unique opportunities for SAAV associated biomarker discovery. In the present study, an isobaric labeling quantitative strategy was applied to identify and quantify variant peptides in serum samples of pancreatic cancer patients and other benign controls. The largest number of SAAV peptides to date in serum including 96 unique variant peptides were quantified in this quantitative analysis, of which five variant peptides showed a statistically significant difference between pancreatic cancer and other controls (p-value < 0.05). Significant differences in the variant peptide SDNCEDTPEAGYFAVAVVK from serotransferrin were detected between pancreatic cancer and controls, which was further validated by selected reaction monitoring (SRM) analysis. The novel biomarker panel obtained by combining α-1-antichymotrypsin (AACT), Thrombospondin-1 (THBS1) and this variant peptide showed an excellent diagnostic performance in discriminating pancreatic cancer from healthy controls (AUC = 0.98) and chronic pancreatitis (AUC = 0.90). These results suggest that large-scale analysis of SAAV peptides in serum may provide a new direction for biomarker discovery research. PMID:25393578

  20. Development of a Charged Particle Microbeam for Targeted and Single Particle Subcellular Irradiation

    SciTech Connect

    Yanch, Jacquelyn C.

    2004-03-12

    The development of a charged particle microbeam for single particle, subcellular irradiations at the Massachusetts Institute of Technology Laboratory for Accelerator Beam Applications (MIT LABA) was initiated under this NEER aeard. The Microbeam apparatus makes use of a pre-existing electrostatic accelerator with a horizontal beam tube.

  1. Ion/Ion Reactions of MALDI-Derived Peptide Ions: Increased Sequence Coverage via Covalent and Electrostatic Modification upon Charge Inversion

    PubMed Central

    Stutzman, John R.; McLuckey, Scott A.

    2012-01-01

    Atmospheric pressure matrix assisted laser desorption/ionization (AP-MALDI)-derived tryptic peptide ions have been subjected to ion/ion reactions with doubly deprotonated 4-formyl-1,3-benzenedisulfonic acid (FBDSA) in the gas phase. The ion/ion reaction produces a negatively charged electrostatic complex composed of the peptide cation and reagent dianion, whereupon dehydration of the complex via collision-induced dissociation (CID) produces a Schiff base product anion. Collisional activation of modified lysine-terminated tryptic peptide anions is consistent with a covalent modification of unprotonated primary amines (i.e. N-terminus and ε-NH2 of lysine). Modified arginine-terminated tryptic peptides have shown evidence of a covalent modification at the N-terminus and a non-covalent interaction with the arginine residue. The modified anions yield at least as much sequence information upon CID as the unmodified cations for the small tryptic peptides examined here and more sequence information for the large tryptic peptides. This study represents the first demonstration of gas phase ion/ion reactions involving MALDI-derived ions. In this case, covalent modification upon charge inversion is shown to enhance MALDI tandem mass spectrometry of tryptic peptides. PMID:23078018

  2. Ion/ion reactions of MALDI-derived peptide ions: increased sequence coverage via covalent and electrostatic modification upon charge inversion.

    PubMed

    Stutzman, John R; McLuckey, Scott A

    2012-12-18

    Atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI)-derived tryptic peptide ions have been subjected to ion/ion reactions with doubly deprotonated 4-formyl-1,3-benzenedisulfonic acid (FBDSA) in the gas-phase. The ion/ion reaction produces a negatively charged electrostatic complex composed of the peptide cation and reagent dianion, whereupon dehydration of the complex via collision-induced dissociation (CID) produces a Schiff base product anion. Collisional activation of modified lysine-terminated tryptic peptide anions is consistent with a covalent modification of unprotonated primary amines (i.e., N-terminus and ε-NH(2) of lysine). Modified arginine-terminated tryptic peptides have shown evidence of a covalent modification at the N-terminus and a noncovalent interaction with the arginine residue. The modified anions yield at least as much sequence information upon CID as the unmodified cations for the small tryptic peptides examined here and more sequence information for the large tryptic peptides. This study represents the first demonstration of gas-phase ion/ion reactions involving MALDI-derived ions. In this case, covalent and electrostatic modification charge inversion is shown to enhance MALDI tandem mass spectrometry of tryptic peptides.

  3. Development of Novel Drug and Gene Delivery Carriers Composed of Single-Walled Carbon Nanotubes and Designed Peptides With PEGylation.

    PubMed

    Ohta, Takahisa; Hashida, Yasuhiko; Yamashita, Fumiyoshi; Hashida, Mitsuru

    2016-09-01

    Single-walled carbon nanotubes (SWCNTs) attract great interest in biomedical applications including drug and gene delivery. In this study, we developed a novel delivery system using SWCNTs associated with designed polycationic and amphiphilic peptides. Wrapping of SWCNTs with H-(-Lys-Trp-Lys-Gly-)7-OH [(KWKG)7] resulted in stable dispersion in water, but the composite aggregated in the buffered solution. This dispersion instability was also evident in a cell culture medium with fetal bovine serum. To improve the aqueous dispersibility, the SWCNTs-(KWKG)7 composite was further modified with polyethylene glycol (PEG) at the lysine residues via amide bond formation and the highest modification extent of 13.3% of the amino groups which corresponded to 2 PEG chains in each peptide molecule was achieved with fluorescein isothiocyanate-labeled carboxyl-PEG12. The uptake of the SWCNTs composite by A549 human lung adenocarcinoma epithelial cells was evaluated by visual observation and fluorescence activated cell sorting analysis for SWCNTs wrapped with a mixture of (KWKG)7 with PEGylation and H-(-Cys-Trp-Lys-Gly-)-OH-(KWKG)6 [CWKG(KWKG)6] labeled with fluorescent boron-dipyrromethene tetramethylrhodamine and 7-fold higher uptake comparing with SWCNTs-peptide composite without PEGylation was obtained suggesting the importance of dispersibility in addition to a cationic charge. The superior potential of SWCNTs composites assisted by polycationic and amphiphilic peptides with PEGylation was thus demonstrated.

  4. Peptide derived from anti-idiotypic single-chain antibody is a potent antifungal agent compared to its parent fungicide HM-1 killer toxin peptide.

    PubMed

    Kabir, M Enamul; Karim, Nurul; Krishnaswamy, Senthilkumar; Selvakumar, Dakshnamurthy; Miyamoto, Masahiko; Furuichi, Yasuhiro; Komiyama, Tadazumi

    2011-12-01

    Based on anti-idiotypic network theory in light of the need for new antifungal drugs, we attempted to identify biologically active fragments from HM-1 yeast killer toxin and its anti-idiotypic antibody and to compare their potency as an antifungal agent. Thirteen overlapping peptides from HM-1 killer toxin and six peptides from its anti-idiotypic single-chain variable fragment (scFv) antibodies representing the complementarity determining regions were synthesized. The binding affinities of these peptides were investigated and measured by Dot blot and surface plasmon resonance analysis and finally their antifungal activities were investigated by inhibition of growth, colony forming unit assay. Peptide P6, containing the potential active site of HM-1 was highly capable of inhibiting the growth of Saccharomyces cerevisiae but was less effective on pathogenic fungi. However, peptide fragments derived from scFv antibody exerted remarkable inhibitory effect on the growth of pathogenic strains of Candida and Cryptococcus species in vitro. One scFv-derived decapeptide (SP6) was selected as the strongest killer peptide for its high binding affinity and antifungal abilities on both Candida and Cryptococcus species with IC(50) values from 2.33 × 10(-7) M to 36.0 × 10(-7) M. SP6 peptide activity was neutralized by laminarin, a β-1,3-glucan molecule, indicating this peptide derived from scFv anti-idiotypic antibody retains antifungal activity through interaction with cell wall β-glucan of their target fungal cells. Experimental evidence strongly suggested the possibility of development of anti-idiotypic scFv peptide-based antifungal agents which may lead to improve therapeutics for the management of varieties of fungal infections.

  5. Characterizing SRAM Single Event Upset in Terms of Single and Double Node Charge Collection

    NASA Technical Reports Server (NTRS)

    Black, J. D.; Ball, D. R., II; Robinson, W. H.; Fleetwood, D. M.; Schrimpf, R. D.; Reed, R. A.; Black, D. A.; Warren, K. M.; Tipton, A. D.; Dodd, P. E.; hide

    2008-01-01

    A well-collapse source-injection mode for SRAM SEU is demonstrated through TCAD modeling. The recovery of the SRAM s state is shown to be based upon the resistive path from the p+-sources in the SRAM to the well. Multiple cell upset patterns for direct charge collection and the well-collapse source-injection mechanisms are then predicted and compared to recent SRAM test data.

  6. Measurement of charged current single charged pion production cross-section on water with P0D detector

    NASA Astrophysics Data System (ADS)

    Assylbekov, Shamil; Wilson, Robert; Wachala, Tomasz; T2K Collaboration

    2015-04-01

    This work describes the first neutrino cross-section measurement of charged-current (CC) single charged pion (1 π+) interaction channel on water as a target. There is some disagreement between measurements on carbon for this process, which effects the precision of neutrino oscillation results. P0D detector of the T2K experiment has been taking neutrino interaction data since 2009 in configurations with and without a water target. Using a statistical water-in/water-out event rate subtraction, a measurement of νμ-induced CC1π+ cross-section on water is reported to be σ = 1 . 10 .10-39 -32.38%+35.27% cm2 , integrated over the entire T2K energy range. The measurement is based on a sample of 2703 events selected from beam runs of 2 . 64 ×1020 protons-on-target with the P0D water-in configuration, and 2187 events selected from 3 . 71 ×1020 protons-on-target with the water-out configuration. The corresponding Monte Carlo (MC) simulation predicted numbers of background events to be 1387.2 and 1046.0 for the water-in and water-out configurations, respectively. Data favors a smaller cross-section when compared with the model, but within uncertainty is consistent with σ = 1 . 26 .10-39cm2 predicted by MC.

  7. Direct charge sharing observation in single-photon-counting pixel detector

    NASA Astrophysics Data System (ADS)

    Pellegrini, G.; Maiorino, M.; Blanchot, G.; Chmeissani, M.; Garcia, J.; Lozano, M.; Martinez, R.; Puigdengoles, C.; Ullan, M.

    2007-04-01

    In photon-counting imaging devices, charge sharing can limit the detector spatial resolution and contrast, as multiple counts can be induced in adjacent pixels as a result of the spread of the charge cloud generated from a single X-ray photon of high energy in the detector bulk. Although debated for a long time, the full impact of charge sharing has not been completely assessed. In this work, the importance of charge sharing in pixellated CdTe and silicon detectors is studied by exposing imaging devices to different low activity sources. These devices are made of Si and CdTe pixel detector bump-bonded to Medipix2 single-photon-counting chips with a 55 μm pixel pitch. We will show how charge sharing affects the spatial detector resolution depending on incident particle type (alpha, beta and gamma), detector bias voltage and read-out chip threshold. This study will give an insight on the impact on the design and operation of pixel detectors coupled to photon-counting devices for imaging applications.

  8. An instrument for charge measurement due to a single collision between two spherical particles

    NASA Astrophysics Data System (ADS)

    Xie, L.; Bao, N.; Jiang, Y.; Han, K.; Zhou, J.

    2016-01-01

    It universally exists in moving particular systems that particles can be electrified, in which the particles are chemically identical, just as toner particles, coal dust, and pharmaceutical powders. However, owing to the limit of experimental instruments, so far, there are yet no experiments to illustrate whether a particle can be electrified due to a single collision between two spherical particles, and there are also no experiments to measure the charge carried by a single particle due to a single collision between two particles. So we have developed an instrument for charge measurement due to a single collision between two spheres. The instrument consists of two-sphere collision device, collision charge measurement apparatus, and particles' trajectory tracking system. By using this instrument, we can investigate the collision contact electrification due to a single collision between two spheres and simultaneously record the moving trajectories of spheres after the collision to calculate the rebound angles to identify the contribution of the triboelectrification due to the rubbing between the contact surfaces and the collision contact electrification due to the normal pressure between the contact surfaces.

  9. Impact of charge carrier injection on single-chain photophysics of conjugated polymers

    SciTech Connect

    Hofmann, Felix J.; Vogelsang, Jan Lupton, John M.

    2016-06-27

    Charges in conjugated polymer materials have a strong impact on the photophysics and their interaction with the primary excited state species has to be taken into account in understanding device properties. Here, we employ single-molecule spectroscopy to unravel the influence of charges on several photoluminescence (PL) observables. The charges are injected either stochastically by a photochemical process or deterministically in a hole-injection sandwich device configuration. We find that upon charge injection, besides a blue-shift of the PL emission and a shortening of the PL lifetime due to quenching and blocking of the lowest-energy chromophores, the non-classical photon arrival time distribution of the multichromophoric chain is modified towards a more classical distribution. Surprisingly, the fidelity of photon antibunching deteriorates upon charging, whereas one would actually expect the opposite: the number of chromophores to be reduced. A qualitative model is presented to explain the observed PL changes. The results are of interest to developing a microscopic understanding of the intrinsic charge-exciton quenching interaction in devices.

  10. Charge-driven feedback loop in the resonance fluorescence of a single quantum dot

    NASA Astrophysics Data System (ADS)

    Merkel, B.; Kurzmann, A.; Schulze, J.-H.; Strittmatter, A.; Geller, M.; Lorke, A.

    2017-03-01

    We demonstrate a feedback loop that manifests itself in a strong hysteresis and bistability of the exciton resonance fluorescence signal. Field ionization of photogenerated quantum dot excitons leads to the formation of a charged interface layer that drags the emission line along over a frequency range of more than 30 GHz . These measurements are well described by a rate equation model. With a time-resolved resonance fluorescence measurement we determined the buildup times for the hole gas in the orders of milliseconds. This internal charge-driven feedback loop could be used to reduce the spectral wandering in the emission spectra of single self-assembled quantum dots.

  11. Photovoltaic effect and charge storage in single ZnO nanowires

    SciTech Connect

    Liao Zhimin; Xu Jun; Zhang Jingmin; Yu Dapeng

    2008-07-14

    Asymmetric Schottky barriers between ZnO nanowire and metal electrode have been fabricated at the two ends of the nanowire. An obvious photocurrent generated from the device at zero voltage bias can be switched on/off with quick response by controlling the light irradiation. Moreover, the device can still afford a current at zero bias after switching off light illumination, which is ascribed to the charge storage effect in single ZnO nanowires. The underlying mechanisms related to the photovoltaic effect and charge storage were discussed.

  12. Secondary ions from condensed gas solids by singly and multiply charged ion impacts

    NASA Astrophysics Data System (ADS)

    Tachibana, T.; Fukai, K.; Naemura, I.; Koizumi, T.; Hirayama, T.

    2009-11-01

    Ion desorption from a condensed gas solid Ne impacted by singly- and multiply-charged Arq+ ions (q = 1-7) has been investigated. Various secondary ions such as cluster ions, Ne+n (n = 2-20) as well as atomic ions are observed. Mass spectral patterns, thickness dependence of the yields, and kinetic energy distributions of the desorbed Ne+n (n = 1,2) depend strongly on the projectile charge state. These results indicate that the dissipation of the projectile potential energy on the surface leads to the desorption of the monomer and small cluster ions by a Coulomb repulsion between adjacent target ions.

  13. Defect mediated desorption of the KBr(001) surface induced by single highly charged ion impact.

    PubMed

    Heller, R; Facsko, S; Wilhelm, R A; Möller, W

    2008-08-29

    The individual impacts of slow (300 eV/amu) highly charged Xe ions induce nanometer sized pitlike structures on the KBr (001) surface. The volume of these structures shows a strong dependence on the ions potential energy. Total potential sputter yields from atomically flat (001) terraces are determined by imaging single ion impact sites. The dependence of the sputter yield on the ions initial charge state combined with structure formation at low and high-fluence irradiations indicates that agglomeration of defects into complex centers plays a major role in the desorption process induced by the potential energy.

  14. Migration of a carbon adatom on a charged single-walled carbon nanotube

    DOE PAGES

    Han, Longtao; Krstic, Predrag; Kaganovich, Igor; ...

    2017-02-02

    Here we find that negative charges on an armchair single-walled carbon nanotube (SWCNT) can significantly enhance the migration of a carbon adatom on the external surfaces of SWCNTs, along the direction of the tube axis. Nanotube charging results in stronger binding of adatoms to SWCNTs and consequent longer lifetimes of adatoms before desorption, which in turn increases their migration distance several orders of magnitude. These results support the hypothesis of diffusion enhanced SWCNT growth in the volume of arc plasma. This process could enhance effective carbon flux to the metal catalyst.

  15. Charge-based separation of proteins and peptides by electrically induced dynamic pH profiles.

    PubMed

    Brod, E; S Ben-Yosef, V; Bandhakavi, S; Sivan, U

    2016-01-29

    A new method for generating complex, dynamic pH profiles in an ampholyte-free separation channel is presented together with the theory behind its operation. The pH is modulated by an array of proton and hydroxide ion injectors placed along the separation channel. The ions generated in-situ by electrically driven water splitting across a bipolar membrane are injected to the channel in the presence of a longitudinal electric field, leading to the formation of a multi-step pH profile. Real-time control over the pH profile along the channel facilitates new dynamic separation strategies as well as steering and harvesting of focused molecules, which are both impossible with conventional separation methods. These freedoms are particularly attractive for Lab-on-a-Chip applications. The pH step-like profile alleviates one of the main hurdles of conventional isoelectric separation methods, namely, the slowing down of focused molecules as they approach their focusing spot. As a result, separation is completed within minutes for both peptides and proteins, even with low applied electric fields. We demonstrate protein and peptide separation within minutes, and resolution of ΔpI=0.2. Novel separation strategies based on spatio-temporal pH control are demonstrated as well.

  16. Synthesis, purification, and characterization of single helix membrane peptides and proteins for NMR spectroscopy.

    PubMed

    Itaya, Miki; Brett, Ian C; Smith, Steven O

    2012-01-01

    Membrane proteins function as receptors, channels, transporters, and enzymes. These proteins are generally difficult to express and purify in a functional form due to the hydrophobic nature of their membrane spanning sequences. Studies on membrane proteins with a single membrane spanning helix have been particularly challenging. Single-pass membrane proteins will often form dimers or higher order oligomers in cell membranes as a result of sequence motifs that mediate specific transmembrane helix interactions. Understanding the structural basis for helix association provides insights into how these proteins function. Nevertheless, nonspecific association or aggregation of hydrophobic membrane spanning sequences can occur when isolated transmembrane domains are reconstituted into membrane bilayers or solubilized into detergent micelles for structural studies by solid-state or solution NMR spectroscopy. Here, we outline the methods used to synthesize, purify, and characterize single transmembrane segments for structural studies. Two synthetic strategies are discussed. The first strategy is to express hydrophobic peptides as protein chimera attached to the maltose binding protein. The second strategy is by direct chemical synthesis. Purification is carried out by several complementary chromatography methods. The peptides are solubilized in detergent for solution NMR studies or reconstituted into model membranes for solid-state NMR studies. We describe the methods used to characterize the reconstitution of these systems prior to NMR structural studies to establish if there is nonspecific aggregation.

  17. Prediction of drift time in ion mobility-mass spectrometry based on Peptide molecular weight.

    PubMed

    Wang, Bing; Valentine, Steve; Plasencia, Manolo; Zhang, Xiang

    2010-09-01

    A computational model is introduced for predicting peptide drift time in ion mobility-mass spectrometry (IMMS). Each peptide was represented using a numeric descriptor: molecular weight. A simple linear regression predictor was constructed for peptides drift time prediction. Three datasets with different charge state assignments were used for the model training and testing. The dataset one contains 212 singly charged peptides, dataset two has 306 doubly charged peptides, and dataset three contains 77 triply charged peptides. Our proposed method achieved a prediction accuracy of 86.3%, 72.6%, and 59.7% for the dataset one, two and three, respectively. Peptide drift time prediction in IMMS will improve the confidence of peptide identifications by limiting the peptide search space during MS/MS database searching and therefore, reducing false discovery rate (FDR) of protein identification.

  18. Real-time attack on single Escherichia coli cells by the human antimicrobial peptide LL-37.

    PubMed

    Sochacki, Kem A; Barns, Kenneth J; Bucki, Robert; Weisshaar, James C

    2011-04-19

    Natural antimicrobial peptides (AMPs) provide prototypes for the design of unconventional antimicrobial agents. Existing bulk assays measure AMP activity but do not provide details of the growth-halting mechanism. We use fluorescence microscopy to directly observe the attack of the human antimicrobial peptide LL-37 on single Escherichia coli cells in real time. Our findings strongly suggest that disruption of the cytoplasmic membrane is not the growth-halting mechanism. At 8 μM, LL-37 binding saturates the outer membrane (OM) within 1 min. Translocation across the OM and access to the periplasmic space (5-25 min later) correlates in time with the halting of growth. Septating cells are attacked more readily than nonseptating cells. The halting of growth may occur because of LL-37 interference with cell wall biogenesis. Only well after growth halts does the peptide permeabilize the cytoplasmic membrane to GFP and the small dye Sytox Green. The assay enables dissection of antimicrobial design criteria into two parts: translocation across the OM and the subsequent halting of growth.

  19. Single liposome analysis of peptide translocation by the ABC transporter TAPL.

    PubMed

    Zollmann, Tina; Moiset, Gemma; Tumulka, Franz; Tampé, Robert; Poolman, Bert; Abele, Rupert

    2015-02-17

    ATP-binding cassette (ABC) transporters use ATP to drive solute transport across biological membranes. Members of this superfamily have crucial roles in cell physiology, and some of the transporters are linked to severe diseases. However, understanding of the transport mechanism, especially of human ABC exporters, is scarce. We reconstituted the human lysosomal polypeptide ABC transporter TAPL, expressed in Pichia pastoris, into lipid vesicles (liposomes) and performed explicit transport measurements. We analyzed solute transport at the single liposome level by monitoring the coincident fluorescence of solutes and proteoliposomes in the focal volume of a confocal microscope. We determined a turnover number of eight peptides per minute, which is two orders of magnitude higher than previously estimated from macroscopic measurements. Moreover, we show that TAPL translocates peptides against a large concentration gradient. Maximal filling is not limited by an electrochemical gradient but by trans-inhibition. Countertransport and reversibility studies demonstrate that peptide translocation is a strictly unidirectional process. Altogether, these data are included in a refined model of solute transport by ABC exporters.

  20. Effect of the hydrophobicity to net positive charge ratio on antibacterial and anti-endotoxin activities of structurally similar antimicrobial peptides.

    PubMed

    Rosenfeld, Yosef; Lev, Naama; Shai, Yechiel

    2010-02-09

    The interaction between host-defense antimicrobial peptides (AMPs) and the bacterial lipopolysaccharide (LPS) governs both the susceptibility of the bacteria to the peptide and the ability of the peptide to inhibit LPS activation of immune cells. Both functions depend on the biophysical properties of the peptides. However, the sequence and structural diversity of AMPs makes it difficult to determine common denominators required for antimicrobial and LPS neutralizing activities. Toward this end, we synthesized and investigated a series of nine 12-amino acid peptides and their fatty acid-conjugated analogues composed of both D- and L-isomers of Leu and Lys at various ratios. The positions of the D-amino acids were preserved. These peptides differ in their net positive charge and hydrophobicity. However, their overall structure in the membrane is similar, as determined by Fourier transform infrared spectroscopy. The peptides and their analogues were functionally tested for their antibacterial and hemolytic activity, their ability to permeate LPS vesicles, their ability to neutralize LPS activation of macrophages, and their effect on LPS morphology, determined by negative staining electron microscopy. The data revealed that increasing the ratio between hydrophobicity and the net positive charge increases both antimicrobial and LPS neutralization activities, but with different modes of contributions. Whereas antimicrobial activity increases linearly with the increase in the peptides' hydrophobicity, peptides with different hydrophobicities are endowed with similar LPS neutralizing activities. Besides adding important information regarding AMP parameters involved in antimicrobial and anti-LPS activities, this study suggests the use of such diastereomers as potential templates for the development of simple molecules that conduct both types of functions.

  1. Fabrication of Supramolecular n/p-Nanowires via Coassembly of Oppositely Charged Peptide-Chromophore Systems in Aqueous Media.

    PubMed

    Khalily, Mohammad Aref; Bakan, Gokhan; Kucukoz, Betul; Topal, Ahmet Emin; Karatay, Ahmet; Yaglioglu, H Gul; Dana, Aykutlu; Guler, Mustafa O

    2017-07-25

    Fabrication of supramolecular electroactive materials at the nanoscale with well-defined size, shape, composition, and organization in aqueous medium is a current challenge. Herein we report construction of supramolecular charge-transfer complex one-dimensional (1D) nanowires consisting of highly ordered mixed-stack π-electron donor-acceptor (D-A) domains. We synthesized n-type and p-type β-sheet forming short peptide-chromophore conjugates, which assemble separately into well-ordered nanofibers in aqueous media. These complementary p-type and n-type nanofibers coassemble via hydrogen bonding, charge-transfer complex, and electrostatic interactions to generate highly uniform supramolecular n/p-coassembled 1D nanowires. This molecular design ensures highly ordered arrangement of D-A stacks within n/p-coassembled supramolecular nanowires. The supramolecular n/p-coassembled nanowires were found to be formed by A-D-A unit cells having an association constant (KA) of 5.18 × 10(5) M(-1). In addition, electrical measurements revealed that supramolecular n/p-coassembled nanowires are approximately 2400 and 10 times more conductive than individual n-type and p-type nanofibers, respectively. This facile strategy allows fabrication of well-defined supramolecular electroactive nanomaterials in aqueous media, which can find a variety of applications in optoelectronics, photovoltaics, organic chromophore arrays, and bioelectronics.

  2. Modulation of pharmacokinetics of radioiodinated sugar-conjugated somatostatin analogues by variation of peptide net charge and carbohydration chemistry.

    PubMed

    Schottelius, Margret; Rau, Friederike; Reubi, Jean Claude; Schwaiger, Markus; Wester, Hans-Jürgen

    2005-01-01

    Sugar conjugation of biooactive peptides has been shown to be a powerful tool to modulate peptide pharmacokinetics. In the case of radiolabeled somatostatin analogues developed for in vivo scintigraphy of somatostatin receptor (sst) expressing tumors, it generally led to tracers with predominant renal excretion and low uptake in nontarget organs, and in some cases also with enhanced tumor accumulation. Especially with respect to endoradiotherapeutic applicability of these tracers, however, understanding the structural requirements for minimal kidney accumulation and maximal tumor uptake is important. The aim of this study was therefore the evaluation of the potential of specific glycoside structures in combination with reduced peptide net charge to reduce kidney accumulation without affecting tumor accumulation. Three glyco analogues of radioiodinated Tyr(3)-octreotate (TOCA) with z = 0 were evaluated in a comparative study using [(125)I]Mtr-TOCA (z = +1), the maltotriose-Amadori analogue of [(125)I]TOCA, as a reference, [(125)I]Glucuron-TOCA, the Amadori conjugate with glucuronic acid, and [(125)I]Gluc-S- and [(125)I]Gal-S-TOCA, the coupling products with glucosyl- and mannosyl-mercaptopropionate. In cells transfected with sst(1)-sst(5), all three new analogues show sst-subtype binding profiles similar to I-Mtr-TOCA with high, but somewhat reduced, affinity for sst(2). In contrast, internalization into sst(2)-expressing cells (in % of [(125)I]Tyr(3)-octreotide ([(125)I]TOC)) as well as the EC(50,R) of unlabeled TOC for internalization determined in dual-tracer experiments are substantially enhanced for [(123)I]Gal-S-TOCA and [(123)I]Gluc-S-TOCA (internalization, 190% +/- 12% and 265% +/- 20%, respectively, vs 168% +/- 6% of [(125)I]TOC for [(123)I]Mtr-TOCA; EC(50,R), 2.62 +/- 0.07 and 2.96 +/- 0.14, respectively, vs 1.81 +/- 0.07 for [(123)I]Mtr-TOCA). The tumor accumulation of [(125)I]Gal-S-TOCA and [(125)I]Gluc-S-TOCA in AR42J tumor-bearing nude mice 1 h p.i. is

  3. Single-crystal charge transfer interfaces for efficient photonic devices (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Alves, Helena; Pinto, Rui M.; Maçôas, Ermelinda M. S.; Baleizão, Carlos; Santos, Isabel C.

    2016-09-01

    Organic semiconductors have unique optical, mechanical and electronic properties that can be combined with customized chemical functionality. In the crystalline form, determinant features for electronic applications such as molecular purity, the charge mobility or the exciton diffusion length, reveal a superior performance when compared with materials in a more disordered form. Combining crystals of two different conjugated materials as even enable a new 2D electronic system. However, the use of organic single crystals in devices is still limited to a few applications, such as field-effect transistors. In 2013, we presented the first system composed of single-crystal charge transfer interfaces presenting photoconductivity behaviour. The system composed of rubrene and TCNQ has a responsivity reaching 1 A/W, corresponding to an external quantum efficiency of nearly 100%. A similar approach, with a hybrid structure of a PCBM film and rubrene single crystal also presents high responsivity and the possibility to extract excitons generated in acceptor materials. This strategy led to an extended action towards the near IR. By adequate material design and structural organisation of perylediimides, we demonstrate that is possible to improve exciton diffusion efficiency. More recently, we have successfully used the concept of charge transfer interfaces in phototransistors. These results open the possibility of using organic single-crystal interfaces in photonic applications.

  4. Investigation of charge multiplication in single crystalline CVD diamond particle detectors

    NASA Astrophysics Data System (ADS)

    Muškinja, M.; Cindro, V.; Gorišek, A.; Kagan, H.; Kramberger, G.; Mandić, I.; Mikuž, M.; Phan, S.; Smith, D. S.; Zavrtanik, M.

    2017-01-01

    A special metallization pattern was created on a single crystalline diamond detector aimed at creating high enough electric field for impact ionization in the detector material. Electric field line focusing through electrode design and very high bias voltages were used to obtain high electric fields. Previous measurements and theoretical calculations indicated that drifting charge multiplication by impact ionization could take place. A large increase of induced charge was observed for the smallest dot electrode which points to charge multiplication while for the large dot and pad detector structure no such effect was observed. The evolution of induced currents was also monitored with the transient current technique. Induced current pulses with duration of order 1 μs were measured. The multiplication gain was found to depend on the particle rate.

  5. Unraveling the Electronic Heterogeneity of Charge Traps in Conjugated Polymers by Single-Molecule Spectroscopy.

    PubMed

    Adachi, Takuji; Vogelsang, Jan; Lupton, John M

    2014-02-06

    Charge trapping is taken for granted in modeling the characteristics of organic semiconductor devices, but very few techniques actually exist to spectroscopically pinpoint trap states. For example, trap levels are often assumed to be discrete in energy. Using the well-known keto defect in polyfluorene as a model, we demonstrate how single-molecule spectroscopy can directly track the formation of charge and exciton traps in conjugated polymers in real time, providing crucial information on the energetic distribution of trap sites relative to the polymer optical gap. Charge traps with universal spectral fingerprints scatter by almost 1 eV in depth, implying that substantial heterogeneity must be taken into account when modeling devices.

  6. Charge Transfer Between Quantum Dots and Peptide-Coupled Redox Complexes

    DTIC Science & Technology

    2009-01-01

    scale ) Ruthenium complex 190 2009 NRL REVIEW NANOSCIENCE TECHNOLOGY N or m al iz ed C ur re nt (µ A ) Potential, V vs...DHLA QDs Abs 2 Ru /QD Abs 5 Ru /QD FIGURE 4 Enzymatic assay of chymotrypsin activity utilizing QD–Ru peptide conjugates, showing enzymatic ve ...0.01 0.02 0.03 0.04 Vmax = 0.04 +/- 0.02 µM/min KM = 0.83 +/- 0.16 µM KM = 2.2 +/- 0.5 µM Vmax = 0.01 +/- 0.004 µM/min No inhibitor + Chymostatin inhibitor V el oc ity (µ M C hy m -R u cl ea ve d

  7. Spectroscopy of Charge Carriers and Traps in Field-Doped Single Crystal Organic Semiconductors

    SciTech Connect

    Zhu, Xiaoyang

    2014-12-10

    The proposed research aims to achieve quantitative, molecular level understanding of charge carriers and traps in field-doped crystalline organic semiconductors via in situ linear and nonlinear optical spectroscopy, in conjunction with transport measurements and molecular/crystal engineering. Organic semiconductors are emerging as viable materials for low-cost electronics and optoelectronics, such as organic photovoltaics (OPV), organic field effect transistors (OFETs), and organic light emitting diodes (OLEDs). Despite extensive studies spanning many decades, a clear understanding of the nature of charge carriers in organic semiconductors is still lacking. It is generally appreciated that polaron formation and charge carrier trapping are two hallmarks associated with electrical transport in organic semiconductors; the former results from the low dielectric constants and weak intermolecular electronic overlap while the latter can be attributed to the prevalence of structural disorder. These properties have lead to the common observation of low charge carrier mobilities, e.g., in the range of 10-5 - 10-3 cm2/Vs, particularly at low carrier concentrations. However, there is also growing evidence that charge carrier mobility approaching those of inorganic semiconductors and metals can exist in some crystalline organic semiconductors, such as pentacene, tetracene and rubrene. A particularly striking example is single crystal rubrene (Figure 1), in which hole mobilities well above 10 cm2/Vs have been observed in OFETs operating at room temperature. Temperature dependent transport and spectroscopic measurements both revealed evidence of free carriers in rubrene. Outstanding questions are: what are the structural features and physical properties that make rubrene so unique? How do we establish fundamental design principles for the development of other organic semiconductors of high mobility? These questions are critically important but not comprehensive, as the nature of

  8. Improved memory behaviour of single-walled carbon nanotubes charge storage nodes

    NASA Astrophysics Data System (ADS)

    Alba-Martin, Maria; Firmager, Timothy; Atherton, Joseph; Rosamond, Mark C.; Ashall, Daniel; Ghaferi, Amal Al; Ayesh, Ahmad; Gallant, Andrew J.; Mabrook, Mohammed F.; Petty, Michael C.; Zeze, Dagou A.

    2012-07-01

    To investigate their memory behaviours, single-walled carbon nanotubes (SWCNTs) were embedded in the floating gate of a hybrid metal-insulator-semiconductor structure using layer-by-layer deposition, and polymethylmethacrylate (PMMA) as the dielectric. Unlike longer SWCNT-based structures, shortened SWCNTs were shown to exhibit reliable and large memory windows by virtue of a better encapsulation which reduces charge leakage. The capacitance-voltage characteristics of the devices were consistent with electron injection into the SWCNT charge storage elements (in the floating) from the top electrode through the PMMA, using localized defects and crossing the PMMA energy barrier. In terms of material formulation, a combination of SWCNTs dispersed in sodium dodecyl sulfate and polyethyleneimine used as charge storage elements in the floating gate was shown to lead to repeatable and reliable memory characteristics. Fast switching and very large memory windows (˜7 V) exhibiting high charge density (2.6 × 1012 cm-2) and charge retention in excess of ˜76% were achieved under a ±10 V sweep voltage range. These results suggest that SWCNTs could lead to improved memory behaviour with the potential for application in plastic electronics.

  9. A sensitive charge scanning probe based on silicon single electron transistor

    NASA Astrophysics Data System (ADS)

    Lina, Su; Xinxing, Li; Hua, Qin; Xiaofeng, Gu

    2016-04-01

    Single electron transistors (SETs) are known to be extremely sensitive electrometers owing to their high charge sensitivity. In this work, we report the design, fabrication, and characterization of a silicon-on-insulator-based SET scanning probe. The fabricated SET is located about 10 μm away from the probe tip. The SET with a quantum dot of about 70 nm in diameter exhibits an obvious Coulomb blockade effect measured at 4.1 K. The Coulomb blockade energy is about 18 meV, and the charge sensitivity is in the order of 10-5-10-3 e/Hz1/2. This SET scanning probe can be used to map charge distribution and sense dynamic charge fluctuation in nanodevices or circuits under test, realizing high sensitivity and high spatial resolution charge detection. Project supported by the Instrument Developing Project of the Chinese Academy of Sciences (No. YZ201152), the National Natural Science Foundation of China (No. 11403084), the Fundamental Research Funds for Central Universities (Nos. JUSRP51510, JUDCF12032), and the Graduate Student Innovation Program for Universities of Jiangsu Province (No. CXLX12_0724).

  10. Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

    PubMed Central

    Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

    2016-01-01

    Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures—formed by a single sequence—may be a key feature in preventing bacterial resistance and could explain why sequence–function relationships in AMPs remain elusive. PMID:27874004

  11. Single-molecule visualization of dynamic transitions of pore-forming peptides among multiple transmembrane positions

    PubMed Central

    Li, Ying; Qian, Zhenyu; Ma, Li; Hu, Shuxin; Nong, Daguan; Xu, Chunhua; Ye, Fangfu; Lu, Ying; Wei, Guanghong; Li, Ming

    2016-01-01

    Research on the dynamics of single-membrane proteins remains underdeveloped due to the lack of proper approaches that can probe in real time the protein's insertion depth in lipid bilayers. Here we report a single-molecule visualization method to track both vertical insertion and lateral diffusion of membrane proteins in supported lipid bilayers by exploiting the surface-induced fluorescence attenuation (SIFA) of fluorophores. The attenuation follows a d−4 dependency, where d is the fluorophore-to-surface distance. The method is validated by observing the antimicrobial peptide LL-37 to transfer among five transmembrane positions: the surface, the upper leaflet, the centre, the lower leaflet and the bottom of the lipid bilayer. These results demonstrate the power of SIFA to study protein-membrane interactions and provide unprecedented in-depth understanding of molecular mechanisms of the insertion and translocation of membrane proteins. PMID:27686409

  12. Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

    NASA Astrophysics Data System (ADS)

    Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

    2016-11-01

    Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures--formed by a single sequence--may be a key feature in preventing bacterial resistance and could explain why sequence-function relationships in AMPs remain elusive.

  13. Multiple tunnel junctions based nanowire photodetector model for single charge detection

    NASA Astrophysics Data System (ADS)

    Chatbouri, Samir; Touati, A.; Troudi, M.; Sghaier, N.; Kalboussi, A.

    2013-07-01

    In this paper we propose a new silicon nanowire photodetector model based on a single-electron transistor for single charge detection (photo-NWSET). In the first part of this work we present the two blocks of the device structure (reading and detection blocks). The presented model is consisting of two blocks capacitively coupled. The first SET (SET1) is supposed to read the charge whereas the detection block is represented by the nanowire (NW) system associated to an optical source. We modeled the NW by a series of seven islands separated by eight tunnel junctions (8TJs). In the second part of this work, we investigate the effects of photoexcitation on Id-Vg curves and we present results obtained on the output (photo-NWSET) characteristics after variation of power illumination and response time.

  14. Unsupervised vector-based classification of single-molecule charge transport data

    PubMed Central

    Lemmer, Mario; Inkpen, Michael S.; Kornysheva, Katja; Long, Nicholas J.; Albrecht, Tim

    2016-01-01

    The stochastic nature of single-molecule charge transport measurements requires collection of large data sets to capture the full complexity of a molecular system. Data analysis is then guided by certain expectations, for example, a plateau feature in the tunnelling current distance trace, and the molecular conductance extracted from suitable histogram analysis. However, differences in molecular conformation or electrode contact geometry, the number of molecules in the junction or dynamic effects may lead to very different molecular signatures. Since their manifestation is a priori unknown, an unsupervised classification algorithm, making no prior assumptions regarding the data is clearly desirable. Here we present such an approach based on multivariate pattern analysis and apply it to simulated and experimental single-molecule charge transport data. We demonstrate how different event shapes are clearly separated using this algorithm and how statistics about different event classes can be extracted, when conventional methods of analysis fail. PMID:27694904

  15. Charge noise, spin-orbit coupling, and dephasing of single-spin qubits

    SciTech Connect

    Bermeister, Adam; Keith, Daniel; Culcer, Dimitrie

    2014-11-10

    Quantum dot quantum computing architectures rely on systems in which inversion symmetry is broken, and spin-orbit coupling is present, causing even single-spin qubits to be susceptible to charge noise. We derive an effective Hamiltonian for the combined action of noise and spin-orbit coupling on a single-spin qubit, identify the mechanisms behind dephasing, and estimate the free induction decay dephasing times T{sub 2}{sup *} for common materials such as Si and GaAs. Dephasing is driven by noise matrix elements that cause relative fluctuations between orbital levels, which are dominated by screened whole charge defects and unscreened dipole defects in the substrate. Dephasing times T{sub 2}{sup *} differ markedly between materials and can be enhanced by increasing gate fields, choosing materials with weak spin-orbit, making dots narrower, or using accumulation dots.

  16. Single-charge transport in ambipolar silicon nanoscale field-effect transistors

    SciTech Connect

    Mueller, Filipp; Konstantaras, Georgios; Wiel, Wilfred G. van der; Zwanenburg, Floris A.

    2015-04-27

    We report single-charge transport in ambipolar nanoscale MOSFETs, electrostatically defined in near-intrinsic silicon. We use the ambipolarity to demonstrate the confinement of either a few electrons or a few holes in exactly the same crystalline environment underneath a gate electrode. We find similar electron and hole quantum dot properties while the mobilities differ quantitatively like in microscale devices. The understanding and control of individual electrons and holes are essential for spin-based quantum information processing.

  17. The single-zone numerical model of homogeneous charge compression ignition engine performance

    NASA Astrophysics Data System (ADS)

    Fedyanov, E. A.; Itkis, E. M.; Kuzmin, V. N.; Shumskiy, S. N.

    2017-02-01

    The single-zone model of methane-air mixture combustion in the Homogeneous Charge Compression Ignition engine was developed. First modeling efforts resulted in the selection of the detailed kinetic reaction mechanism, most appropriate for the conditions of the HCCI process. Then, the model was completed so as to simulate the performance of the four-stroke engine and was coupled by physically reasonable adjusting functions. Validation of calculations against experimental data showed acceptable agreement.

  18. Structure guided RP-HPLC chromatography of diastereomeric α-helical peptide analogs substituted with single amino acid stereoisomers

    PubMed Central

    Huang, YiBing; Pan, Ling; Zhao, LianJing; Mant, Colin T.; Hodges, Robert S.; Chen, Yuxin

    2013-01-01

    An α-helical model peptide (Ac-EAEKAAKE-X-EKAAKEAEK-amide) was used as a template to examine the efficacy of conventional reversed-phase high-performance liquid chromatography (RP-HPLC) in separating peptide analogs with single substitutions (at position X) of diasteromeric amino acids Ile, allo-Ile, D-Ile and D-allo-Ile. We compared differences of peptide retention behavior on a C8 column and a C18 column at different temperatures. We demonstrated how subtle differences in peptide secondary structure affected by the different substitutions of amino acids with identical overall hydrophobicity enabled effective resolution of these peptide analogs. We also demonstrated the ability of RP-HPLC to separate Ile- and allo-Ile-substituted analogs of a 26-residue α-helical antimicrobial peptide (AMP), with the substitution site towards the C-terminus of the α-helix. These peptides show different values of antibacterial activity and hemolytic activity, and different selectivity against bacteria and human cells. Our results underline the ability of RP-HPLC to resolve even difficult diasteromeric peptide mixtures as well as its value in monitoring very subtle hydrophobicity changes in de novo-designed AMP. PMID:24127254

  19. Antimicrobial/cytolytic peptides from the venom of the North African scorpion, Androctonus amoreuxi: biochemical and functional characterization of natural peptides and a single site-substituted analog.

    PubMed

    Almaaytah, Ammar; Zhou, Mei; Wang, Lei; Chen, Tianbao; Walker, Brian; Shaw, Chris

    2012-06-01

    The venoms of scorpions are complex cocktails of polypeptide toxins that fall into two structural categories: those that contain cysteinyl residues with associated disulfide bridges and those that do not. As the majority of lethal toxins acting upon ion channels fall into the first category, most research has been focused there. Here we report the identification and structural characterization of two novel 18-mer antimicrobial peptides from the venom of the North African scorpion, Androctonus amoreuxi. Named AamAP1 and AamAP2, both peptides are C-terminally amidated and differ in primary structure at just two sites: Leu-->Pro at position 2 and Phe-->Ile at position 17. Synthetic replicates of both peptides exhibited a broad-spectrum of antimicrobial activity against a Gram-positive bacterium (Staphylococcus aureus), a Gram-negative bacterium (Escherichia coli) and a yeast (Candida albicans), at concentrations ranging between 20 μM and 150 μM. In this concentration range, both peptides produced significant degrees of hemolysis. A synthetic replicate of AamAP1 containing a single substitution (His-->Lys) at position 8, generated a peptide (AamAP-S1) with enhanced antimicrobial potency (3-5 μM) against the three test organisms and within this concentration range, hemolytic effects were negligible. In addition, this His-->Lys variant exhibited potent growth inhibitory activity (ID(50) 25-40 μm) against several human cancer cell lines and endothelial cells that was absent in both natural peptides. Natural bioactive peptide libraries, such as those that occur in scorpion venoms, thus constitute a unique source of novel lead compounds with drug development potential whose biological properties can be readily manipulated by simple synthetic chemical means. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. Soft matter interactions at the molecular scale: interaction forces and energies between single hydrophobic model peptides.

    PubMed

    Stock, Philipp; Utzig, Thomas; Valtiner, Markus

    2017-02-08

    In all realms of soft matter research a fundamental understanding of the structure/property relationships based on molecular interactions is crucial for developing a framework for the targeted design of soft materials. However, a molecular picture is often difficult to ascertain and yet essential for understanding the many different competing interactions at play, including entropies and cooperativities, hydration effects, and the enormous design space of soft matter. Here, we characterized for the first time the interaction between single hydrophobic molecules quantitatively using atomic force microscopy, and demonstrated that single molecular hydrophobic interaction free energies are dominated by the area of the smallest interacting hydrophobe. The interaction free energy amounts to 3-4 kT per hydrophobic unit. Also, we find that the transition state of the hydrophobic interactions is located at 3 Å with respect to the ground state, based on Bell-Evans theory. Our results provide a new path for understanding the nature of hydrophobic interactions at the single molecular scale. Our approach enables us to systematically vary hydrophobic and any other interaction type by utilizing peptide chemistry providing a strategic advancement to unravel molecular surface and soft matter interactions at the single molecular scale.

  1. Allatotropin-related peptide in cockroaches: identification via mass spectrometric analysis of single identified neurons.

    PubMed

    Neupert, Susanne; Schattschneider, Sebastian; Predel, Reinhard

    2009-03-01

    The first insect allatotropin-related peptide (ATRP) was isolated from head extracts of the adult sphinx moth Manduca sexta [Kataoka H, Toschi A, Li JP, Carney RL, Schooley DA, Kramer SJ. Identification of an allatotropin from adult Manduca sexta. Science 1989;243:1481-3.]. Meanwhile ATRPs are known from different holometabolous insects but only a single ATRP could be identified from hemimetabolous insects [Paemen L, Tips A, Schoofs L, Proost P, Van Damme J, De Loof A. Lom-AG-myotropin: a novel myotropic peptide from the male accessory glands of Locusta migratoria. Peptides 1991;12:7-10.]. This means that the extensive analysis of neuropeptides from Leucophaea maderae and Periplaneta americana, which led to the discovery of many novel insect neuropeptides, did not result in the detection of any ATRP. In this study, we used another approach to find a cockroach ATRP by first identifying Manse-AT immunoreactive neurons in the terminal ganglion that can be stained by retrograde labeling and are suitable for dissection and subsequent mass spectrometric analysis. The peptidomic analysis of these putative ATRP neurons paved the way for the identification of the first cockroach ATRP. MALDI-TOF/TOF tandem mass spectrometry revealed a sequence identity with Locmi-AG-MT-1 which classifies this ATRP as a highly conserved neuropeptide. A mass spectrometric screening of the nervous system allowed the detection of ATRP-ion signals in different parts of the CNS of P. americana as well as L. maderae. The data obtained in this study will be incorporated in a map of peptidergic neurons from the CNS of the American cockroach, P. americana.

  2. Raman Spectroscopy of Charge Transfer Interactions Between Single Wall Carbon Nanotubes and [FeFe] Hydrogenase

    SciTech Connect

    Blackburn, J. L. Svedruzic, D.; McDonald, T. J.; Kim, Y. H.; King, P. W.; Heben, M. J.

    2008-01-01

    We report a Raman spectroscopy study of charge transfer interactions in complexes formed by single-walled carbon nanotubes (SWNTs) and [FeFe] hydrogenase I (CaHydI) from Clostridium acetobutylicum. The choice of Raman excitation wavelength and sample preparation conditions allows differences to be observed for complexes involving metallic (m) and semiconducting (s) species. Adsorbed CaHydI can reversibly inject electronic charge into the LUMOs of s-SWNTs, while charge can be injected and removed from m-SWNTs at lower potentials just above the Fermi energy. Time-dependent enzymatic assays demonstrated that the reduced and oxidized forms of CaHydI are deactivated by oxygen, but at rates that varied by an order of magnitude. The time evolution of the oxidative decay of the CaHydI activity reveals different time constants when complexed with m-SWNTs and s-SWNTs. The correlation of enzymatic assays with time-dependent Raman spectroscopy provides a novel method by which the charge transfer interactions may be investigated in the various SWNT-CaHydI complexes. Surprisingly, an oxidized form of CaHydI is apparently more resistant to oxygen deactivation when complexed to m-SWNTs rather than s-SWNTs.

  3. Thermally Induced Charge Reversal of Layer-by-Layer Assembled Single-Component Polymer Films.

    PubMed

    Richardson, Joseph J; Tardy, Blaise L; Ejima, Hirotaka; Guo, Junling; Cui, Jiwei; Liang, Kang; Choi, Gwan H; Yoo, Pil J; De Geest, Bruno G; Caruso, Frank

    2016-03-23

    Temperature can be harnessed to engineer unique properties for materials useful in various contexts and has been shown to affect the layer-by-layer (LbL) assembly of polymer thin films and cause physical changes in preassembled polymer thin films. Herein we demonstrate that exposure to relatively low temperatures (≤ 100 °C) can induce physicochemical changes in cationic polymer thin films. The surface charge of polymer films containing primary and secondary amines reverses after heating (from positive to negative), and different characterization techniques are used to show that the change in surface charge is related to oxidation of the polymer that specifically occurs in the thin film state. This charge reversal allows for single-polymer LbL assembly to be performed with poly(allylamine) hydrochloride (PAH) through alternating heat/deposition steps. Furthermore, the negative charge induced by heating reduces the fouling and cell-association of PAH-coated planar and particulate substrates, respectively. This study highlights a unique property of thin films which is relevant to LbL assembly and biofouling and is of interest for the future development of thin polymer films for biomedical systems.

  4. Structure and switching of single-stranded DNA tethered to a charged nanoparticle surface

    NASA Astrophysics Data System (ADS)

    Xin-Jun, Zhao; Zhi-Fu, Gao

    2016-07-01

    Using a molecular theory, we investigate the temperature-dependent self-assembly of single-stranded DNA (ssDNA) tethered to a charged nanoparticle surface. Here the size, conformations, and charge properties of ssDNA are taken into account. The main results are as follows: i) when the temperature is lower than the critical switching temperature, the ssDNA will collapse due to the existence of electrostatic interaction between ssDNA and charged nanoparticle surface; ii) for the short ssDNA chains with the number of bases less than 10, the switching of ssDNA cannot happen, and the critical temperature does not exist; iii) when the temperature increases, the electrostatic attractive interaction between ssDNA and charged nanoparticle surface becomes weak dramatically, and ssDNA chains will stretch if the electrostatic attractive interaction is insufficient to overcome the elastic energy of ssDNA and the electrostatic repulsion energy. These findings accord well with the experimental observations. It is predicted that the switching of ssDNA will not happen if the grafting densities are too high. Project supported by the Joint Funds of Xinjiang Natural Science Foundation, China (Grant No. 2015211C298).

  5. Transport and Charge Manipulation in a Single Electron Silicon Double Quantum Dot

    NASA Astrophysics Data System (ADS)

    Wang, K.; Payette, C.; Dovzhenko, Y.; Petta, J. R.

    2013-03-01

    Silicon is one of the most promising candidates for ultra-coherent qubits due to its relatively early position in periodical table and the absence of nuclear spin in its naturally abundant isotope. Here we demonstrate a reliable recipe that enables us to reproducibly fabricate an accumulation mode few electron double quantum dot (DQD). We demonstrate tunable interdot tunnel coupling at single electron occupancy in the device. The charge state of the qubit is monitored by measuring the amplitude of the radio frequency signal that is reflected from a resonant circuit coupled to a charge sensor. By applying microwave radiation to the depletion gates, we probe the energy level structure of the DQD using photon assisted tunneling (PAT). We apply bursts of microwave radiation and monitor the dependence of the PAT peak height on the burst period to extract the charge relaxation time, T1. By experimentally tuning the charge qubit Hamiltonian, we measure the tunnel coupling and detuning dependence of T1. Supported by the United States Department of Defense. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressly or implied, of the U.S. Government.

  6. Lattice Boltzmann simulation of a single charged particle in a Newtonian fluid.

    PubMed

    Wan, Rong-Zhen; Fang, Hai-Ping; Lin, Zhifang; Chen, Shiyi

    2003-07-01

    The lattice Boltzmann method is used to study the sedimentaion of a single charged circular cylinder in a two-dimensional channel in a Newtonian fluid. When the dielectric constant of the liquid is smaller than that of the walls, there are attractive forces between the particle and the walls. The hydrodynamic force pushes the particle towards the centerline at low Reynolds numbers. Due to the competition between the Coulomb force and the hydrodynamic force in opposite directions, there is a critical linear charge density q(c) at which the particle will fall vertically off centerline, which is a metastable state in addition to the stable state on centerline, for any initial position of the particle sufficiently far from the proximal wall. It is found that the rotation of the particle plays an important role in the stability of such metastable states. The particle hits on the wall or falls on the centerline when the linear charge density on the particle is greater or less than q(c). The simulation method and the new phenomena are also helpful in the study of charged multiparticle suspensions.

  7. Single Molecule Spectroelectrochemistry of Interfacial Charge Transfer Dynamics In Hybrid Organic Solar Cell

    SciTech Connect

    Pan, Shanlin

    2014-11-16

    Our research under support of this DOE grant is focused on applied and fundamental aspects of model organic solar cell systems. Major accomplishments are: 1) we developed a spectroelectorchemistry technique of single molecule single nanoparticle method to study charge transfer between conjugated polymers and semiconductor at the single molecule level. The fluorescence of individual fluorescent polymers at semiconductor surfaces was shown to exhibit blinking behavior compared to molecules on glass substrates. Single molecule fluorescence excitation anisotropy measurements showed the conformation of the polymer molecules did not differ appreciably between glass and semiconductor substrates. The similarities in molecular conformation suggest that the observed differences in blinking activity are due to charge transfer between fluorescent polymer and semiconductor, which provides additional pathways between states of high and low fluorescence quantum efficiency. Similar spectroelectrochemistry work has been done for small organic dyes for understand their charge transfer dynamics on various substrates and electrochemical environments; 2) We developed a method of transferring semiconductor nanoparticles (NPs) and graphene oxide (GO) nanosheets into organic solvent for a potential electron acceptor in bulk heterojunction organic solar cells which employed polymer semiconductor as the electron donor. Electron transfer from the polymer semiconductor to semiconductor and GO in solutions and thin films was established through fluorescence spectroscopy and electroluminescence measurements. Solar cells containing these materials were constructed and evaluated using transient absorption spectroscopy and dynamic fluorescence techniques to understand the charge carrier generation and recombination events; 3) We invented a spectroelectorchemistry technique using light scattering and electroluminescence for rapid size determination and studying electrochemistry of single NPs in an

  8. A single-layer peptide nanofiber for enhancing the cytotoxicity of trastuzumab (anti-HER)

    NASA Astrophysics Data System (ADS)

    Malik, Ruchi; Wagh, Anil; Qian, Steven; Law, Benedict

    2013-06-01

    A multivalent system is often employed to enhance the effectiveness of a targeted therapy. In the present study, we report a single-layer peptide nanofiber (NFP) as a multivalent targeting platform to improve the cytotoxicity of trastuzumab (anti-HER), a monoclonal antibody targeting the human epidermal growth factor receptor 2 (HER-2) in approximately 20 % of breast cancer patients. The trastuzumab-conjugated nanofiber (anti-HER/NFP) was 100 × 4 nm in size and was assembled from multiple peptide units (mPEG-BK( FITC)SGASNRA-kldlkldlkldl-CONH2). The optimized preparation was attached with approximately 10 antibodies at the surface. Because of an increase in the multivalency, anti-HER/NFP was able to truncate more cell surface HER-2 and, thus, showed an enhanced cytotoxicity toward HER-2 positive SKBr-3 human breast cancer as compared to the free anti-HER. Western blot analysis and fluorescence microscopic studies confirmed that there was a significant downregulation of the HER-2 level and also inhibition of the cell survival cell signaling pathways including the phosphatidylinositol 3-kinase (PI3K) and the mitogen activated protein kinase (MAPK) pathway. Our data suggested that NFP can be useful as a multivalent platform for immunotherapy, especially in combination with other chemotherapeutic agents in the future.

  9. Charge-Density Wave Driven Phase Transitions in Single-Layer MoS2

    NASA Astrophysics Data System (ADS)

    Zhuang, Houlong L.; Johannes, Michelle D.; Hennig, Richard G.

    2014-03-01

    Phase transitions in single-layer MoS2 are frequently observed in experiments. We reveal that charge doping can induce the phase transition of single-layer MoS2 from the 2 H to the 1 T structure. Further, the 1 T structure undergoes a second phase transition due to the occurrence of a charge-density wave (CDW). By comparing the energies of several possible resulting CDW structures, we find that the √{ 3} a × a orthorhombic structure is the most stable one, consistent with experimental observations. Moreover, we discover that the band structure of the √{ 3} a × a structure possesses a Dirac cone, which is split by spin-orbit interactions into a bandgap of 50 meV. We show that the underlying CDW transition mechanism is not electronic, but can be controlled by charge doping nonetheless. Finally, we calculate the interface energy and band offsets of a lateral heterostructure formed by the 2 H and √{ 3} a × a structures.

  10. Superconducting single electron transistor for charge sensing in Si/SiGe-based quantum dots

    NASA Astrophysics Data System (ADS)

    Yang, Zhen

    Si-based quantum devices, including Si/SiGe quantum dots (QD), are promising candidates for spin-based quantum bits (quits), which are a potential platform for quantum information processing. Meanwhile, qubit readout remains a challenging task related to semiconductor-based quantum computation. This thesis describes two readout devices for Si/SiGe QDs and the techniques for developing them from a traditional single electron transistor (SET). By embedding an SET in a tank circuit and operating it in the radio-frequency (RF) regime, a superconducting RF-SET has quick response as well as ultra high charge sensitivity and can be an excellent charge sensor for the QDs. We demonstrate such RF-SETs for QDs in a Si/SiGe heterostructure. Characterization of the SET in magnetic fields is studied for future exploration of advanced techniques such as spin detection and spin state manipulation. By replacing the tank circuit with a high-quality-factor microwave cavity, the embedded SET will be operated in the supercurrent regime as a single Cooper pair transistor (CPT) to further increase the charge sensitivity and reduce any dissipation. The operating principle and implementation of the cavity-embedded CPT (cCPT) will be introduced.

  11. On the relationship between peptide adsorption resistance and surface contact angle: a combined experimental and simulation single-molecule study.

    PubMed

    Schwierz, Nadine; Horinek, Dominik; Liese, Susanne; Pirzer, Tobias; Balzer, Bizan N; Hugel, Thorsten; Netz, Roland R

    2012-12-05

    The force-induced desorption of single peptide chains from mixed OH/CH(3)-terminated self-assembled monolayers is studied in closely matched molecular dynamics simulations and atomic force microscopy experiments with the goal to gain microscopic understanding of the transition between peptide adsorption and adsorption resistance as the surface contact angle is varied. In both simulations and experiments, the surfaces become adsorption resistant against hydrophilic as well as hydrophobic peptides when their contact angle decreases below θ ≈ 50°-60°, thus confirming the so-called Berg limit established in the context of protein and cell adsorption. Entropy/enthalpy decomposition of the simulation results reveals that the key discriminator between the adsorption of different residues on a hydrophobic monolayer is of entropic nature and thus is suggested to be linked to the hydrophobic effect. By pushing a polyalanine peptide onto a polar surface, simulations reveal that the peptide adsorption resistance is caused by the strongly bound water hydration layer and characterized by the simultaneous gain of both total entropy in the system and total number of hydrogen bonds between water, peptide, and surface. This mechanistic insight into peptide adsorption resistance might help to refine design principles for anti-fouling surfaces.

  12. Floating gate memory with charge storage dots array formed by Dps protein modified with site-specific binding peptides

    NASA Astrophysics Data System (ADS)

    Kamitake, Hiroki; Uenuma, Mutsunori; Okamoto, Naofumi; Horita, Masahiro; Ishikawa, Yasuaki; Yamashita, Ichro; Uraoka, Yukiharu

    2015-05-01

    We report a nanodot (ND) floating gate memory (NFGM) with a high-density ND array formed by a biological nano process. We utilized two kinds of cage-shaped proteins displaying SiO2 binding peptide (minTBP-1) on their outer surfaces: ferritin and Dps, which accommodate cobalt oxide NDs in their cavities. The diameters of the cobalt NDs were regulated by the cavity sizes of the proteins. Because minTBP-1 is strongly adsorbed on the SiO2 surface, high-density cobalt oxide ND arrays were obtained by a simple spin coating process. The densities of cobalt oxide ND arrays based on ferritin and Dps were 6.8 × 1011 dots cm-2 and 1.2 × 1012 dots cm-2, respectively. After selective protein elimination and embedding in a metal-oxide-semiconductor (MOS) capacitor, the charge capacities of both ND arrays were evaluated by measuring their C-V characteristics. The MOS capacitor embedded with the Dps ND array showed a wider memory window than the device embedded with the ferritin ND array. Finally, we fabricated an NFGM with a high-density ND array based on Dps, and confirmed its competent writing/erasing characteristics and long retention time.

  13. Charge Manipulation in Molecules Encapsulated Inside Single-Wall Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Yanagi, Kazuhiro; Moriya, Rieko; Cuong, Nguyen Thanh; Otani, Minoru; Okada, Susumu

    2013-02-01

    We report clear experimental evidence for the charge manipulation of molecules encapsulated inside single-wall carbon nanotubes (SWCNTs) using electrochemical doping techniques. We encapsulated β-carotene (Car) inside SWCNTs and clarified electrochemical doping characteristics of their Raman spectra. C=C streching modes of encapsulated Car and a G band of SWCNTs showed clearly different doping behaviors as the electrochemical potentials were shifted. Electron extraction from encapsulated Car was clearly achieved. However, electrochemical characteristics of Car inside SWCNTs and doping mechanisms elucidated by calculations based on density-functional theory indicate the difficulty of charge manipulation of molecules inside SWCNTs due to the presence of strong on-site Coulomb repulsion energy at the molecules.

  14. Charge manipulation in molecules encapsulated inside single-wall carbon nanotubes.

    PubMed

    Yanagi, Kazuhiro; Moriya, Rieko; Cuong, Nguyen Thanh; Otani, Minoru; Okada, Susumu

    2013-02-22

    We report clear experimental evidence for the charge manipulation of molecules encapsulated inside single-wall carbon nanotubes (SWCNTs) using electrochemical doping techniques. We encapsulated β-carotene (Car) inside SWCNTs and clarified electrochemical doping characteristics of their Raman spectra. C=C streching modes of encapsulated Car and a G band of SWCNTs showed clearly different doping behaviors as the electrochemical potentials were shifted. Electron extraction from encapsulated Car was clearly achieved. However, electrochemical characteristics of Car inside SWCNTs and doping mechanisms elucidated by calculations based on density-functional theory indicate the difficulty of charge manipulation of molecules inside SWCNTs due to the presence of strong on-site Coulomb repulsion energy at the molecules.

  15. Tuning charge and correlation effects for a single molecule on a graphene device

    NASA Astrophysics Data System (ADS)

    Wickenburg, Sebastian; Lu, Jiong; Lischner, Johannes; Tsai, Hsin-Zon; Omrani, Arash A.; Riss, Alexander; Karrasch, Christoph; Bradley, Aaron; Jung, Han Sae; Khajeh, Ramin; Wong, Dillon; Watanabe, Kenji; Taniguchi, Takashi; Zettl, Alex; Neto, A. H. Castro; Louie, Steven G.; Crommie, Michael F.

    2016-11-01

    The ability to understand and control the electronic properties of individual molecules in a device environment is crucial for developing future technologies at the nanometre scale and below. Achieving this, however, requires the creation of three-terminal devices that allow single molecules to be both gated and imaged at the atomic scale. We have accomplished this by integrating a graphene field effect transistor with a scanning tunnelling microscope, thus allowing gate-controlled charging and spectroscopic interrogation of individual tetrafluoro-tetracyanoquinodimethane molecules. We observe a non-rigid shift in the molecule's lowest unoccupied molecular orbital energy (relative to the Dirac point) as a function of gate voltage due to graphene polarization effects. Our results show that electron-electron interactions play an important role in how molecular energy levels align to the graphene Dirac point, and may significantly influence charge transport through individual molecules incorporated in graphene-based nanodevices.

  16. Ultrafast electron microscopy: Instrument response from the single-electron to high bunch-charge regimes

    NASA Astrophysics Data System (ADS)

    Plemmons, Dayne A.; Flannigan, David J.

    2017-09-01

    We determine the instrument response of an ultrafast electron microscope equipped with a conventional thermionic electron gun and absent modifications beyond the optical ports. Using flat, graphite-encircled LaB6 cathodes, we image space-charge effects as a function of photoelectron-packet population and find that an applied Wehnelt bias has a negligible effect on the threshold levels (>103 electrons per pulse) but does appear to suppress blurring at the upper limits (∼105 electrons). Using plasma lensing, we determine the instrument-response time for 700-fs laser pulses and find that single-electron packets are laser limited (1 ps), while broadening occurs well below the space-charge limit.

  17. Tuning charge and correlation effects for a single molecule on a graphene device

    PubMed Central

    Wickenburg, Sebastian; Lu, Jiong; Lischner, Johannes; Tsai, Hsin-Zon; Omrani, Arash A.; Riss, Alexander; Karrasch, Christoph; Bradley, Aaron; Jung, Han Sae; Khajeh, Ramin; Wong, Dillon; Watanabe, Kenji; Taniguchi, Takashi; Zettl, Alex; Neto, A.H. Castro; Louie, Steven G.; Crommie, Michael F.

    2016-01-01

    The ability to understand and control the electronic properties of individual molecules in a device environment is crucial for developing future technologies at the nanometre scale and below. Achieving this, however, requires the creation of three-terminal devices that allow single molecules to be both gated and imaged at the atomic scale. We have accomplished this by integrating a graphene field effect transistor with a scanning tunnelling microscope, thus allowing gate-controlled charging and spectroscopic interrogation of individual tetrafluoro-tetracyanoquinodimethane molecules. We observe a non-rigid shift in the molecule's lowest unoccupied molecular orbital energy (relative to the Dirac point) as a function of gate voltage due to graphene polarization effects. Our results show that electron–electron interactions play an important role in how molecular energy levels align to the graphene Dirac point, and may significantly influence charge transport through individual molecules incorporated in graphene-based nanodevices. PMID:27886170

  18. Charge trapping in aligned single-walled carbon nanotube arrays induced by ionizing radiation exposure

    SciTech Connect

    Esqueda, Ivan S.; Cress, Cory D.; Che, Yuchi; Cao, Yu; Zhou, Chongwu

    2014-02-07

    The effects of near-interfacial trapping induced by ionizing radiation exposure of aligned single-walled carbon nanotube (SWCNT) arrays are investigated via measurements of gate hysteresis in the transfer characteristics of aligned SWCNT field-effect transistors. Gate hysteresis is attributed to charge injection (i.e., trapping) from the SWCNTs into radiation-induced traps in regions near the SWCNT/dielectric interface. Self-consistent calculations of surface-potential, carrier density, and trapped charge are used to describe hysteresis as a function of ionizing radiation exposure. Hysteresis width (h) and its dependence on gate sweep range are investigated analytically. The effects of non-uniform trap energy distributions on the relationship between hysteresis, gate sweep range, and total ionizing dose are demonstrated with simulations and verified experimentally.

  19. Full control of quadruple quantum dot circuit charge states in the single electron regime

    SciTech Connect

    Delbecq, M. R. Nakajima, T.; Otsuka, T.; Amaha, S.; Watson, J. D.; Manfra, M. J.; Tarucha, S.

    2014-05-05

    We report the realization of an array of four tunnel coupled quantum dots in the single electron regime, which is the first required step toward a scalable solid state spin qubit architecture. We achieve an efficient tunability of the system but also find out that the conditions to realize spin blockade readout are not as straightforwardly obtained as for double and triple quantum dot circuits. We use a simple capacitive model of the series quadruple quantum dots circuit to investigate its complex charge state diagrams and are able to find the most suitable configurations for future Pauli spin blockade measurements. We then experimentally realize the corresponding charge states with a good agreement to our model.

  20. Adsorption of polyelectrolyte versus surface charge: in situ single-molecule atomic force microscopy experiments on similarly, oppositely, and heterogeneously charged surfaces.

    PubMed

    Roiter, Yuri; Minko, Sergiy

    2007-07-26

    We have studied the effect of the pH and surface charge of mica on the adsorption of the positively charged weak polyelectrolyte (PE) poly(2-vinylpyridine) (P2VP) using atomic force microscopy (AFM) single-molecule experiments. These AFM experiments were performed in situ directly under aqueous media. If the mica's surface and the PE are oppositely charged (pH > 3), the PE forms a flat adsorbed layer of two-dimensionally (2D) equilibrated self-avoiding random walk coils. The adsorbed layer's structure remains almost unchanged if the pH is decreased to pH 3 (the mica's surface is weakly charged). At pH 2 (the mica surface is decorated by spots of different electrical charges), the polyelectrolyte chains take the form of a 2D compressed coil. In this pH range, at an increased P2VP concentration in solution, the PE segments preferentially adsorb onto the top of previously adsorbed segments, rather than onto an unoccupied surface. We explain this behavior as being caused by the heterogeneous character of the charged surface and the competitive adsorption of hydronium ions. The further increase of polymer concentration results in a complete coverage of the mica substrate and the charge overcompensation by P2VP chains adsorbed on the similarly charged substrate, due to van der Waals forces.

  1. Novel designs of single-chain MHC I/peptide complex for the magnetosome display system.

    PubMed

    Honda, Toru; Maeda, Yoshiaki; Yasuda, Takayuki; Tanaka, Tsuyoshi; Matsunaga, Tadashi; Yoshino, Tomoko

    2015-02-01

    The magnetic nanoparticles displaying the class I major histocompatibility complex (MHC I) were biologically synthesized using the magnetotactic bacterium Magnetospirillum magneticum AMB-1. Expression level and antigen peptide (HER263-71)-binding capability of the MHC I were evaluated on bacterial magnetic particles (BacMPs, also known as magnetosomes). Furthermore, the single-chain complexes of MHC I and HER263-71 were de novo designed for the magnetosome display system in order to improve the interaction between MHC I and HER263-71. Two types of the fusion arrangements were tested, and one of the complexes was estimated to fold into the correct conformation at the level of over 70%. In addition to the high folding ratio, an advantage of this system is that any refolding processes were not required even though the N-terminus of HER263-71 peptide is not free, which conventional bacterial expression systems have never demonstrated. The as-prepared single-chain MHC I/HER263-71 complex-displaying BacMPs (MHC I/HER2-BacMPs) specifically interacted with, and magnetically separated the HER263-71-induced cells, suggesting that the native T-cell receptor could recognize the engineered MHC I/HER2 complex on the BacMPs. By optimizing the magnetic sorting method, the MHC I/HER2-BacMPs developed in this study would be useful in immunotherapeutic applications. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Cationized phenylalanine conformations characterized by IRMPD and computation for singly and doubly charged ions.

    PubMed

    Dunbar, Robert C; Steill, Jeffrey D; Oomens, Jos

    2010-11-07

    Electrospray ionization produces phenylalanine (Phe) complexes of the alkali metal ion series, plus Ag(+) and Ba(2+). Infrared multiple photon dissociation (IRMPD) spectroscopy using the FELIX free electron laser light source is used to characterize the conformations of the ions, in conjunction with density functional theory (DFT) calculations giving thermochemical information and computed infrared spectra for likely candidate conformations. For complexes of small, singly charged ions (Li(+), Na(+), K(+) and Ag(+)) a single tridentate, charge-solvated conformational theme (N/O/Ring) binding amino nitrogen, carbonyl oxygen and the aromatic ring to the metal ion accounts for all the observations. The larger alkalis Rb(+) and Cs(+) show clear spectroscopic evidence of mixed populations, containing substantial fractions of both tridentate and also bidentate chelation. For Rb(+) the bidentate fraction is assigned as the (O/Ring) chelation pattern, while for Cs(+) a mixture of (O/Ring) and (O/O) chelation patterns seems likely. All of the smaller ions with high positive charge density have a clear preference for cation-π interaction with the side-chain aromatic ring, but for the larger ions Rb(+) and particularly Cs(+) this interaction becomes sufficiently weak to allow conformations having the metal ion remote from the π system. The Ba(2+) complex is unique in showing clear evidence of a major fraction of salt-bridge (zwitterionic) ions along with charge-solvated conformations. Plots of the frequency shifts of the two highly perturbed ligand vibrational modes (C[double bond, length as m-dash]O stretch and NH(2) frustrated inversion) give good linear correlations with the binding energy of the metal to the ligand.

  3. Single Amino Acid Variation Underlies Species-Specific Sensitivity to Amphibian Skin-Derived Opioid-like Peptides.

    PubMed

    Vardy, Eyal; Sassano, Maria F; Rennekamp, Andrew J; Kroeze, Wesley K; Mosier, Philip D; Westkaemper, Richard B; Stevens, Craig W; Katritch, Vsevolod; Stevens, Raymond C; Peterson, Randall T; Roth, Bryan L

    2015-06-18

    It has been suggested that the evolution of vertebrate opioid receptors (ORs) follow a vector of increased functionality. Here, we test this idea by comparing human and frog ORs. Interestingly, some of the most potent opioid peptides known have been isolated from amphibian skin secretions. Here we show that such peptides (dermorphin and deltorphin) are highly potent in the human receptors and inactive in frog ORs. The molecular basis for the insensitivity of the frog ORs to these peptides was studied using chimeras and molecular modeling. The insensitivity of the delta OR (DOR) to deltorphin was due to variation of a single amino acid, Trp7.35, which is a leucine in mammalian DORs. Notably, Trp7.35 is completely conserved in all known DOR sequences from lamprey, fish, and amphibians. The deltorphin-insensitive phenotype was verified in fish. Our results provide a molecular explanation for the species selectivity of skin-derived opioid peptides.

  4. Single amino acid variation underlies species-specific sensitivity to amphibian skin-derived opioid-like peptides

    PubMed Central

    Vardy, Eyal; Sassano, Maria F.; Rennekamp, Andrew J.; Kroeze, Wesley K.; Mosier, Philip D.; Westkaemper, Richard B.; Stevens, Craig W.; Katritch, Vsevolod; Stevens, Raymond C.; Peterson, Randel T.; Roth, Bryan L.

    2015-01-01

    It has been suggested that the evolution of vertebrate opioid receptors (ORs) follow a vector of increased functionality. Here we test this idea comparing human and frog ORs. Interestingly, some of the most potent opioid peptides known have been isolated from amphibian skin secretions. Here we show that such peptides (dermorphin and deltorphin) are highly potent in the human receptors and inactive in frog ORs. The molecular basis for the insensitivity of the frog ORs to these peptides was studied using chimeras and molecular modeling. Interestingly, the insensitivity of the delta opioid receptor (DOR) to deltorphin was due to variation of a single amino acid– Trp7.35—which is a leucine in mammalian DORs. Notably, Trp7.35 is completely conserved in all known DOR sequences from lamprey, fish and amphibians. The deltorphin-insensitive phenotype was verified in fish. Our results provide a molecular explanation for the species selectivity of skin-derived opioid peptides. PMID:26091169

  5. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling

    NASA Astrophysics Data System (ADS)

    Zhao, Yanan; Ashcroft, Brian; Zhang, Peiming; Liu, Hao; Sen, Suman; Song, Weisi; Im, Jongone; Gyarfas, Brett; Manna, Saikat; Biswas, Sovan; Borges, Chad; Lindsay, Stuart

    2014-06-01

    The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic `fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore.

  6. Rapid screening of peptide probes through in situ single-bead sequencing microarray.

    PubMed

    Wang, Weizhi; Wei, Zewen; Zhang, Di; Ma, Huailei; Wang, Zihua; Bu, Xiangli; Li, Menglin; Geng, Lingling; Lausted, Christopher; Hood, Leroy; Fang, Qiaojun; Wang, Hao; Hu, Zhiyuan

    2014-12-02

    Peptide ligands as targeting probes for in vivo imaging and drug delivery have attracted great interest in the biomedical community. However, high affinity and specificity screening of large peptide libraries remains a tedious process. Here, we report a continuous-flow microfluidic method for one-bead-one-compound (OBOC) combinatorial peptide library screening. We screened a library with 2 × 10(5) peptide beads within 4 h and discovered 140 noncanonical peptide hits targeting the tumor marker, aminopeptidase N (APN). Using the Clustal algorithm, we identified the conserved sequence Tyr-XX-Tyr in the N terminal. We demonstrated that the novel sequence YVEYHLC peptides have both nanomolar affinity and high specificity for APN in ex vivo and in vivo models. We envision that the successful demonstration of this integrated novel nanotechnology for peptide screening and identification open a new avenue for rapid discovery of new peptide-based reagents for disease diagnostics and therapeutics.

  7. Guiding Of Slow Highly Charged Ions Through A Single Mesoscopic Glass Capillary

    SciTech Connect

    Bereczky, R. J.; Tokesi, K.; Kowarik, G.; Lemaignan, C.; Mace, A.; Ladinig, F.; Raab, R.; Aumayr, F.

    2011-06-01

    We present experimental studies of the transmission of slow 4.5 keV Ar{sup 9+} ions through a single cylindrical-shaped glass capillary of macroscopic dimension with large aspect ratio. We find stable transmission of a micrometer-scale beam with considerable intensity after a charge-up phase, in which a self-organized process leads to the formation of a guiding electric field. We show the time evolution of the transmitted intensity through the sample for various capillary tilt angles.

  8. Charging a capacitor from an external fluctuating potential using a single conical nanopore.

    PubMed

    Gomez, Vicente; Ramirez, Patricio; Cervera, Javier; Nasir, Saima; Ali, Mubarak; Ensinger, Wolfgang; Mafe, Salvador

    2015-04-01

    We explore the electrical rectification of large amplitude fluctuating signals by an asymmetric nanostructure operating in aqueous solution. We show experimentally and theoretically that a load capacitor can be charged to voltages close to 1 V within a few minutes by converting zero time-average potentials of amplitudes in the range 0.5-3 V into average net currents using a single conical nanopore. This process suggests that significant energy conversion and storage from an electrically fluctuating environment is feasible with a nanoscale pore immersed in a liquid electrolyte solution, a system characteristic of bioelectronics interfaces, electrochemical cells, and nanoporous membranes.

  9. Charging a Capacitor from an External Fluctuating Potential using a Single Conical Nanopore

    PubMed Central

    Gomez, Vicente; Ramirez, Patricio; Cervera, Javier; Nasir, Saima; Ali, Mubarak; Ensinger, Wolfgang; Mafe, Salvador

    2015-01-01

    We explore the electrical rectification of large amplitude fluctuating signals by an asymmetric nanostructure operating in aqueous solution. We show experimentally and theoretically that a load capacitor can be charged to voltages close to 1 V within a few minutes by converting zero time-average potentials of amplitudes in the range 0.5–3 V into average net currents using a single conical nanopore. This process suggests that significant energy conversion and storage from an electrically fluctuating environment is feasible with a nanoscale pore immersed in a liquid electrolyte solution, a system characteristic of bioelectronics interfaces, electrochemical cells, and nanoporous membranes. PMID:25830563

  10. On the charge transfer between single-walled carbon nanotubes and graphene

    SciTech Connect

    Rao, Rahul Pierce, Neal; Dasgupta, Archi

    2014-08-18

    It is important to understand the electronic interaction between single-walled carbon nanotubes (SWNTs) and graphene in order to use them efficiently in multifunctional hybrid devices. Here, we deposited SWNT bundles on graphene-covered copper and SiO{sub 2} substrates by chemical vapor deposition and investigated the charge transfer between them by Raman spectroscopy. Our results revealed that, on both copper and SiO{sub 2} substrates, graphene donates electrons to the SWNTs, resulting in p-type doped graphene and n-type doped SWNTs.

  11. Creation of nanohillocks on CaF2 surfaces by single slow highly charged ions.

    PubMed

    El-Said, A S; Heller, R; Meissl, W; Ritter, R; Facsko, S; Lemell, C; Solleder, B; Gebeshuber, I C; Betz, G; Toulemonde, M; Möller, W; Burgdörfer, J; Aumayr, F

    2008-06-13

    Upon impact on a solid surface, the potential energy stored in slow highly charged ions is primarily deposited into the electronic system of the target. By decelerating the projectile ions to kinetic energies as low as 150 x q eV, we find first unambiguous experimental evidence that potential energy alone is sufficient to cause permanent nanosized hillocks on the (111) surface of a CaF(2) single crystal. Our investigations reveal a surprisingly sharp and well-defined threshold of potential energy for hillock formation which can be linked to a solid-liquid phase transition.

  12. Binding of β-Amyloid (1–42) Peptide to Negatively Charged Phospholipid Membranes in the Liquid-Ordered State: Modeling and Experimental Studies

    PubMed Central

    Ahyayauch, Hasna; Raab, Michal; Busto, Jon V.; Andraka, Nagore; Arrondo, José-Luis R.; Masserini, Massimo; Tvaroska, Igor; Goñi, Félix M.

    2012-01-01

    To explore the initial stages of amyloid β peptide (Aβ42) deposition on membranes, we have studied the interaction of Aβ42 in the monomeric form with lipid monolayers and with bilayers in either the liquid-disordered or the liquid-ordered (Lo) state, containing negatively charged phospholipids. Molecular dynamics (MD) simulations of the system have been performed, as well as experimental measurements. For bilayers in the Lo state, in the absence of the negatively charged lipids, interaction is weak and it cannot be detected by isothermal calorimetry. However, in the presence of phosphatidic acid, or of cardiolipin, interaction is detected by different methods and in all cases interaction is strongest with lower (2.5–5 mol %) than higher (10–20 mol %) proportions of negatively charged phospholipids. Liquid-disordered bilayers consistently allowed a higher Aβ42 binding than Lo ones. Thioflavin T assays and infrared spectroscopy confirmed a higher proportion of β-sheet formation under conditions when higher peptide binding was measured. The experimental results were supported by MD simulations. We used 100 ns MD to examine interactions between Aβ42 and three different 512 lipid bilayers consisting of palmitoylsphingomyelin, dimyristoyl phosphatidic acid, and cholesterol in three different proportions. MD pictures are different for the low- and high-charge bilayers, in the former case the peptide is bound through many contact points to the bilayer, whereas for the bilayer containing 20 mol % anionic phospholipid only a small fragment of the peptide appears to be bound. The MD results indicate that the binding and fibril formation on the membrane surface depends on the composition of the bilayer, and is the result of a subtle balance of many inter- and intramolecular interactions between the Aβ42 and membrane. PMID:22947861

  13. Electronic transport in single-helical protein molecules: Effects of multiple charge conduction pathways and helical symmetry

    NASA Astrophysics Data System (ADS)

    Kundu, Sourav; Karmakar, S. N.

    2016-07-01

    We propose a tight-binding model to investigate electronic transport properties of single helical protein molecules incorporating both the helical symmetry and the possibility of multiple charge transfer pathways. Our study reveals that due to existence of both the multiple charge transfer pathways and helical symmetry, the transport properties are quite rigid under influence of environmental fluctuations which indicates that these biomolecules can serve as better alternatives in nanoelectronic devices than its other biological counterparts e.g., single-stranded DNA.

  14. Single-particle thermal diffusion of charged colloids: double-layer theory in a temperature gradient.

    PubMed

    Dhont, J K G; Briels, W J

    2008-01-01

    The double-layer contribution to the single-particle thermal diffusion coefficient of charged, spherical colloids with arbitrary double-layer thickness is calculated and compared to experiments. The calculation is based on an extension of the Debye-Hückel theory for the double-layer structure that includes a small temperature gradient. There are three forces that constitute the total thermophoretic force on a charged colloidal sphere due to the presence of its double layer: i) the force F W that results from the temperature dependence of the internal electrostatic energy W of the double layer, ii) the electric force Fel with which the temperature-induced non-spherically symmetric double-layer potential acts on the surface charges of the colloidal sphere and iii) the solvent-friction force Fsol on the surface of the colloidal sphere due to the solvent flow that is induced in the double layer because of its asymmetry. The force F W will be shown to reproduce predictions based on irreversible-thermodynamics considerations. The other two forces Fel and Fsol depend on the details of the temperature-gradient-induced asymmetry of the double-layer structure which cannot be included in an irreversible-thermodynamics treatment. Explicit expressions for the thermal diffusion coefficient are derived for arbitrary double-layer thickness, which complement the irreversible-thermodynamics result through the inclusion of the thermophoretic velocity resulting from the electric- and solvent-friction force.

  15. Vibrational investigations of guanine, thioguanine and their singly charged cations and anions

    NASA Astrophysics Data System (ADS)

    Singh, R.; Yadav, R. A.

    2017-01-01

    The complete vibrational studies have been done with help of quantum mechanics for the neutral Guanine (Gua) and Thioguanine (TGua) molecules and their singly charged cations and anions employing the B3LYP/6-311++G** method. Neutral Thioguanine and cations of Guanine and Thioguanine show planar structures and belong to Cs point group symmetry while the neutral Guanine and anions of Guanine and Thioguanine possess non-planar structure with C1 point group symmetry. Vibrational studies of ionic radicals of Gua and its thio- derivative are not available in literatures. Such extensive studies have been attempted for the first time. The normal modes of all the species have been assigned on the basis using potential energy distributions (PEDs) using GAR2PED software. The PEDs have also been calculated to make a conspicuous assignment as animation available in GaussView is not a guarantee for correct normal mode assignment. Charge transfer occurs in the molecule have been shown by the calculated highest occupied molecular orbital—lowest unoccupied molecular orbital (HOMO-LUMO) energies. The mapping of electron density iso-surface with electrostatic potential, has been carried out to get the information about the size, shape, charge density distribution and site of chemical reactivity of the molecule. The electronic properties HOMO and LUMO energies have been measured. The energy gap from HOMO to LUMO of the Gua is 5.0547 eV and TGua 4.0743 eV.

  16. Field-induced conductance switching by charge-state alternation in organometallic single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Schwarz, Florian; Kastlunger, Georg; Lissel, Franziska; Egler-Lucas, Carolina; Semenov, Sergey N.; Venkatesan, Koushik; Berke, Heinz; Stadler, Robert; Lörtscher, Emanuel

    2016-02-01

    Charge transport through single molecules can be influenced by the charge and spin states of redox-active metal centres placed in the transport pathway. These intrinsic properties are usually manipulated by varying the molecule's electrochemical and magnetic environment, a procedure that requires complex setups with multiple terminals. Here we show that oxidation and reduction of organometallic compounds containing either Fe, Ru or Mo centres can solely be triggered by the electric field applied to a two-terminal molecular junction. Whereas all compounds exhibit bias-dependent hysteresis, the Mo-containing compound additionally shows an abrupt voltage-induced conductance switching, yielding high-to-low current ratios exceeding 1,000 at bias voltages of less than 1.0 V. Density functional theory calculations identify a localized, redox-active molecular orbital that is weakly coupled to the electrodes and closely aligned with the Fermi energy of the leads because of the spin-polarized ground state unique to the Mo centre. This situation provides an additional slow and incoherent hopping channel for transport, triggering a transient charging effect in the entire molecule with a strong hysteresis and large high-to-low current ratios.

  17. Surface Charge Density Determination of Single Conical Nanopores based on Normalized Ion Current Rectification

    SciTech Connect

    Liu, J.; Kvetny, M.; Feng, J.; Wang, D.; Wu, B.; Brown, W.; Wang, G.

    2011-01-01

    Current rectification is well known in ion transport through nanoscale pores and channel devices. The measured current is affected by both the geometry and fixed interfacial charges of the nanodevices. In this article, an interesting trend is observed in steady-state current–potential measurements using single conical nanopores. A threshold low-conductivity state is observed upon the dilution of electrolyte concentration. Correspondingly, the normalized current at positive bias potentials drastically increases and contributes to different degrees of rectification. This novel trend at opposite bias polarities is employed to differentiate the ion flux affected by the fixed charges at the substrate–solution interface (surface effect), with respect to the constant asymmetric geometry (volume effect). The surface charge density (SCD) of individual nanopores, an important physical parameter that is challenging to measure experimentally and is known to vary from one nanopore to another, is directly quantified by solving Poisson and Nernst–Planck equations in the simulation of the experimental results. The flux distribution inside the nanopore and the SCD of individual nanopores are reported. The respective diffusion and migration translocations are found to vary at different positions inside the nanopore. This knowledge is believed to be important for resistive pulse sensing applications because the detection signal is determined by the perturbation of the ion current by the analytes.

  18. Surface Charge Density Determination of Single Conical Nanopores Based on Normalized Ion Current Rectification

    SciTech Connect

    Liu, Juan; Kvetny, Maksim; Feng, Jingyu; Wang, Dengchao; Wu, Baohua; Brown, Warren; Wang, Gangli

    2011-12-19

    Current rectification is well-known in ion transport through nanoscale pores and channel devices. The measured current is affected by both the geometry and fixed interfacial charges of the nanodevices. In this paper, an interesting trend is observed in steady-state current-potential measurements using single conical nanopores. A threshold low conductivity state is observed upon the dilution of electrolyte concentration. Correspondingly, the normalized current at positive bias potentials drastically increases and contributes to different degree of rectification. The novel opposite trend at opposite bias polarities is employed to differentiate the ion flux affected by the fixed charges at the substrate-solution interface (surface effect), with respect to the constant asymmetric geometry (volume effect). The surface charge density (SCD) of individual nanopores, an important physical parameter that is challenging to measure experimentally and is known to vary from one nanopore to another, are directly quantified by solving Poisson and Nernst-Planck equations in the simulation of the experimental results. Flux distribution inside the nanopore and SCD of individual nanopores are reported. The respective diffusion and migration translocations are found to vary at different positions inside the nanopore. The knowledge is believed important for resistive pulse sensing applications, as the detection signal is determined by the perturbation of ion current by the analytes.

  19. Single electron charging in deterministically positioned InAs/InP quantum dots

    NASA Astrophysics Data System (ADS)

    Reimer, M. E.; Dalacu, D.; Lapointe, J.; Poole, P. J.; Kim, D.; Aers, G. C.; McKinnon, W. R.; Williams, R. L.

    2009-01-01

    We demonstrate precise control of electron charging within a single deterministically positioned InAs/InP quantum dot emitting in the telecommunications band around 1500 nm. Photolumine-scence emission as a function of vertical electric field is used to monitor the electron number within the dot. From Stark shift spectroscopy, we extract strength and orientation for the built-in dipole moment that suggests a uniform InAs dot composition and a configuration in which the electron lies above the hole at zero electric field. The scalable gating technology we employ to electrically contact individual prepositioned quantum dots promises arrays of initialized single spins that can be used for fiber-based quantum information applications.

  20. Spiro-OMeTAD single crystals: Remarkably enhanced charge-carrier transport via mesoscale ordering

    PubMed Central

    Shi, Dong; Qin, Xiang; Li, Yuan; He, Yao; Zhong, Cheng; Pan, Jun; Dong, Huanli; Xu, Wei; Li, Tao; Hu, Wenping; Brédas, Jean-Luc; Bakr, Osman M.

    2016-01-01

    We report the crystal structure and hole-transport mechanism in spiro-OMeTAD [2,2′,7,7′-tetrakis(N,N-di-p-methoxyphenyl-amine)9,9′-spirobifluorene], the dominant hole-transporting material in perovskite and solid-state dye-sensitized solar cells. Despite spiro-OMeTAD’s paramount role in such devices, its crystal structure was unknown because of highly disordered solution-processed films; the hole-transport pathways remained ill-defined and the charge carrier mobilities were low, posing a major bottleneck for advancing cell efficiencies. We devised an antisolvent crystallization strategy to grow single crystals of spiro-OMeTAD, which allowed us to experimentally elucidate its molecular packing and transport properties. Electronic structure calculations enabled us to map spiro-OMeTAD’s intermolecular charge-hopping pathways. Promisingly, single-crystal mobilities were found to exceed their thin-film counterparts by three orders of magnitude. Our findings underscore mesoscale ordering as a key strategy to achieving breakthroughs in hole-transport material engineering of solar cells. PMID:27152342

  1. Single ionization in highly charged ion-atom collisions at low to intermediate velocities

    NASA Astrophysics Data System (ADS)

    Abdallah, Mohammad Abdallah

    1998-11-01

    Single electron ejection from neutral targets (He and Ne) by the impact of low to highly charged ions (p, He+,/ Ne+,/ He2+,/ C6+,/ O8+, and Ne10+) at low to intermediate impact velocities is studied. A novel technique of electron momentum imaging is implemented. In this technique two-dimensional electron momentum distributions are produced in coincidence with recoil ions and projectile ions. In first generation experiments we studied the ejected electron momentum distributions without analyzing recoil ions momentum. This series of experiments revealed a charge-state dependence and velocity dependence that are contradictory to a dominant saddle point ionization mechanism at intermediate velocities. It showed a possibility of an agreement with a saddle centered distributions for low charge states at low collision velocities. To pursue the problem in more detail, we developed a second generation spectrometer which allowed us to fully determine the recoil ions momentum. This allowed us to determine the collision plane, energy loss (Q-value), and impact parameter for every collision that resulted in a single (target) electron ejection. This series of experiments revealed for the first time very marked structure in electron spectra that were impossible to observe in other experiments. These structures indicate the quasi-molecular nature of the collision process even at velocities comparable to the electron 'classical' orbital velocity. For the collisions of p, He+, and He2+ with He, a π-orbital shape of the electron momentum distribution is observed. This indicates the importance of the rotational coupling 2p/sigma/to2p/pi in the initial promotion of the ground state electron. This is followed by further promotions to the continuum. This agrees with the 'classical' description implied by the saddle-point ionization mechanism picture.

  2. Optimization for Single-Spike X-Ray FELs at LCLS with a Low Charge Beam

    SciTech Connect

    Wang, L.; Ding, Y.; Huang, Z.; /SLAC

    2011-12-14

    The Linac Coherent Light Source is an x-ray free-electron laser at the SLAC National Accelerator Laboratory, which is operating at x-ray wavelengths of 20-1.2 Angstrom with peak brightness nearly ten orders of magnitude beyond conventional synchrotron radiation sources. At the low charge operation mode (20 pC), the x-ray pulse length can be <10 fs. In this paper we report our numerical optimization and simulations to produce even shorter x-ray pulses by optimizing the machine and undulator setup at 20 pC charge. In the soft x-ray regime, with combination of slotted-foil or undulator taper, a single spike x-ray pulse is achievable with peak FEL power of a few 10s GW. Linac Coherent Light Source (LCLS), the world's first hard x-ray Free electron laser (FEL), has started operation since 2009. With nominal operation charge of 250 pC, the generated x-ray pulse length is from 70 fs to a few hundred fs. This marks the beginning of a new era of ultrashort x-ray sciences. In addition, a low charge (20pC) operation mode has also been established. Since the collective effects are reduced at the low charge mode, we can increase the compression factor and still achieve a few kA peak current. The expected electron beam and x-ray pulses are less than 10 fs. There are growing interests in even shorter x-ray pulses, such as fs to sub-fs regime. One of the simple solutions is going to even lower charge. As discussed, single-spike x-ray pulses can be generated using 1 pC charge. However, this charge level is out of the present LCLS diagnostic range. 20 pC is a reasonable operation charge at LCLS, based on the present diagnostic system. At 20 pC in the soft x-ray wavelength regime, we have experimentally demonstrated that FEL can work at undercompression or over-compression mode, such as 1 degree off the full-compression; at full-compression, however, there is almost no lasing. In hard x-ray wavelength regime, we observed that there are reasonable photons generated even at full

  3. Mutagenesis and nuclear magnetic resonance analyses of the fusion peptide of Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus F protein.

    PubMed

    Tan, Ying; Jiang, Ling; Wang, Manli; Yin, Feifei; Deng, Fei; Liu, Maili; Hu, Zhihong; Wang, Hualin

    2008-08-01

    The entry of enveloped viruses into cells is normally mediated by fusion between viral and cellular membranes, in which the fusion peptide plays a crucial role. The fusion peptides of group II nucleopolyhedrovirus (NPV) F proteins are quite conserved, with a hydrophobic region located at the N terminal of the F(1) fragment. For this report, we used mutagenesis and nuclear magnetic resonance (NMR) to study the structure and function of the fusion peptide of the Helicoverpa armigera single-nucleocapsid NPV (HearNPV) F protein (HaF). Five mutations in the fusion peptide of HaF, N(1)G, N(1)L, I(2)N, G(3)L, and D(11)L, were generated separately, and the mutated f genes were transformed into the f-null HearNPV bacmid. The mutations N(1)L, I(2)N, and D(11)L were found to completely abolish the ability of the recombinant bacmids to produce infectious budded virus, while the mutations N(1)G and G(3)L did not. The low-pH-induced envelope fusion assay demonstrated that the N(1)G substitution increased the fusogenicity of HaF, while the G(3)L substitution reduced its fusogenicity. NMR spectroscopy was used to determine the structure of a synthetic fusion peptide of HaF in the presence of sodium dodecyl sulfate micelles at pH 5.0. The fusion peptide appeared to be an amphiphilic structure composed of a flexible coil in the N terminus from N(1) to N(5), a 3(10)-helix from F(6) to G(8), a turn at S(9), and a regular alpha-helix from V(10) to D(19). The data provide the first NMR structure of a baculovirus fusion peptide and allow us to further understand the relationship of structure and function of the fusion peptide.

  4. Ion-induced nucleation of dibutyl phthalate vapors on spherical and nonspherical singly and multiply charged polyethylene glycol ions.

    PubMed

    Nasibulin, Albert G; de la Mora, Juan Fernandez; Kauppinen, Esko I

    2008-02-14

    Dibutyl phthalate vapor nucleation induced by positive polyethylene glycol (PEG) ions with controlled sizes and charges was experimentally studied. The ions were produced by electrospray ionization, classified in a high-resolution differential mobility analyzer, and studied in a nano condensation nucleus counter of the mixing type. Ionic radii of PEG varied from 0.52 to 1.56 nm, including from singly to quadruply charged ions. Some of these ions are fully stretched chains, other are spherical, and others have intermediate forms, all of them having been previously characterized by mobility and mass spectrometry studies. Activation of PEG1080(+2) requires a supersaturation almost as high as that required for small singly charged ions and higher than for PEG1080(+). This anomaly is explained by the Coulombic stretching of the ion into a long chain, where the two charged centers appear to be relatively decoupled from each other. The critical supersaturation for singly charged spherical ions falls below Thomson's (capillary) theory and even below the already low values seen previously for tetraheptyl ammonium bromide clusters. Spherical PEG4120(+2) falls close to the Thomson curve. The trends observed for slightly nonspherical PEG4120(+3) and highly nonspherical (but not quite linear) PEG4120(+4) are intermediate between those of multiply charged spheres and small singly charged ions.

  5. Gas-phase doubly charged complexes of cyclic peptides with copper in +1, +2 and +3 formal oxidation states: formation, structures and electron capture dissociation.

    PubMed

    Afonso, Carlos; Tabet, Jean-Claude; Giorgi, Gianluca; Tureček, František

    2012-02-01

    Copper complexes with a cyclic D-His-β-Ala-L-His-L-Lys and all-L-His-β-Ala-His-Lys peptides were generated by electrospray which were doubly charged ions that had different formal oxidation states of Cu(I), Cu(II) and Cu(III) and different protonation states of the peptide ligands. Electron capture dissociation showed no substantial differences between the D-His and L-His complexes. All complexes underwent peptide cross-ring cleavages upon electron capture. The modes of ring cleavage depended on the formal oxidation state of the Cu ion and peptide protonation. Density functional theory (DFT) calculations, using the B3LYP with an effective core potential at Cu and M06-2X functionals, identified several precursor ion structures in which the Cu ion was threecoordinated to pentacoordinated by the His and Lys side-chain groups and the peptide amide or enolimine groups. The electronic structure of the formally Cu(III) complexes pointed to an effective Cu(I) oxidation state with the other charge residing in the peptide ligand. The relative energies of isomeric complexes of the [Cu(c-HAHK + H)](2+) and [Cu(c-HAHK - H)](2+) type with closed electronic shells followed similar orders when treated by the B3LYP and M06-2X functionals. Large differences between relative energies calculated by these methods were obtained for open-shell complexes of the [Cu(c-HAHK)](2+) type. Charge reduction resulted in lowering the coordination numbers for some Cu complexes that depended on the singlet or triplet spin state being formed. For [Cu(c-HAHK - H)](2+) complexes, solution H/D exchange involved only the N-H protons, resulting in the exchange of up to seven protons, as established by ultra-high mass resolution measurements. Contrasting the experiments, DFT calculations found the lowest energy structures for the gas-phase ions that were deprotonated at the peptide C(α) positions.

  6. The Fate of a Normal Human Cell Traversed by a Single Charged Particle

    PubMed Central

    Fournier, C.; Zahnreich, S.; Kraft, D.; Friedrich, T.; Voss, K.-O.; Durante, M.; Ritter, S.

    2012-01-01

    The long-term “fate” of normal human cells after single hits of charged particles is one of the oldest unsolved issues in radiation protection and cellular radiobiology. Using a high-precision heavy-ion microbeam we could target normal human fibroblasts with exactly one or five carbon ions and measured the early cytogenetic damage and the late behaviour using single-cell cloning. Around 70% of the first cycle cells presented visible aberrations in mFISH after a single ion traversal, and about 5% of the cells were still able to form colonies. In one third of selected high-proliferative colonies we observed clonal (radiation-induced) aberrations. Terminal differentiation and markers of senescence (PCNA, p16) in the descendants of cells traversed by one carbon ion occurred earlier than in controls, but no evidence of radiation-induced chromosomal instability was found. We conclude that cells surviving single-ion traversal, often carrying clonal chromosome aberrations, undergo accelerated senescence but maintain chromosomal stability. PMID:22966418

  7. The Fate of a Normal Human Cell Traversed by a Single Charged Particle

    NASA Astrophysics Data System (ADS)

    Fournier, C.; Zahnreich, S.; Kraft, D.; Friedrich, T.; Voss, K.-O.; Durante, M.; Ritter, S.

    2012-09-01

    The long-term ``fate'' of normal human cells after single hits of charged particles is one of the oldest unsolved issues in radiation protection and cellular radiobiology. Using a high-precision heavy-ion microbeam we could target normal human fibroblasts with exactly one or five carbon ions and measured the early cytogenetic damage and the late behaviour using single-cell cloning. Around 70% of the first cycle cells presented visible aberrations in mFISH after a single ion traversal, and about 5% of the cells were still able to form colonies. In one third of selected high-proliferative colonies we observed clonal (radiation-induced) aberrations. Terminal differentiation and markers of senescence (PCNA, p16) in the descendants of cells traversed by one carbon ion occurred earlier than in controls, but no evidence of radiation-induced chromosomal instability was found. We conclude that cells surviving single-ion traversal, often carrying clonal chromosome aberrations, undergo accelerated senescence but maintain chromosomal stability.

  8. Single housing during early adolescence causes time-, area- and peptide-specific alterations in endogenous opioids of rat brain.

    PubMed

    Granholm, L; Roman, E; Nylander, I

    2015-01-01

    A number of experimental procedures require single housing to assess individual behaviour and physiological responses to pharmacological treatments. The endogenous opioids are closely linked to social interaction, especially early in life, and disturbance in the social environment may affect opioid peptides and thereby confound experimental outcome. The aim of the present study was to examine time-dependent effects of single housing on opioid peptides in rats. Early adolescent Sprague Dawley rats (post-natal day 22) were subjected to either prolonged (7 days) or short (30 min) single housing. Several brain regions were dissected and immunoreactive levels of Met-enkephalin-Arg(6) Phe(7) (MEAP), dynorphin B and nociception/orphanin FQ, as well as serum corticosterone were measured using RIA. Prolonged single housing reduced immunoreactive MEAP in hypothalamus, cortical regions, amygdala, substantia nigra and periaqueductal grey. Short single housing resulted in an acute stress response as indicated by high levels of corticosterone, accompanied by elevated immunoreactive nociceptin/orphanin FQ in medial prefrontal cortex, nucleus accumbens and amygdala. Neither short nor prolonged single housing affected dynorphin B. Disruption in social environmental conditions of rats, through single housing during early adolescence, resulted in time-, area- and peptide-specific alterations in endogenous opioids in the brain. These results provide further evidence for an association between early life social environment and opioids. Furthermore, the results have implications for experimental design; in any pharmacological study involving opioid peptides, it is important to distinguish between effects induced by housing and treatment. This article is part of a themed section on Opioids: New Pathways to Functional Selectivity. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue-2. © 2014 The Authors. British Journal of Pharmacology

  9. Single housing during early adolescence causes time-, area- and peptide-specific alterations in endogenous opioids of rat brain

    PubMed Central

    Granholm, L; Roman, E; Nylander, I

    2015-01-01

    BACKGROUND AND PURPOSE A number of experimental procedures require single housing to assess individual behaviour and physiological responses to pharmacological treatments. The endogenous opioids are closely linked to social interaction, especially early in life, and disturbance in the social environment may affect opioid peptides and thereby confound experimental outcome. The aim of the present study was to examine time-dependent effects of single housing on opioid peptides in rats. EXPERIMENTAL APPROACH Early adolescent Sprague Dawley rats (post-natal day 22) were subjected to either prolonged (7 days) or short (30 min) single housing. Several brain regions were dissected and immunoreactive levels of Met-enkephalin-Arg6Phe7 (MEAP), dynorphin B and nociception/orphanin FQ, as well as serum corticosterone were measured using RIA. KEY RESULTS Prolonged single housing reduced immunoreactive MEAP in hypothalamus, cortical regions, amygdala, substantia nigra and periaqueductal grey. Short single housing resulted in an acute stress response as indicated by high levels of corticosterone, accompanied by elevated immunoreactive nociceptin/orphanin FQ in medial prefrontal cortex, nucleus accumbens and amygdala. Neither short nor prolonged single housing affected dynorphin B. CONCLUSIONS AND IMPLICATIONS Disruption in social environmental conditions of rats, through single housing during early adolescence, resulted in time-, area- and peptide-specific alterations in endogenous opioids in the brain. These results provide further evidence for an association between early life social environment and opioids. Furthermore, the results have implications for experimental design; in any pharmacological study involving opioid peptides, it is important to distinguish between effects induced by housing and treatment. LINKED ARTICLES This article is part of a themed section on Opioids: New Pathways to Functional Selectivity. To view the other articles in this section visit http

  10. Charge transfer effects, thermo and photochromism in single crystal CVD synthetic diamond.

    PubMed

    Khan, R U A; Martineau, P M; Cann, B L; Newton, M E; Twitchen, D J

    2009-09-09

    We report on the effects of thermal treatment and ultraviolet irradiation on the point defect concentrations and optical absorption profiles of single crystal CVD synthetic diamond. All thermal treatments were below 850 K, which is lower than the growth temperature and unlikely to result in any structural change. UV-visible absorption spectroscopy measurements showed that upon thermal treatment (823 K), various broad absorption features diminished: an absorption band at 270 nm (used to deduce neutral single substitutional nitrogen (N(S)(0)) concentrations) and also two broad features centred at approximately 360 and 520 nm. Point defect centre concentrations as a function of temperature were also deduced using electron paramagnetic resonance (EPR) spectroscopy. Above ∼500 K, we observed a decrease in the concentration of N(S)(0) centres and a concomitant increase in the negatively charged nitrogen-vacancy-hydrogen (NVH) complex (NVH(-)) concentration. Both transitions exhibited an activation energy between 0.6 and 1.2 eV, which is lower than that for the N(S)(0) donor (∼1.7 eV). Finally, it was found that illuminating samples with intense short-wave ultraviolet light recovered the N(S)(0) concentration and also the 270, 360 and 520 nm absorption features. From these results, we postulate a valence band mediated charge transfer process between NVH and single nitrogen centres with an acceptor trap depth for NVH of 0.6-1.2 eV. Because the loss of N(S)(0) concentration is greater than the increase in NVH(-) concentration we also suggest the presence of another unknown acceptor existing at a similar energy to NVH. The extent to which the colour in CVD synthetic diamond is dependent on prior history is discussed.

  11. Single-Molecule Protein Folding: A Study of the Surface-Mediated Conformational Dynamics of a Model Amphipathic Peptide

    NASA Astrophysics Data System (ADS)

    Cunningham, Joy; English, Douglas

    2004-03-01

    Most surface-active polypeptides, composed of 10-50 amino acids, are devoid of well-defined tertiary structure. The conformation of these proteins is greatly dependent upon their environment and may assume totally different characteristics in an aqueous environment, in a detergent micelle, or in an organic solvent. Most antimicrobial peptides are helix-forming and are activated upon interaction with a membrane-mimicking environment. We are seeking to physically characterize the mechanism of membrane-peptide interaction through studying a simple model peptide, MT-1. MT-1 was designed as a nonhomologous analogue of melittin, the principle component in bee venom. We are using single molecule spectroscopy to examine the induction of secondary structure upon interaction of MT-1 with various membrane-mimicking interfaces. Specifically, we monitor coil-to-helix transition through single molecule fluorescence resonance energy transfer (sm-FRET) to determine conformational distributions of folded and unfolded peptides at an interface. Studies with MT-1 will focus upon the biologically relevant issues of orientation, aggregation, and folding at surfaces using both ensemble and single molecule experiments.

  12. Synthetic Peptide Vaccine Development: Designing Dual Epitopes into a Single Pilin Peptide Immunogen Generates Antibody Cross-reactivity between Two Strains of Pseudomonas aeruginosa

    PubMed Central

    Hackbarth, Clifton; Hodges, Robert S.

    2010-01-01

    One of the main challenges of Pseudomonas aeruginosa (P. aeruginosa) vaccine development is the design of an antigen that elicits cross-reactive antibodies against multiple virulent strains. Using a rational design approach, we have developed a single 17-residue peptide immunogen that generates antibodies that target the receptor binding domain (RBD) of the type IV pilus of more than one strain of P. aeruginosa. Using the RBD sequence, of native strain PAO as a template, we have systematically changed up to five residues in the PAO sequence of the peptide immunogen, into that of the PAK sequence. We show by indirect and competitive ELISA, that the mutant peptide immunogens elicit the development of polyclonal sera that is cross-reactive to both native strain PAO and PAK pilin. We further show that there are at least two separate antibody populations in the polyclonal sera that possess closely-related epitopes but which are each strain specific. Moreover, part of the epitope for the PAO specific antibodies consists of several residues outside the disulfide loop of the receptor binding domain. This allows us to create two unique epitopes within the same receptor binding domain sequence. PMID:20807222

  13. Theoretical Studies of the Interaction of Excitons with Charged Impurities in Single-Walled Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Tayo, Benjamin O.

    A fundamental theory of the electronic and optical properties of semiconductors shows the importance of impurities, which are often unavoidable and can alter intrinsic properties of semiconductor materials substantially. While the subject of impurity doping is well understood in bulk semiconductors, the role and impact of doping in low dimensional materials like carbon nanotubes is still under investigation and there exists significant debate on the exact nature of electronic impurity levels in single-walled carbon nanotubes associated with adatoms. In this work, we address the role of impurities in single-walled carbon nanotubes. A simple model is developed for studying the interaction of bright (singlet) excitons in semiconducting single-wall nanotubes with charged impurities. The model reveals a red shift in the energy of excitonic states in the presence of an impurity, thus indicating binding of excitons in the impurity potential well. Signatures of several bound states were found in the absorption spectrum below the onset of excitonic optical transitions in the bare nanotube. The dependence of the binding energy on the model parameters, such as impurity charge and position, was determined and analytical fits were derived for a number of tubes of different diameter. The nanotube family splitting is seen in the diameter dependence, gradually decreasing with the diameter. By calculating the partial absorption coefficient for a small segment of nanotube the local nature of the wave function of the bound states was derived. Our studies provide useful insights into the role of the physical environment (here, a charged impurity atom) in the manipulation of the excited states of carbon nanotubes. We performed very detailed calculations of the electronic and optical properties of carbon nanotubes in the presence of an immobile impurity atom, thus going beyond previous many-body perturbation theory (MBPT) studies in which the carbon nanotubes were considered in vacuum

  14. Plantaricin A, a cationic peptide produced by Lactobacillus plantarum, permeabilizes eukaryotic cell membranes by a mechanism dependent on negative surface charge linked to glycosylated membrane proteins.

    PubMed

    Sand, Sverre L; Nissen-Meyer, Jon; Sand, Olav; Haug, Trude M

    2013-02-01

    Lactobacillus plantarum C11 releases plantaricin A (PlnA), a cationic peptide pheromone that has a membrane-permeabilizing, antimicrobial effect. We have previously shown that PlnA may also permeabilize eukaryotic cells, with a potency that differs between cell types. It is generally assumed that cationic antimicrobial peptides exert their effects through electrostatic attraction to negatively charged phospholipids in the membrane. The aim of the present study was to investigate if removal of the negative charge linked to glycosylated proteins at the cell surface reduces the permeabilizing potency of PlnA. The effects of PlnA were tested on clonal rat anterior pituitary cells (GH(4) cells) using patch clamp and microfluorometric techniques. In physiological extracellular solution, GH(4) cells are highly sensitive to PlnA, but the sensitivity was dramatically reduced in solutions that partly neutralize the negative surface charge of the cells, in agreement with the notion that electrostatic interactions are probably important for the PlnA effects. Trypsination of cells prior to PlnA exposure also rendered the cells less sensitive to the peptide, suggesting that negative charges linked to membrane proteins are involved in the permeabilizing action. Finally, pre-exposure of cells to a mixture of enzymes that split carbohydrate residues from the backbone of glycosylated proteins also impeded the PlnA-induced membrane permeabilization. We conclude that electrostatic attraction between PlnA and glycosylated membrane proteins is probably an essential first step before PlnA can interact with membrane phospholipids. Deviating glycosylation patterns may contribute to the variation in PlnA sensitivity of different cell types, including cancerous cells and their normal counterparts.

  15. Formation of peptides from amino acids by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles

    NASA Technical Reports Server (NTRS)

    Nakashima, T.; Fox, S. W.

    1981-01-01

    The synthesis of peptides from individual amino acids or pairs of amino acids and ATP in the presence of catalysis by nucleoproteinoid microparticles is investigated. Experiments were performed with suspensions formed from the condensation of lysine-rich and acidic proteinoids with polyadenylic acid, to which were added glycine, phenylalanine, proline, lysine or glycine-phenylalanine mixtures, and ATP either at once or serially. Peptide yields are found to be greatest for equal amounts of acidic and basic proteinoids. The addition of imidazole is found to alter the preference of glycine-phenylalanine mixtures to form mixed heteropeptides rather than homopeptides. A rapid ATP decay in the peptide synthesis reaction is observed, and a greater yield is obtained for repeated small additions than for a single addition of ATP. The experimental system has properties similar to modern cells, and represents an organizational unit ready for the evolution of associated biochemical pathways.

  16. Formation of peptides from amino acids by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles

    NASA Technical Reports Server (NTRS)

    Nakashima, T.; Fox, S. W.

    1981-01-01

    The synthesis of peptides from individual amino acids or pairs of amino acids and ATP in the presence of catalysis by nucleoproteinoid microparticles is investigated. Experiments were performed with suspensions formed from the condensation of lysine-rich and acidic proteinoids with polyadenylic acid, to which were added glycine, phenylalanine, proline, lysine or glycine-phenylalanine mixtures, and ATP either at once or serially. Peptide yields are found to be greatest for equal amounts of acidic and basic proteinoids. The addition of imidazole is found to alter the preference of glycine-phenylalanine mixtures to form mixed heteropeptides rather than homopeptides. A rapid ATP decay in the peptide synthesis reaction is observed, and a greater yield is obtained for repeated small additions than for a single addition of ATP. The experimental system has properties similar to modern cells, and represents an organizational unit ready for the evolution of associated biochemical pathways.

  17. Nanocapillary electrokinetic tracking for monitoring charge fluctuations on a single nanoparticle.

    PubMed

    Faez, Sanli; Samin, Sela; Baasanjav, Dashdeleg; Weidlich, Stefan; Schmidt, Markus; Mosk, Allard P

    2016-12-12

    We introduce nanoCapillary Electrokinetic Tracking (nanoCET), an optofluidic platform for continuously measuring the electrophoretic mobility of a single colloidal nanoparticle or macromolecule in vitro with millisecond time resolution and high charge sensitivity. This platform is based on using a nanocapillary optical fiber in which liquids may flow inside a channel embedded inside the light-guiding core and nanoparticles are tracked using elastic light scattering. Using this platform we have experimentally measured the electrophoretic mobility of 60 nm gold nanoparticles in an aqueous environment. Further, using numerical simulations, we demonstrate the underlying electrokinetic dynamics inside the nanocapillary and the necessary steps for extending this method to probing single biomolecules, which can be achieved with existing technologies. This achievement will immensely facilitate the daunting challenge of monitoring biochemical or catalytic reactions on a single entity over a wide range of timescales. The unique measurement capabilities of this platform pave the way for a wide range of discoveries in colloid science, analytical biochemistry, and medical diagnostics.

  18. Single bunch transverse instability in a circular accelerator with chromaticity and space charge

    NASA Astrophysics Data System (ADS)

    Balbekov, V.

    2015-10-01

    The transverse instability of a bunch in a circular accelerator is elaborated in this paper. A new tree-modes model is proposed and developed to describe the most unstable modes of the bunch. This simple and flexible model includes chromaticity and space charge, and can be used with any bunch and wake forms. The dispersion equation for the bunch eigentunes is obtained in form of a third-order algebraic equation. The known head-tail and TMCI modes appear as the limiting cases which are distinctly bounded at zero chromaticity only. It is shown that the instability parameters depend only slightly on the bunch model but they are rather sensitive to the wake shape. In particular, space charge effects are investigated in the paper and it is shown that their influence depends on sign of wake field enhancing the bunch stability if the wake is negative. The resistive wall wake is considered in detail including a comparison of single and collective effects. A comparison of the results with earlier publications is carried out.

  19. Single bunch transverse instability in a circular accelerator with chromaticity and space charge

    DOE PAGES

    Balbekov, V.

    2015-10-21

    The transverse instability of a bunch in a circular accelerator is elaborated in this paper. A new tree-modes model is proposed and developed to describe the most unstable modes of the bunch. This simple and flexible model includes chromaticity and space charge, and can be used with any bunch and wake forms. The dispersion equation for the bunch eigentunes is obtained in form of a third-order algebraic equation. The known head-tail and TMCI modes appear as the limiting cases which are distinctly bounded at zero chromaticity only. It is shown that the instability parameters depend only slightly on the bunchmore » model but they are rather sensitive to the wake shape. In particular, space charge effects are investigated in the paper and it is shown that their influence depends on sign of wake field enhancing the bunch stability if the wake is negative. In addition, the resistive wall wake is considered in detail including a comparison of single and collective effects. A comparison of the results with earlier publications is carried out.« less

  20. Single bunch transverse instability in a circular accelerator with chromaticity and space charge

    SciTech Connect

    Balbekov, V.

    2015-10-21

    The transverse instability of a bunch in a circular accelerator is elaborated in this paper. A new tree-modes model is proposed and developed to describe the most unstable modes of the bunch. This simple and flexible model includes chromaticity and space charge, and can be used with any bunch and wake forms. The dispersion equation for the bunch eigentunes is obtained in form of a third-order algebraic equation. The known head-tail and TMCI modes appear as the limiting cases which are distinctly bounded at zero chromaticity only. It is shown that the instability parameters depend only slightly on the bunch model but they are rather sensitive to the wake shape. In particular, space charge effects are investigated in the paper and it is shown that their influence depends on sign of wake field enhancing the bunch stability if the wake is negative. In addition, the resistive wall wake is considered in detail including a comparison of single and collective effects. A comparison of the results with earlier publications is carried out.

  1. Probing the origin of structural stability of single and double stapled p53 peptide analogs bound to MDM2.

    PubMed

    Guo, Zuojun; Streu, Kristina; Krilov, Goran; Mohanty, Udayan

    2014-06-01

    The stabilization of secondary structure is believed to play an important role in the peptide-protein binding interaction. In this study, the α-helical conformation and structural stability of single and double stapled all-hydrocarbon cross-linked p53 peptides when bound and unbound to MDM2 are investigated. We determined the effects of the peptide sequence, the stereochemistry of the cross-linker, the conformation of the double bond in the alkene bridge, and the length of the bridge, to the relative stability of the α-helix structure. The binding affinity calculations by WaterMap provided over one hundred hydration sites in the MDM2 binding pocket where water density is greater than twice that of the bulk, and the relative value of free energy released by displacing these hydration sites. In agreement with the experimental data, potentials of mean force obtained by weighted histogram analysis methods indicated the order of peptides from lowest to highest binding affinity. Our study provides a comprehensive rationalization of the relationship between peptide stapling strategy, the secondary structural stability, and the binding affinity of p53/MDM2 complex. We hope our efforts can help to further the development of a new generation p53/MDM2 inhibitors that can reactivate the function of p53 as tumor suppressor gene.

  2. Development of single vial kits for preparation of (68)Ga-labelled peptides for PET imaging of neuroendocrine tumours.

    PubMed

    Mukherjee, Archana; Pandey, Usha; Chakravarty, Rubel; Sarma, Haladhar Dev; Dash, Ashutosh

    2014-08-01

    The present work was aimed at the formulation and evaluation of freeze-dried kits of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA)-peptides for the preparation of (68)Ga-labelled peptides for PET imaging of neuroendocrine tumours. The (68)GaCl3 was obtained from the locally produced nanoceria-PAN, composite-sorbent-based (68)Ge/(68)Ga generator. Single vial kits of somatostatin analogues DOTA-[Tyr(3)]-octreotide (DOTA-TOC), DOTA-[NaI(3)]-octreotide (DOTA-NOC) and DOTA-Tyr(3)-Thre(8)-octreotide (DOTA-TATE) were formulated. Optimization of radiolabelling with (68)Ga from the in-house generator, characterization, long term evaluation of stability of kits and bioevaluation studies in animals was carried out. DOTA-TOC, DOTA-NOC and DOTA-TATE kits could be successfully formulated. Consistently high radiochemical yields (>95 %) were obtained on radiolabelling with (68)Ga. The radiolabelled peptides exhibited excellent in vitro stability. Biodistribution studies in normal non-tumour bearing Swiss mice revealed fast clearance of activity via renal route as reported for the respective peptides. Availability of ready to use DOTA-peptide kits in conjunction with (68)Ge/(68)Ga generators would pave way for the establishment of (68)Ga radiopharmacy, a long-felt need of the nuclear medicine community.

  3. Impact of single-residue mutations on the structure and function of ovispirin/novispirin antimicrobial peptides.

    PubMed

    Sawai, Monali V; Waring, Alan J; Kearney, William R; McCray, Paul B; Forsyth, William R; Lehrer, Robert I; Tack, Brian F

    2002-03-01

    We studied three model antibacterial peptides that resembled the N-terminal 18 amino acids of SMAP-29, an alpha-helical, antimicrobial peptide of sheep. Although the parent compound, ovispirin-1 (KNLRR IIRKI IHIIK KYG), was potently antimicrobial, it was also highly cytotoxic to human epithelial cells and hemolytic for human erythrocytes. Single residue substitutions to ovispirin-1 yielded two substantially less cytotoxic peptides (novispirins), with intact antimicrobial properties. One of these, novispirin G-10, differed from ovispirin-1 only by containing glycine at position 10, instead of isoleucine. The other, novispirin T-7, contained threonine instead of isoleucine at position 7. We determined the three-dimensional solution structures of all three peptides by circular dichroism spectroscopy and two-dimensional nuclear magnetic resonance spectroscopy. Although all retained an amphipathic helical structure in 2,2,2-trifluoroethanol, they manifested subtle fine-structural changes that evidently impacted their activities greatly. These findings show that simple structural modifications can 'fine-tune' an antimicrobial peptide to minimize unwanted cytotoxicity while retaining its desired activity.

  4. Charge regulation phenomenon predicted from the modeling of polypeptide electrophoretic mobilities as a relevant mechanism of amyloid-beta peptide oligomerization.

    PubMed

    Deiber, Julio A; Peirotti, Marta B; Piaggio, Maria V

    2016-03-01

    Electrophoretic mobilities of amyloid-beta (1-40) and (1-42) peptides and their aggregates are modeled to study the amyloidogenic pathway associated with Alzheimer´s Disease. The near molecule pH generated by the intraparticle charge regulation phenomenon during the oligomerization of amyloid-beta (1-40) and (1-42) peptides is evaluated and discussed as a relevant mechanism supporting the "amyloid cascade hypothesis" proposed in the literature. A theoretical framework associated with the oligomerization of amyloid-beta peptides including simple scaling laws and the consideration of electrokinetic and hydrodynamic global properties of oligomers is presented. The central finding is the explanation of the near molecule pH change toward the pI when the oligomerization number increases. These results allow one to rationalize consecutive physical stages that validate the amyloid cascade hypothesis. Concluding remarks involving mainly the effects of pair and intraparticle charge regulation phenomena on the amyloidogenic pathway with some suggestions for future research are provided.

  5. Charge transport in single Au / alkanedithiol / Au junctions: coordination geometries and conformational degrees of freedom.

    PubMed

    Li, Chen; Pobelov, Ilya; Wandlowski, Thomas; Bagrets, Alexei; Arnold, Andreas; Evers, Ferdinand

    2008-01-09

    Recent STM molecular break-junction experiments have revealed multiple series of peaks in the conductance histograms of alkanedithiols. To resolve a current controversy, we present here an in-depth study of charge transport properties of Au|alkanedithiol|Au junctions. Conductance histograms extracted from our STM measurements unambiguously confirm features showing more than one set of junction configurations. On the basis of quantum chemistry calculations, we propose that certain combinations of different sulfur-gold couplings and trans/gauche conformations act as the driving agents. The present study may have implications for experimental methodology: whenever conductances of different junction conformations are not statistically independent, the conductance histogram technique can exhibit a single series only, even though a much larger abundance of microscopic realizations exists.

  6. Modifications of gallium phosphide single crystals using slow highly charged ions and swift heavy ions

    NASA Astrophysics Data System (ADS)

    El-Said, A. S.; Wilhelm, R. A.; Heller, R.; Akhmadaliev, Sh.; Schumann, E.; Sorokin, M.; Facsko, S.; Trautmann, C.

    2016-09-01

    GaP single crystals were irradiated with slow highly charged ions (HCI) using 114 keV 129Xe(33-40)+ and with various swift heavy ions (SHI) of 30 MeV I9+ and 374 MeV-2.2 GeV 197Au25+. The irradiated surfaces were investigated by scanning force microscopy (SFM). The irradiations with SHI lead to nanohillocks protruding from the GaP surfaces, whereas no changes of the surface topography were observed after the irradiation with HCI. This result indicates that a potential energy above 38.5 keV is required for surface nanostructuring of GaP. In addition, strong coloration of the GaP crystals was observed after irradiation with SHI. The effect was stronger for higher energies. This was confirmed by measuring an increased extinction coefficient in the visible light region.

  7. Structural properties of reciprocal form factor in neutral atoms and singly charged ions.

    PubMed

    Romera, E; Angulo, J C

    2004-04-22

    Structural characteristics of the spherically averaged internally folded density or reciprocal form factor Br are studied within the Hartree-Fock framework for 103 neutral atoms, 54 singly charged cations, and 43 anions in their ground state. The function Br is classified throughout the Periodic Table into three types: (i) monotonic decrease from the origin, (ii) maximum at r=0 and a negative minimum at r>0, and (iii) a local maximum at r=0 and a pair maximum-minimum out of the origin. A detailed study of the corresponding properties for individual subshells as well as their relative weight for the total Br is also carried out. For completeness, the analytical Br for hydrogenlike atoms in both ground and excited states is also analyzed.

  8. Single-sheet identification method of heavy charged particles using solid state nuclear track detectors

    NASA Astrophysics Data System (ADS)

    Zaki, M. F.; Abdel-Naby, A.; Morsy, A. Ahmed

    2007-08-01

    The theoretical and experimental investigations of the penetration of charged particles in matter played a very important role in the development of modern physics. Solid state nuclear track detectors have become one of the most important tools for many branches of science and technology. An attempt has been made to examine the suitability of the single-sheet particle identification technique in CR-39 and CN-85 polycarbonate by plotting track cone length vs. residual range for different heavy ions in these detectors. So, the maximum etchable ranges of heavy ions such as ^{93}Nb, ^{86}Kr and ^{4}He in CR-39 and ^{4}He and ^{132}Xe in CN-85 polycarbonate have been determined. The ranges of these ions in these detectors have also been computed theoretically using the Henke-Benton program. A reasonably good agreement has been observed between the experimentally and theoretically computed values.

  9. Characterization of Single-Sided Charge-Sharing CZT Strip Detectors for Gamma-Ray Astronomy

    NASA Technical Reports Server (NTRS)

    Donmez, Burcin; Macri, John R.; Ryan, James M.; Legere, Jason S.; McConnell, Mark L.; Widholm, Mark; Narita, Tomohiko; Hamel, Louis-Andre

    2006-01-01

    We report progress in the study of thick single-sided charge-sharing cadmium zinc telluride (CZT) strip detector modules designed to perform spectroscopy and 3-D imaging of gamma-rays. We report laboratory measurements including spectroscopy, efficiency and 3-D imaging capability of prototype detectors (15 15 7.5 cu mm) with 11x11 unit cells. We also report on Monte Carlo simulations (GEANT4 v7.1) to investigate the effect of multihits on detector performance in both spectroscopy and imaging. We compare simulation results with data obtained from laboratory measurements and discuss the implications for future strip detector designs. Keywords: CZT, strip detectors, gamma-ray

  10. Characterization of Single-Sided Charge-Sharing CZT Strip Detectors for Gamma-Ray Astronomy

    NASA Technical Reports Server (NTRS)

    Donmez, Burcin; Macri, John R.; Ryan, James M.; Legere, Jason S.; McConnell, Mark L.; Widholm, Mark; Narita, Tomohiko; Hamel, Louis-Andre

    2006-01-01

    We report progress in the study of thick single-sided charge-sharing cadmium zinc telluride (CZT) strip detector modules designed to perform spectroscopy and 3-D imaging of gamma-rays. We report laboratory measurements including spectroscopy, efficiency and 3-D imaging capability of prototype detectors (15 15 7.5 cu mm) with 11x11 unit cells. We also report on Monte Carlo simulations (GEANT4 v7.1) to investigate the effect of multihits on detector performance in both spectroscopy and imaging. We compare simulation results with data obtained from laboratory measurements and discuss the implications for future strip detector designs. Keywords: CZT, strip detectors, gamma-ray

  11. Isotope-Resolved and Charge-Sensitive Force Imaging Using Scanned Single Molecules

    NASA Astrophysics Data System (ADS)

    Sun, Yan; Rastawicki, Dominik; Liu, Yang; Mar, Warren; Manoharan, Hari; Miglio, Anna; Melinte, Sorin; Charlier, Jean-Christophe; Rignanese, Gian-Marco; He, Lianhua; Liu, Fang; Zhou, Aihui

    Originally conceived as surface imaging instruments, the scanning tunnelling microscope (STM) and the atomic force microscope (AFM) were recently used to probe molecular chemical bonds with exquisite sensitivity. Remarkably, molecule-functionalized scanning tips can also provide direct access to the inelastic electron tunneling spectrum (IETS) of the terminal molecule. Here we report atomic manipulation experiments addressing carbon monoxide (CO) isotopes at low temperatures. The unique and quantifiable dependence of the CO vibrational modes offers insight into tip-controlled force and charge sensing of surface adsorbates, subsurface defects, and quantum nanostructures. The specific behavior of the monitored vibrational modes originates from the interplay of interaction forces between the top electrode--a scanned tip functionalized with a single molecule--and the atomic scale force field surrounding the target atomically-assembled nanostructure. We also present density functional theory (DFT) computations that have been performed in order to scrutinize and visualize the vibrational spectroscopic fingerprints and local force fields.

  12. Peptide-catalyzed, bioinspired silicification for single-cell encapsulation in the imidazole-buffered system.

    PubMed

    Park, Ji Hun; Choi, Insung S; Yang, Sung Ho

    2015-03-28

    Inspired by biosilicification of glass sponges, we designed a catalytic peptide, which formed silica structures in the imidazole-buffered solution. The peptide was adsorbed selectively onto the surface of yeast cells, and the bioinspired silicification led to the formation of a cytoprotective silica shell on individual yeast cells.

  13. Imidate-Based Cross-Linkers for Structural Proteomics: Increased Charge of Protein and Peptide Ions and CID and ECD Fragmentation Studies

    NASA Astrophysics Data System (ADS)

    Koolen, Hector H. F.; Gomes, Alexandre F.; Schwab, Nicolas V.; Eberlin, Marcos N.; Gozzo, Fabio C.

    2014-07-01

    Chemical cross-linking is an attractive low-resolution technique for structural studies of protein complexes. Distance constraints obtained from cross-linked peptides identified by mass spectrometry (MS) are used to construct and validate protein models. Amidinating cross-linkers such as diethyl suberthioimidate (DEST) have been used successfully in chemical cross-linking experiments. In this work, the application of a commercial diimidate cross-linking reagent, dimethyl suberimidate (DMS), was evaluated with model peptides and proteins. The peptides were designed with acetylated N-termini followed by random sequences containing two Lys residues separated by an Arg residue. After cross-linking reactions, intra- and intermolecular cross-linked species were submitted to CID and ECD dissociations to study their fragmentation features in the gas phase. Fragmentation of intramolecular peptides by collision induced dissociation (CID) demonstrates a unique two-step fragmentation pathway involving formation of a ketimine as intermediate. Electron capture and electron transfer dissociation (ECD and ETD) experiments demonstrated that the cyclic moiety is not dissociated. Intermolecular species demonstrated previously described fragmentation behavior in both CID and ECD experiments. The charge state distributions (CSD) obtained after reaction with DMS were compared with those obtained with disuccinimidyl suberate (DSS). CSDs for peptides and proteins were increased after their reaction with DMS, owing to the higher basicity of DMS modified species. These features were also observed in LC-MS experiments with bovine carbonic anhydrase II (BCA) after cross-linking with DMS and tryptic proteolysis. Cross-linked peptides derived from this protein were identified at high confidence and those species were in agreement with the crystal structure of BCA.

  14. Processing integral-skin polyolefin foams in single-charge rotational foam molding

    NASA Astrophysics Data System (ADS)

    Pop-Iliev, Remon

    This thesis focuses on establishing the scientific and engineering foundations for gaining a fundamental understanding of the mechanisms and critical parameters governing the processing of integral-skin low-density polyolefin foams in rotational foam molding. The presented research is particularly intended to broaden the knowledge in the field of manufacturing adjacent, but clearly distinct, layers of non-cellular and cellular structures, consisting of identical or compatible plastic grades, using a single-charge processing concept. Although this technology is beneficial for the efficacy of the molding process and the structural homogeneity of the moldings, its optimization raised a fairly large number of fundamental issues that had to be resolved through further research. In this context, an attempt has been made to establish rigorous, experimentally validated, theoretical models that describe the phenomena identified as the fundamental challenges of this technology. The major contributions of this thesis include: (i) optimization of the single-charge rotational foam molding process for the manufacture of both PE/PE and PE/PP integral-skin cellular composites, (ii) development of a two-step oven temperature profile that prevents the foamable resins invading the solid skin layer and ensures that skin formation always completes prior to the activation of the foamable resin, (iii) fundamental study of the adherence behavior of powders and foamable pellets to a high-temperature rotating mold wall, (iv) fundamental study of the lifespan of CBA-blown bubbles in non-pressurized non-isothermal polymer melts using hot-stage optical microscopy and digital imaging, (v) development of a detailed theoretical model involving diffusion, surface tension, and viscosity to simulate the observed foaming mechanism, and (vi) fundamental study of the rotofoamablility of polyolefin resins using both dry blending and melt compounding based methods and characterization of rheological and

  15. Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene

    NASA Astrophysics Data System (ADS)

    Shankla, Manish; Aksimentiev, Aleksei

    2014-10-01

    Control over interactions with biomolecules holds the key to applications of graphene in biotechnology. One such application is nanopore sequencing, where a DNA molecule is electrophoretically driven through a graphene nanopore. Here we investigate how interactions of single-stranded DNA and a graphene membrane can be controlled by electrically biasing the membrane. The results of our molecular dynamics simulations suggest that electric charge on graphene can force a DNA homopolymer to adopt a range of strikingly different conformations. The conformational response is sensitive to even very subtle nucleotide modifications, such as DNA methylation. The speed of DNA motion through a graphene nanopore is strongly affected by the graphene charge: a positive charge accelerates the motion, whereas a negative charge arrests it. As a possible application of the effect, we demonstrate stop-and-go transport of DNA controlled by the charge of graphene. Such on-demand transport of DNA is essential for realizing nanopore sequencing.

  16. Heparin-Promoted Cellular Uptake of the Cell-Penetrating Glycosaminoglycan Binding Peptide, GBPECP, Depends on a Single Tryptophan.

    PubMed

    Hung, Li-Chun; Jiang, Ingjye; Chen, Chien-Jung; Lu, Jia-Yin; Hsieh, Yi-Fen; Kuo, Ping-Hsieh; Hung, Yi-Lin; Wang, Lily Hui-Ching; Chang, Margaret Dah-Tsyr; Sue, Shih-Che

    2017-02-17

    A 10-residue, glycosaminoglycan-binding peptide, GBPECP, derived from human eosinophil cationic protein has been recently designated as a potent cell-penetrating peptide. A model system containing peptide, glycan, and lipid was monitored by nuclear magnetic resonance (NMR) spectroscopy to determine the cell-penetrating mechanism. Heparin octasaccharide with dodecylphosphocholine (DPC) lipid micelle was titrated into the GBPECP solution. Our data revealed substantial roles for the charged residues Arg5 and Lys7 in recognizing heparin, whereas Arg3 had less effect. The aromatic residue Trp4 acted as an irreplaceable moiety for membrane insertion, as the replacement of Trp4 with Arg4 abolished cell penetration, although it significantly improved the heparin-binding ability. GBPECP bound either heparin or lipid in the presence or absence of the other ligand indicating that the peptide has two alternative binding sites: Trp4 is responsible for lipid insertion, and Arg5 and Lys7 are for GAG binding. We developed a molecular model showing that the two effects synergistically promote the penetration. The loss of either effect would abolish the penetration. GBPECP has been proven to enter cells through macropinocytosis. The GBPECP treatment inhibited A549 lung cancer cell migration and invasion, implying that the cellular microenvironment would be modulated by GBPECP internalization. The intracellular penetration of GBPECP leading to inhibition of epithelial cell migration and invasion depends on the presence of the tryptophan residue in its sequence compared with similar derivative peptides. Therefore, GBPECP shows substantial potential as a novel delivery therapeutic through rapid and effective internalization and interference with cell mobility.

  17. Folded structure and insertion depth of the frog-skin antimicrobial Peptide esculentin-1b(1-18) in the presence of differently charged membrane-mimicking micelles.

    PubMed

    Manzo, Giorgia; Casu, Mariano; Rinaldi, Andrea C; Montaldo, Nicola P; Luganini, Anna; Gribaudo, Giorgio; Scorciapino, Mariano A

    2014-11-26

    Antimicrobial peptides (AMPs) are effectors of the innate immunity of most organisms. Their role in the defense against pathogen attack and their high selectivity for bacterial cells make them attractive for the development of a new class of antimicrobial drugs. The N-terminal fragment of the frog-skin peptide esculentin-1b (Esc(1-18)) has shown broad-spectrum antimicrobial activity. Similarly to most cationic AMPs, it is supposed to act by binding to and damaging the negatively charged plasma membrane of bacteria. Differently from many other AMPs, Esc(1-18) activity is preserved in biological fluids such as serum. In this work, a structural investigation was performed through NMR spectroscopy. The 3D structure was obtained in the presence of either zwitterionic or negatively charged micelles as membrane models for eukaryotic and prokaryotic membranes, respectively. Esc(1-18) showed a higher affinity for and deeper insertion into the latter and adopted an amphipathic helical structure characterized by a kink at the residue G8. These findings were confirmed by measuring penetration into lipid monolayers. The presence of negatively charged lipids in the bilayer appears to be necessary for Esc(1-18) to bind, to fold in the right three-dimensional structure, and, ultimately, to exert its biological role as an AMP.

  18. Increase of Positive Net Charge and Conformational Rigidity Enhances the Efficacy of d-Enantiomeric Peptides Designed to Eliminate Cytotoxic Aβ Species.

    PubMed

    Ziehm, Tamar; Brener, Oleksandr; van Groen, Thomas; Kadish, Inga; Frenzel, Daniel; Tusche, Markus; Kutzsche, Janine; Reiß, Kerstin; Gremer, Lothar; Nagel-Steger, Luitgard; Willbold, Dieter

    2016-08-17

    Alzheimer's disease (AD) is a neurodegenerative disorder and the most common type of dementia. Until now, there is no curative therapy available. Previously, we selected the amyloid-beta (Aβ) targeting peptide D3 consisting of 12 d-enantiomeric amino acid residues by mirror image phage display as a potential drug candidate for the treatment of AD. In the current approach, we investigated the optimization potential of linear D3 with free C-terminus (D3COOH) by chemical modifications. First, the impact of the net charge was investigated and second, cyclization was introduced which is a well-known tool for the optimization of peptides for enhanced target affinity. Following this strategy, three D3 derivatives in addition to D3COOH were designed: C-terminally amidated linear D3 (D3CONH2), cyclic D3 (cD3), and cyclic D3 with an additional arginine residue (cD3r) to maintain the net charge of linear D3CONH2. These four compounds were compared to each other according to their binding affinities to Aβ(1-42), their efficacy to eliminate cytotoxic oligomers, and consequently their potency to neutralize Aβ(1-42) oligomer induced neurotoxicity. D3CONH2 and cD3r versions with equally increased net charge showed superior properties over D3COOH and cD3, respectively. The cyclic versions showed superior properties compared to their linear version with equal net charge, suggesting cD3r to be the most efficient compound among these four. Indeed, treatment of the transgenic AD mouse model Tg-SwDI with cD3r significantly enhanced spatial memory and cognition of these animals as revealed by water maze performance. Therefore, charge increase and cyclization imply suitable modification steps for an optimization approach of the Aβ targeting compound D3.

  19. Gold Ion-Angiotensin Peptide Interaction by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Lee, Jenny; Jayathilaka, Lasanthi P.; Gupta, Shalini; Huang, Jin-Sheng; Lee, Bao-Shiang

    2012-05-01

    Stimulated by the interest in developing gold compounds for treating cancer, gold ion-angiotensin peptide interactions are investigated by mass spectrometry. Under the experimental conditions used, the majority of gold ion-angiotensin peptide complexes contain gold in the oxidation states I and III. Both ESI-MS and MALDI-TOF MS detect singly/multiply charged ions for mononuclear/multinuclear gold-attached peptides, which are represented as [peptide + a Au(I) + b Au(III) + (e - a -3b) H]e+, where a,b ≥ 0 and e is charge. ESI-MS data shows singly/multiply charged ions of Au(I)-peptide and Au(III)-peptide complexes. This study reveals that MALDI-TOF MS mainly detects singly charged Au(I)-peptide complexes, presumably due to the ionization process. The electrons in the MALDI plume seem to efficiently reduce Au(III) to Au(I). MALDI also tends to enhance the higher polymeric forms of gold-peptide complexes regardless of the laser power used. Collision-induced dissociation experiments of the mononuclear and dinuclear gold-attached peptide ions for angiotensin peptides show that the gold ion (a soft acid) binding sites are in the vicinity of Cys (a soft ligand), His (a major anchor of peptide for metal ion chelation), and the basic residue Arg. Data also suggests that the abundance of gold-attached peptides increases with higher gold concentration until saturation, after which an increase in gold ion concentration leads to the aggregation and/or precipitation of gold-bound peptides.

  20. Efficient Charge Extraction and Slow Recombination in Organic-Inorganic Perovskites Capped with Semiconducting Single-Walled Carbon Nanotubes

    SciTech Connect

    Ihly, Rachelle; Dowgiallo, Anne-Marie; Yang, Mengjin; Schulz, Philip; Stanton, Noah J.; Reid, Obadiah G.; Ferguson, Andrew J.; Zhu, Kai; Berry, Joseph J.; Blackburn, Jeffrey L.

    2016-04-01

    Metal-halide based perovskite solar cells have rapidly emerged as a promising alternative to traditional inorganic and thin-film photovoltaics. Although charge transport layers are used on either side of perovskite absorber layers to extract photogenerated electrons and holes, the time scales for charge extraction and recombination are poorly understood. Ideal charge transport layers should facilitate large discrepancies between charge extraction and recombination rates. Here, we demonstrate that highly enriched semiconducting single-walled carbon nanotube (SWCNT) films enable rapid (sub-picosecond) hole extraction from a prototypical perovskite absorber layer and extremely slow back-transfer and recombination (hundreds of microseconds). The energetically narrow and distinct spectroscopic signatures for charges within these SWCNT thin films enables the unambiguous temporal tracking of each charge carrier with time-resolved spectroscopies covering many decades of time. The efficient hole extraction by the SWCNT layer also improves electron extraction by the compact titanium dioxide electron transport layer, which should reduce charge accumulation at each critical interface. Finally, we demonstrate that the use of thin interface layers of semiconducting single-walled carbon nanotubes between the perovskite absorber layer and a prototypical hole transport layer improves device efficiency and stability, and reduces hysteresis.

  1. Single-Hole Charging and Discharging Phenomena in Carbon Nanotube Field-Effect-Transistor-Based Nonvolatile Memory

    NASA Astrophysics Data System (ADS)

    Ohori, Takahiro; Nagaso, Satoshi; Ohno, Yasuhide; Maehashi, Kenzo; Inoue, Koichi; Matsumoto, Kazuhiko

    2010-06-01

    We have fabricated nonvolatile memory based on top-gated carbon nanotube field-effect transistors (CNTFETs). Two kinds of insulating films, SiNx and SiO2, were deposited to control the hysteresis characteristics after the removal of water molecules around the single-walled CNT channels. The interface between the SiNx and SiO2 films is expected to act as a charge storage node of nonvolatile memory. The fabricated CNTFET-based memory devices clearly exhibited not only a memory effect but also good retention characteristics for charge storage. Furthermore, single-hole charging and discharging phenomena were clearly observed in the CNTFET-based memory devices by reducing the number of carriers trapped in the interface between the SiNx and SiO2 films. These results indicate that the CNTFET-based nonvolatile memory can be potentially used to realize single-electron memory.

  2. Charging the quantum capacitance of graphene with a single biological ion channel.

    PubMed

    Wang, Yung Yu; Pham, Ted D; Zand, Katayoun; Li, Jinfeng; Burke, Peter J

    2014-05-27

    The interaction of cell and organelle membranes (lipid bilayers) with nanoelectronics can enable new technologies to sense and measure electrophysiology in qualitatively new ways. To date, a variety of sensing devices have been demonstrated to measure membrane currents through macroscopic numbers of ion channels. However, nanoelectronic based sensing of single ion channel currents has been a challenge. Here, we report graphene-based field-effect transistors combined with supported lipid bilayers as a platform for measuring, for the first time, individual ion channel activity. We show that the supported lipid bilayers uniformly coat the single layer graphene surface, acting as a biomimetic barrier that insulates (both electrically and chemically) the graphene from the electrolyte environment. Upon introduction of pore-forming membrane proteins such as alamethicin and gramicidin A, current pulses are observed through the lipid bilayers from the graphene to the electrolyte, which charge the quantum capacitance of the graphene. This approach combines nanotechnology with electrophysiology to demonstrate qualitatively new ways of measuring ion channel currents.

  3. Charging the Quantum Capacitance of Graphene with a Single Biological Ion Channel

    PubMed Central

    2015-01-01

    The interaction of cell and organelle membranes (lipid bilayers) with nanoelectronics can enable new technologies to sense and measure electrophysiology in qualitatively new ways. To date, a variety of sensing devices have been demonstrated to measure membrane currents through macroscopic numbers of ion channels. However, nanoelectronic based sensing of single ion channel currents has been a challenge. Here, we report graphene-based field-effect transistors combined with supported lipid bilayers as a platform for measuring, for the first time, individual ion channel activity. We show that the supported lipid bilayers uniformly coat the single layer graphene surface, acting as a biomimetic barrier that insulates (both electrically and chemically) the graphene from the electrolyte environment. Upon introduction of pore-forming membrane proteins such as alamethicin and gramicidin A, current pulses are observed through the lipid bilayers from the graphene to the electrolyte, which charge the quantum capacitance of the graphene. This approach combines nanotechnology with electrophysiology to demonstrate qualitatively new ways of measuring ion channel currents. PMID:24754625

  4. Simultaneous demonstrations of neuropeptide Y gene expression and peptide storage in single neurons of the human brain

    SciTech Connect

    Chan-Palay, V.; Yasargil, G.; Hamid, Q.; Polak, J.M.; Palay, S.L.

    1988-05-01

    A combination of in situ hybridization for neuropeptide Y mRNA that used a /sup 32/P-labeled complementary RNA probe and immunocytochemistry with polyclonal antibodies against neuropeptide Y were applied to human cortical brain samples to simultaneously localize neuropeptide Y and its mRNA. These two techniques allowed simultaneous identification of neuropeptide Y gene expression and peptide storage in single neutrons of the human brain.

  5. Lipid surface charge does not influence conductance or calcium block of single sodium channels in planar bilayers.

    PubMed Central

    Worley, J F; French, R J; Pailthorpe, B A; Krueger, B K

    1992-01-01

    We have studied the effects of membrane surface charge on Na+ ion permeation and Ca2+ block in single, batrachotoxin-activated Na channels from rat brain, incorporated into planar lipid bilayers. In phospholipid membranes with no net charge (phosphatidylethanolamine, PE), at low divalent cation concentrations (approximately 100 microM Mg2+), the single channel current-voltage relation was linear and the single channel conductance saturated with increasing [Na+] and ionic strength, reaching a maximum (gamma max) of 31.8 pS, with an apparent dissociation constant (K0.5) of 40.5 mM. The data could be approximated by a rectangular hyperbola. In negatively charged bilayers (70% phosphatidylserine, PS; 30% PE) slightly larger conductances were observed at each concentration, but the hyperbolic form of the conductance-concentration relation was retained (gamma max = 32.9 pS and K0.5 = 31.5 mM) without any preferential increase in conductance at lower ionic strengths. Symmetrical application of Ca2+ caused a voltage-dependent block of the single channel current, with the block being greater at negative potentials. For any given voltage and [Na+] this block was identical in neutral and negatively charged membranes. These observations suggest that both the conduction pathway and the site(s) of Ca2+ block of the rat brain Na channel protein are electrostatically isolated from the negatively charged headgroups on the membrane lipids. PMID:1318097

  6. Noncovalent Protein and Peptide Functionalization of Single-Walled Carbon Nanotubes for Biodelivery and Optical Sensing Applications.

    PubMed

    Antonucci, Alessandra; Kupis-Rozmysłowicz, Justyna; Boghossian, Ardemis A

    2017-04-05

    The exquisite structural and optical characteristics of single-walled carbon nanotubes (SWCNTs), combined with the tunable specificities of proteins and peptides, can be exploited to strongly benefit technologies with applications in fields ranging from biomedicine to industrial biocatalysis. The key to exploiting the synergism of these materials is designing protein/peptide-SWCNT conjugation schemes that preserve biomolecule activity while keeping the near-infrared optical and electronic properties of SWCNTs intact. Since sp(2) bond-breaking disrupts the optoelectronic properties of SWCNTs, noncovalent conjugation strategies are needed to interface biomolecules to the nanotube surface for optical biosensing and delivery applications. An underlying understanding of the forces contributing to protein and peptide interaction with the nanotube is thus necessary to identify the appropriate conjugation design rules for specific applications. This article explores the molecular interactions that govern the adsorption of peptides and proteins on SWCNT surfaces, elucidating contributions from individual amino acids as well as secondary and tertiary protein structure and conformation. Various noncovalent conjugation strategies for immobilizing peptides, homopolypeptides, and soluble and membrane proteins on SWCNT surfaces are presented, highlighting studies focused on developing near-infrared optical sensors and molecular scaffolds for self-assembly and biochemical analysis. The analysis presented herein suggests that though direct adsorption of proteins and peptides onto SWCNTs can be principally applied to drug and gene delivery, in vivo imaging and targeting, or cancer therapy, nondirect conjugation strategies using artificial or natural membranes, polymers, or linker molecules are often better suited for biosensing applications that require conservation of biomolecular functionality or precise control of the biomolecule's orientation. These design rules are intended to

  7. Experimental determination of single-event upset (SEU) as a function of collected charge in bipolar integrated circuits

    NASA Technical Reports Server (NTRS)

    Zoutendyk, J. A.; Malone, C. J.; Smith, L. S.

    1984-01-01

    Single-Event Upset (SEU) in bipolar integrated circuits (ICs) is caused by charge collection from ion tracks in various regions of a bipolar transistor. This paper presents experimental data which have been obtained wherein the range-energy characteristics of heavy ions (Br) have been utilized to determine the cross section for soft-error generation as a function of charge collected from single-particle tracks which penetrate a bipolar static RAM. The results of this work provide a basis for the experimental verification of circuit-simulation SEU modeling in bipolar ICs.

  8. Time-resolved measurements with single droplet introduction to investigate space-charge effects in plasma mass spectrometry.

    PubMed

    Stewart, I I; Olesik, J W

    1999-02-01

    An investigation of the space-charge induced effects of high concentrations of Pb+ matrix ions on Li+ analyte ions in inductively coupled plasma mass spectrometry (ICP-MS) is presented using a vertically oriented mass spectrometer with single droplet introduction. Greater reproducibility and stability in droplet-to-droplet sample introduction using the monodisperse microparticulate injector (MDMI) was achieved with the vertical orientation. Typical variation (%RSD) in the droplet-to-droplet arrival times, and mass spectrometry peak analytical areas are better than 5%. With this precision, a more quantitative description of the space-charge effect on a single cloud of ions is obtained. Both radial and axial space-charge effects were found to occur in the ion beam. Radial effects result in a loss in intensity because of poor transmission or collisions at surfaces within the mass spectrometer. Axial effects modify the kinetic energy distribution of background ion beam components (e.g., 16O+ and 40Ar+) and sampled ion cloud constituents (e.g., 7Li+). However, axial effects do not appear to generate significant broadening of sampled ion clouds within the mass spectrometer. At the point of charge separation and high ion-beam charge density, the ion cloud maxima for Li and Pb are not coincident. This is because of mass dependent diffusion in the ICP as the ion clouds approach the sampling orifice. Space-charge induced ion loss occurs predominantly at a localized region after the Li+ sampled cloud peak maximum. When the Pb concentration in the sample is sufficiently high the 7Li+ sampled signal has a bimodal peak shape. The existence of the dip and its relative location in the bimodal 7Li+ sampled signal suggests that space-charge effects are localized to the region of high charge density occurring just after charge separation.

  9. Protein nanopore-based, single-molecule exploration of copper binding to an antimicrobial-derived, histidine-containing chimera peptide.

    PubMed

    Mereuta, Loredana; Schiopu, Irina; Asandei, Alina; Park, Yoonkyung; Hahm, Kyung-Soo; Luchian, Tudor

    2012-12-11

    Metal ions binding exert a crucial influence upon the aggregation properties and stability of peptides, and the propensity of folding in various substates. Herein, we demonstrate the use of the α-HL protein as a powerful nanoscopic tool to probe Cu(2+)-triggered physicochemical changes of a 20 aminoacids long, antimicrobial-derived chimera peptide with a His residue as metal-binding site, and simultaneously dissect the kinetics of the free- and Cu(2+)-bound peptide interaction to the α-HL pore. Combining single-molecule electrophysiology on reconstituted lipid membranes and fluorescence spectroscopy, we show that the association rate constant between the α-HL pore and a Cu(2+)-free peptide is higher than that of a Cu(2+)-complexed peptide. We posit that mainly due to conformational changes induced by the bound Cu(2+) on the peptide, the resulting complex encounters a higher energy barrier toward its association with the protein pore, stemming most likely from an extra entropy cost needed to fit the Cu(2+)-complexed peptide within the α-HL lumen region. The lower dissociation rate constant of the Cu(2+)-complexed peptide from α-HL pore, as compared to that of Cu(2+)-free peptide, supports the existence of a deeper free energy well for the protein interaction with a Cu(2+)-complexed peptide, which may be indicative of specific Cu(2+)-mediated contributions to the binding of the Cu(2+)-complexed peptide within the pore lumen.

  10. Testing multistage gain and offset trimming in a single photon counting IC with a charge sharing elimination algorithm

    NASA Astrophysics Data System (ADS)

    Krzyżanowska, A.; Gryboś, P.; Szczygieł, R.; Maj, P.

    2015-12-01

    Designing a hybrid pixel detector readout electronics operating in a single photon counting mode is a very challenging process, where many main parameters are optimized in parallel (e.g. gain, noise, and threshold dispersion). Additional requirements for a smaller pixel size with extended functionality push designers to use new deep sub-micron technologies. Minimizing the channel size is possible, however, with a decreased pixel size, the charge sharing effect becomes a more important issue. To overcome this problem, we designed an integrated circuit prototype produced in CMOS 40 nm technology, which has an extended functionality of a single pixel. A C8P1 algorithm for the charge sharing effect compensation was implemented. In the algorithm's first stage the charge is rebuilt in a signal rebuilt hub fed by the CSA (charge sensitive amplifier) outputs from four neighbouring pixels. Then, the pixel with the biggest amount of charge is chosen, after a comparison with all the adjacent ones. In order to process the data in such a complicated way, a certain architecture of a single channel was proposed, which allows for: ṡ processing the signal with the possibility of total charge reconstruction (by connecting with the adjacent pixels), ṡ a comparison of certain pixel amplitude to its 8 neighbours, ṡ the extended testability of each block inside the channel to measure CSA gain dispersion, shaper gain dispersion, threshold dispersion (including the simultaneous generation of different pulse amplitudes from different pixels), ṡ trimming all the necessary blocks for proper operation. We present a solution for multistage gain and offset trimming implemented in the IC prototype. It allows for minimization of the total charge extraction errors, minimization of threshold dispersion in the pixel matrix and minimization of errors of comparison of certain pixel pulse amplitudes with all its neighbours. The detailed architecture of a single channel is presented together

  11. Single amino acid fingerprinting of the human antibody repertoire with high density peptide arrays.

    PubMed

    Weber, Laura K; Palermo, Andrea; Kügler, Jonas; Armant, Olivier; Isse, Awale; Rentschler, Simone; Jaenisch, Thomas; Hubbuch, Jürgen; Dübel, Stefan; Nesterov-Mueller, Alexander; Breitling, Frank; Loeffler, Felix F

    2017-04-01

    The antibody species that patrol in a patient's blood are an invaluable part of the immune system. While most of them shield us from life-threatening infections, some of them do harm in autoimmune diseases. If we knew exactly all the antigens that elicited all the antibody species within a group of patients, we could learn which ones correlate with immune protection, are irrelevant, or do harm. Here, we demonstrate an approach to this question: First, we use a plethora of phage-displayed peptides to identify many different serum antibody binding peptides. Next, we synthesize identified peptides in the array format and rescreen the serum used for phage panning to validate antibody binding peptides. Finally, we systematically vary the sequence of validated antibody binding peptides to identify those amino acids within the peptides that are crucial for binding "their" antibody species. The resulting immune fingerprints can then be used to trace them back to potential antigens. We investigated the serum of an individual in this pipeline, which led to the identification of 73 antibody fingerprints. Some fingerprints could be traced back to their most likely antigen, for example the immunodominant capsid protein VP1 of enteroviruses, most likely elicited by the ubiquitous poliovirus vaccination. Thus, with our approach, it is possible, to pinpoint those antibody species that correlate with a certain antigen, without any pre-information. This can help to unravel hitherto enigmatic diseases.

  12. Single- and double-electron loss from helium by collisions with v>=v0 multiply charged ions

    NASA Astrophysics Data System (ADS)

    Hvelplund, P.; Haugen, H. K.; Knudsen, H.

    1980-11-01

    Cross sections for single- and double-electron loss (electron capture plus impact ionization) for H+, Heq+, Oq+, and Auq+ incident on helium have been measured at velocities from ~v0 to ~10v0. The charge state q was varied from 1 to 21, depending on velocity and projectile. The energy and charge-state dependence of the single-loss cross section at the lower velocities is reasonably well described by the model of Olson based on Coulomb interaction between particles and classical trajectory Monte Carlo calculations. The results for H+, He+, and He++ at high velocities are in good agreement with earlier experimental values of Pivovar et al. and with Bethe-Born calculations of Gillespie. The double-loss cross section, which for highly charged projectiles amounts to as much as 60% of the single loss, is found to behave quite differently from the single-loss cross section, both as a function of incident charge and velocity. While single-loss cross sections at velocities between v0 and 2v0 are almost independent of energy and proportional to q, the double-loss cross sections are approximately proportional to energy and to q2.

  13. Single residue deletions along the length of the influenza HA fusion peptide lead to inhibition of membrane fusion function

    SciTech Connect

    Langley, William A.; Thoennes, Sudha; Bradley, Konrad C.; Galloway, Summer E.; Talekar, Ganesh R.; Cummings, Sandra F.; Vareckova, Eva; Russell, Rupert J.; Steinhauer, David A.

    2009-11-25

    A panel of eight single amino acid deletion mutants was generated within the first 24 residues of the fusion peptide domain of the of the hemagglutinin (HA) of A/Aichi/2/68 influenza A virus (H3N2 subtype). The mutant HAs were analyzed for folding, cell surface transport, cleavage activation, capacity to undergo acid-induced conformational changes, and membrane fusion activity. We found that the mutant DELTAF24, at the C-terminal end of the fusion peptide, was expressed in a non-native conformation, whereas all other deletion mutants were transported to the cell surface and could be cleaved into HA1 and HA2 to activate membrane fusion potential. Furthermore, upon acidification these cleaved HAs were able to undergo the characteristic structural rearrangements that are required for fusion. Despite this, all mutants were inhibited for fusion activity based on two separate assays. The results indicate that the mutant fusion peptide domains associate with target membranes in a non-functional fashion, and suggest that structural features along the length of the fusion peptide are likely to be relevant for optimal membrane fusion activity.

  14. Solubilization of single-walled carbon nanotubes using a peptide aptamer in water below the critical micelle concentration.

    PubMed

    Li, Zha; Kameda, Tomoshi; Isoshima, Takashi; Kobatake, Eiry; Tanaka, Takeshi; Ito, Yoshihiro; Kawamoto, Masuki

    2015-03-24

    The solubilizing ability of single-walled carbon nanotubes (SWCNTs) in water with several dispersants was investigated. Among the dispersants, including low-molecular-weight surfactants, peptides, DNA, and a water-soluble polymer, the peptide aptamer, A2 (IFRLSWGTYFS), exhibited the highest dispersion capability below the critical micelle concentration at a concentration of 0.02 w/v%. The dispersion of supernatant aqueous solution of SWCNTs containing aptamer A2 was essentially unchanged for several months after high-speed ultracentrifugation and gave rise to an efficient and stable dispersion of the SWCNTs in water. From the results of isothermal titration calorimetry and molecular dynamics simulations, the effective binding capability of A2 was due to π-π interaction between aromatic groups in the peptide aptamer and the side walls of SWCNTs. Interestingly, the peptide aptamer showed the possibility of diameter separation of semiconducting SWCNTs using a uniform density gradient ultracentrifuge. These phenomena are encouraging results toward an effective approach to the dispersion and separation of SWCNTs.

  15. A helical-dipole model describes the single-channel current rectification of an uncharged peptide ion channel.

    PubMed Central

    Kienker, P K; DeGrado, W F; Lear, J D

    1994-01-01

    We are designing simple peptide ion channels as model systems for the study of the physical principles controlling conduction through ion-channel proteins. Here we report on an uncharged peptide, Ac-(Leu-Ser-Ser-Leu-Leu-Ser-Leu)3-CONH2, designed to form an aggregate of parallel, amphiphilic, membrane-spanning alpha-helices around a central water-filled pore. This peptide in planar lipid bilayers forms ion channels that show single-channel current rectification in symmetric 1 M KCl. The current at a given holding membrane potential is larger than the current measured through the same channel when the potential is reversed. Based on our hypothesized gating mechanism, the larger currents flow from the peptide carboxyl terminus toward the amino terminus. We present an ionic electrodiffusion model based on the helical-dipole potential and the dielectric interfacial polarization energy, which with reasonable values for dipole magnitude and dielectric constants, accurately replicates the current-voltage data. PMID:7515180

  16. Mass spectrometry strategies for venom mapping and peptide sequencing from crude venoms: case applications with single arthropod specimen.

    PubMed

    Favreau, Philippe; Menin, Laure; Michalet, Sophie; Perret, Fréderic; Cheneval, Olivier; Stöcklin, Maxime; Bulet, Philippe; Stöcklin, Reto

    2006-05-01

    Due to their complexity and diversity, animal venoms represent an extensive source of bioactive compounds such as peptides and proteins. Conventional approaches for their characterization often require large quantities of biological material. Current mass spectrometry (MS) techniques now give access to a wealth of information in a short working time frame with minute amounts of sample. Such MS approaches may now be used for the discovery of novel compounds, and once their structure has been determined they may be synthesized and tested for functional activity. Molecular mass fingerprints of venoms allow the rapid identification of known toxins as well as preliminary structural characterization of new compounds. De novo peptide sequencing by tandem mass spectrometry (MS/MS) offers rapid access to partial or total primary peptide structures. This article, written as a tutorial, also contains new material: molecular mass fingerprint analysis of Orthochirus innesi scorpion venom, and identification of components from bumblebee Bombus lapidarius venom, both collected from one single specimen. The structure of the three major peptides detected in the Bombus venom was fully characterized in one working day by de novo sequencing using an electrospray ionization hybrid quadrupole time-of-flight instrument (ESI-QqTOF) and a matrix-assisted laser desorption ionization time-of-flight instrument (MALDI-LIFT-TOF-TOF). After presenting the MS-based sequence elucidation, perspectives in using MS and MS/MS techniques in toxinology are discussed.

  17. Quantum computing over long time scales in a singly charged quantum dot

    NASA Astrophysics Data System (ADS)

    Sun, Bo

    In this thesis, we will study the continuous wave optical spectroscopy of self-assembled quantum dots (SAQDs), focusing on the use of these dots toward quantum computing and information processing applications. Probing the strong field interaction between an intense optical pump beam and a neutral quantum dot will reveal Autler-Townes splitting and Mollow absorption spectrum. The presence of these two phenomenon confirm the isolated nature of the exciton trapped in the quantum dot and the suppression of many-body physics due to exciton confinement. This curbs the decoherence caused by exciton-exciton interactions in higher dimensional heterostructures. After confirming the atom-like nature of the SAQD, we then charge the SAQD with a single electron and use the electron spin as our qubit. By applying a magnetic field perpendicular to the sample growth direction, we turn on the spin flip Raman transitions and create two lambda (Λ) systems that can be used to coherently manipulate the spin. A single laser resonant with one of the transitions can quickly initialize the spin state via optical pumping while two lasers, one on each leg of the lambda, can initialize the spin into an arbitrary superposition state through coherent population trapping. The developed dark state spectroscopy is then used to demonstrate interaction between the optically generated hole spin with the background nuclear spins. This hole assisted dynamic nuclear polarization creates a feedback mechanism which locks the nuclear field to the laser detunings and suppresses nuclear spin fluctuations. We use dark state spectroscopy to measure a two orders of magnitude increase of the electron spin coherence time, a result of the narrowing of the nuclear field distribution. Furthermore, we find that this nuclear spin narrowing can persist in the dark, without laser interaction, for well over 1s even in the presence of a fluctuating electron charge and electron spin polarization. We have opened the door

  18. Single-Shot Charge Readout Using a Cryogenic Heterojunction Bipolar Transistor Preamplifier Inline with a Silicon Single Electron Transistor at Millikelvin Temperatures

    NASA Astrophysics Data System (ADS)

    Curry, Matthew; England, Troy; Wendt, Joel; Pluym, Tammy; Lilly, Michael; Carr, Stephen; Carroll, Malcolm

    Single-shot readout is a requirement for many implementations of quantum information processing. The single-shot readout fidelity is dependent on the signal-to-noise-ratio (SNR) and bandwidth of the readout detection technique. Several different approaches are being pursued to enhance read-out including RF-reflectometry, RF-transmission, parametric amplification, and transistor-based cryogenic preamplification. The transistor-based cryogenic preamplifier is attractive in part because of the reduced experimental complexity compared with the RF techniques. Here we present single-shot charge readout using a cryogenic Heterojunction-Bipolar-Transistor (HBT) inline with a silicon SET charge-sensor at millikelvin temperatures. For the relevant range of HBT DC-biasing, the current gain is 100 to 2000 and the power dissipation is 50 nW to 5 μW, with the microfabricated SET and discrete HBT in an integrated package mounted to the mixing chamber stage of a dilution refrigerator. We experimentally demonstrate a SNR of up to 10 with a bandwidth of 1 MHz, corresponding to a single-shot time-domain charge-sensitivity of approximately 10-4 e / √Hz. This measured charge-sensitivity is comparable to the values reported using the RF techniques. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a Lockheed-Martin Company, for the U. S. Department of Energy under Contract No. DE-AC04-94AL85000.

  19. Single charge sensing and transport in double quantum dots fabricated from commercially grown Si/SiGe heterostructures

    NASA Astrophysics Data System (ADS)

    Wang, K.; Payette, C.; Dovzhenko, Y.; Koppinen, P.; Petta, J. R.

    2012-02-01

    We perform quantum Hall measurements on three types of commercially available modulation doped Si/SiGe heterostructures [1] to determine their suitability for depletion gate defined quantum dot devices. By adjusting the growth parameters, we are able to achieve two dimensional electron gases with low charge densities and high mobilities. We extract an electron temperature of 100 mK in the single quantum dot regime. Double quantum dots fabricated on these heterostructures show clear evidence of single charge transitions [2] as measured in dc transport and charge sensing. [4pt] [1] C. B. Simmons et al, Phys. Rev. Lett. 106, 156804 (2011).[0pt] [2] R. Hanson et al, Rev. Mod. Phys. 79, 1217 (2007).

  20. Charge enhancement of single-stranded DNA in negative electrospray ionization using the supercharging reagent meta-nitrobenzyl alcohol.

    PubMed

    Brahim, Bessem; Alves, Sandra; Cole, Richard B; Tabet, Jean-Claude

    2013-12-01

    Charge enhancement of single-stranded oligonucleotide ions in negative ESI mode is investigated. The employed reagent, meta-nitrobenzyl alcohol (m-NBA), was found to improve total signal intensity (Itot), increase the highest observed charge states (zhigh), and raise the average charge states (zavg) of all tested oligonucleotides analyzed in negative ESI. To quantify these increases, signal enhancement ratios (SER1%) and charge enhancement coefficients (CEC1%) were introduced. The SER1%, (defined as the quotient of total oligonucleotide ion abundances with 1% m-NBA divided by total oligonucleotide abundance without m-NBA) was found to be greater than unity for every oligonucleotide tested. The CEC1% values (defined as the average charge state in the presence of 1% m-NBA minus the average charge state in the absence of m-NBA) were found to be uniformly positive. Upon close inspection, the degree of charge enhancement for longer oligonucleotides was found to be dependent upon thymine density (i.e., the number and the location of phospho-thymidine units). A correlation between the charge enhancement induced by the presence of m-NBA and the apparent gas-phase acidity (largely determined by the sequence of thymine units but also by the presence of protons on other nucleobases) of multiply deprotonated oligonucleotide species, was thus established. Ammonium cations appeared to be directly involved in the m-NBA supercharging mechanism, and their role seems to be consistent with previously postulated ESI mechanisms describing desorption/ionization of single-stranded DNA into the gas phase.

  1. Charge Enhancement of Single-Stranded DNA in Negative Electrospray Ionization Using the Supercharging Reagent Meta-nitrobenzyl Alcohol

    NASA Astrophysics Data System (ADS)

    Brahim, Bessem; Alves, Sandra; Cole, Richard B.; Tabet, Jean-Claude

    2013-12-01

    Charge enhancement of single-stranded oligonucleotide ions in negative ESI mode is investigated. The employed reagent, meta-nitrobenzyl alcohol (m-NBA), was found to improve total signal intensity (Itot), increase the highest observed charge states (zhigh), and raise the average charge states (zavg) of all tested oligonucleotides analyzed in negative ESI. To quantify these increases, signal enhancement ratios (SER1%) and charge enhancement coefficients (CEC1%) were introduced. The SER1%, (defined as the quotient of total oligonucleotide ion abundances with 1 % m-NBA divided by total oligonucleotide abundance without m-NBA) was found to be greater than unity for every oligonucleotide tested. The CEC1% values (defined as the average charge state in the presence of 1 % m-NBA minus the average charge state in the absence of m-NBA) were found to be uniformly positive. Upon close inspection, the degree of charge enhancement for longer oligonucleotides was found to be dependent upon thymine density (i.e., the number and the location of phospho-thymidine units). A correlation between the charge enhancement induced by the presence of m-NBA and the apparent gas-phase acidity (largely determined by the sequence of thymine units but also by the presence of protons on other nucleobases) of multiply deprotonated oligonucleotide species, was thus established. Ammonium cations appeared to be directly involved in the m-NBA supercharging mechanism, and their role seems to be consistent with previously postulated ESI mechanisms describing desorption/ionization of single-stranded DNA into the gas phase.

  2. Single active-site histidine in D-xylose isomerase from Streptomyces violaceoruber. Identification by chemical derivatization and peptide mapping.

    PubMed

    Vangrysperre, W; Ampe, C; Kersters-Hilderson, H; Tempst, P

    1989-10-01

    Group-specific chemical modifications of D-xylose isomerase from Streptomyces violaceruber indicated that complete loss of activity is fully correlated with the acylation of a single histidine. Active-site protection, by the ligand combination of xylitol plus Mg2+, completely blocked diethyl pyrocarbonate derivatization of this particular residue [Vangrysperre, Callens, Kersters-Hilderson & De Bruyne (1988) Biochem. J. 250, 153-160]. Differential peptide mapping between D-xylose isomerase, which has previously been treated with diethyl pyrocarbonate in the presence or absence of xylitol plus Mg2+, allowed specific isolation and sequencing of a peptide containing this active-site histidine. For this purpose we used two essentially new techniques: first, a highly reproducible peptide cleavage protocol for protease-resistant, carbethoxylated proteins with guanidinium hydrochloride as denaturing agent and subtilisin for proteolysis; and second, reverse-phase liquid chromatography with dual-wavelength detection at 214 and 238 nm, and calculation of absorbance ratios. It allowed us to locate the single active-site histidine at position 54 in the primary structure of Streptomyces violaceoruber D-xylose isomerase. The sequence around this residue is conserved in D-xylose isomerases from a diversity of micro-organisms, suggesting that this is a structurally and/or functionally essential part of the molecule.

  3. Structural evolution and membrane interactions of Alzheimer's amyloid-beta peptide oligomers: new knowledge from single-molecule fluorescence studies.

    PubMed

    Johnson, Robin D; Steel, Duncan G; Gafni, Ari

    2014-07-01

    Amyloid-β peptide (Aβ) oligomers may represent the proximal neurotoxin in Alzheimer's disease. Single-molecule microscopy (SMM) techniques have recently emerged as a method for overcoming the innate difficulties of working with amyloid-β, including the peptide's low endogenous concentrations, the dynamic nature of its oligomeric states, and its heterogeneous and complex membrane interactions. SMM techniques have revealed that small oligomers of the peptide bind to model membranes and cells at low nanomolar-to-picomolar concentrations and diffuse at rates dependent on the membrane characteristics. These methods have also shown that oligomers grow or dissociate based on the presence of specific inhibitors or promoters and on the ratio of Aβ40 to Aβ42. Here, we discuss several types of single-molecule imaging that have been applied to the study of Aβ oligomers and their membrane interactions. We also summarize some of the recent insights SMM has provided into oligomer behavior in solution, on planar lipid membranes, and on living cell membranes. A brief overview of the current limitations of the technique, including the lack of sensitive assays for Aβ-induced toxicity, is included in hopes of inspiring future development in this area of research. © 2014 The Protein Society.

  4. Structural evolution and membrane interactions of Alzheimer's amyloid-beta peptide oligomers: New knowledge from single-molecule fluorescence studies

    PubMed Central

    Johnson, Robin D; Steel, Duncan G; Gafni, Ari

    2014-01-01

    Amyloid-β peptide (Aβ) oligomers may represent the proximal neurotoxin in Alzheimer's disease. Single-molecule microscopy (SMM) techniques have recently emerged as a method for overcoming the innate difficulties of working with amyloid-β, including the peptide's low endogenous concentrations, the dynamic nature of its oligomeric states, and its heterogeneous and complex membrane interactions. SMM techniques have revealed that small oligomers of the peptide bind to model membranes and cells at low nanomolar-to-picomolar concentrations and diffuse at rates dependent on the membrane characteristics. These methods have also shown that oligomers grow or dissociate based on the presence of specific inhibitors or promoters and on the ratio of Aβ40 to Aβ42. Here, we discuss several types of single-molecule imaging that have been applied to the study of Aβ oligomers and their membrane interactions. We also summarize some of the recent insights SMM has provided into oligomer behavior in solution, on planar lipid membranes, and on living cell membranes. A brief overview of the current limitations of the technique, including the lack of sensitive assays for Aβ-induced toxicity, is included in hopes of inspiring future development in this area of research. PMID:24753305

  5. Charged single alpha-helices in proteomes revealed by a consensus prediction approach.

    PubMed

    Gáspári, Zoltán; Süveges, Dániel; Perczel, András; Nyitray, László; Tóth, Gábor

    2012-04-01

    Charged single α-helices (CSAHs) constitute a recently recognized protein structural motif. Its presence and role is characterized in only a few proteins. To explore its general features, a comprehensive study is necessary. We have set up a consensus prediction method available as a web service (at http://csahserver.chem.elte.hu) and downloadable scripts capable of predicting CSAHs from protein sequences. Using our method, we have performed a comprehensive search on the UniProt database. We found that the motif is very rare but seems abundant in proteins involved in symbiosis and RNA binding/processing. Although there are related proteins with CSAH segments, the motif shows no deep conservation in protein families. We conclude that CSAH-containing proteins, although rare, are involved in many key biological processes. Their conservation pattern and prevalence in symbiosis-associated proteins suggest that they might be subjects of relatively rapid molecular evolution and thus can contribute to the emergence of novel functions.

  6. Production of charged (singly and multiply) phosphorous beams with electron cyclotron resonance ion source

    NASA Astrophysics Data System (ADS)

    Maunoury, L.; Kantas, S.; Leroy, R.; Pacquet, J. Y.

    2006-03-01

    Within the framework of biological application linked to ion irradiation, the fabrication of radioactive stents by ion implantation provides a significant improvement of the recovery of arteries after a treatment of stenosed coronary arteries [P. Fehsenfeld et al., Semin Interv Cardiol. 3, 157 (1998); E. Huttel et al., Rev. Sci. Instrum. 73, 825 (2002); M.-A. Golombeck et al., Nucl. Instrum. Methods Phys. Res. B 206, 495 (2003)]. For this appliance, the suitable radioactive ion is P32. Obviously, in order to have a minimum loss of these radioactive ions through the ionization process, it is imperative to have high ionization efficiency. In this article, the production of such singly and multiply charged phosphorous beams is investigated using two different electron cyclotron resonance ion sources: MONO1000/1001 [P. Jardin et al., Rev. Sci. Instrum. 73, 789 (2002)] and SUPERSHyPIE [J. Y. Pacquet et al., EP Patent No. 97 401294 (pending); R. Leroy et al., 14th International Workshop on ECR Ion Sources, May 1999 (unpublished)]. Spectra and above all efficiencies [J. Y. Pacquet et al., GANIL R 02 07; GANIL R 03 08] (31% of ionization efficiency for phosphorous atoms and compound with MONO1000/1001 and 43% of ionization efficiency for phosphorous atoms with SUPERSHyPIE) of these beams will be presented as well as the intensities (227eμA for P+ with MONO1000/1001 and 145eμA for P7+ with SUPERSHyPIE) of such beams.

  7. Image analysis of single event transient effects on charge coupled devices irradiated by protons

    NASA Astrophysics Data System (ADS)

    Wang, Zujun; Xue, Yuanyuan; Liu, Jing; He, Baoping; Yao, Zhibin; Ma, Wuying

    2016-10-01

    The experiments of single event transient (SET) effects on charge coupled devices (CCDs) irradiated by protons are presented. The radiation experiments have been carried out at the accelerator protons with the energy of 200 MeV and 60 MeV.The incident angles of the protons are at 30°and 90° to the plane of the CCDs to obtain the images induced by the perpendicularity and incline incident angles. The experimental results show that the typical characteristics of the SET effects on a CCD induced by protons are the generation of a large number of dark signal spikes (hot pixels) which are randomly distributed in the "pepper" images. The characteristics of SET effects are investigated by observing the same imaging area at different time during proton radiation to verify the transient effects. The experiment results also show that the number of dark signal spikes increases with increasing integration time during proton radiation. The CCDs were tested at on-line and off-line to distinguish the radiation damage induced by the SET effects or DD effects. The mechanisms of the dark signal spike generation induced by the SET effects and the DD effects are demonstrated respectively.

  8. Silver deposition on a polymer substrate catalyzed by singly charged monodisperse copper nanoparticles.

    PubMed

    Byeon, Jeong Hoon; Roberts, Jeffrey T

    2012-05-01

    Aerosol deposition of singly charged monodisperse copper nanoparticles was used to catalytically activate a polymer substrate for electroless silver deposition. An ambient spark discharge was used to produce aerosol copper nanoparticles, and the particles were electrostatically classified at an equivalent mobility diameter of 10 nm, using a nanodifferential mobility analyzer. Deposition of the copper particles onto the surface of the substrate was enhanced by thermophoresis. The copper-deposited substrate was then immersed in a Ag(I) solution, resulting in the electroless deposition of silver (∼17 μm line width) on the previously deposited copper (∼12 μm line width, using a shadow mask with a 100 μm in width patterned stripe). The arithmetic mean roughness and electrical resistivity of the silver pattern were 44.7 nm and 7.9 μΩ cm, respectively, which showed an enhancement compared to those from the nonclassified copper particles (roughness = 162.2 nm, resistivity = 13.3 μΩ cm), because of a more-uniform copper deposition.

  9. Delay coordinates: a sensitive indicator of nonlinear dynamics in single charged particle motion in magnetic reversals

    NASA Astrophysics Data System (ADS)

    Chapman, Sandra C.; Watkins, Nicholas W.

    1995-08-01

    The delay coordinate technique is examined as an indicator of the regime of particle dynamics for the system of single charged particle motion in magnetic reversals. Examples of numerically integrated trajectories in both static (zero electric field) and time dependent (corresponding nonzero induction electric field) simple models for magnetic reversals are considered. In the static case, the dynamics can in principle be directly classified by constructing Poincaré surfaces of section; here we demonstrate that whilst the Poincaré surface contains the relevant information to classify the dynamics, the corresponding delay coordinate plot can provide a far more sensitive indication of the onset of nonregular behaviour. In the case of nonperiodic time dependence considered here Poincaré plots cannot in general be constructed directly. Nevertheless, delay coordinate plots can still reveal details of the phase space portrait of the system, and here are shown to indicate whether segments of stochastic motion exist in a given trajectory. It is anticipated that the delay coordinate plot technique as realized here will be a valuable tool in characterizing the behaviour in large numbers of trajectories that are evolved in time-dependent systems, thereby giving us insight into the evolution of the distribution function as a whole, either in prescribed fields or in self-consistent numerical simulations.

  10. Factors Associated with Serum B-Type Natriuretic Peptide in Infants with Single Ventricles

    PubMed Central

    Butts, Ryan J.; Zak, Victor; Hsu, Daphne; Cnota, James; Colan, Steven D.; Hehir, David; Kantor, Paul; Levine, Jami C.; Margossian, Renee; Richmond, Marc; Szwast, Anita; Williams, Derek; Williams, Richard; Atz, Andrew M.

    2014-01-01

    Background Data regarding the value of B-type natriuretic peptide measurements (BNP) in infants with single ventricle (SV) physiology are lacking. The objective of this analysis was to describe the changes in BNP in infants with SV physiology before and after superior cavopulmonary connection (SCPC) surgery. Methods BNP levels were measured by a core laboratory pre-SCPC (5.0 ± 1.6 months) and at age 14 months during a multicenter trial of angiotensin converting enzyme inhibition therapy in infants with SV. Multivariable longitudinal analysis was utilized to model the associations between BNP with three sets of grouped variables (echocardiographic, catheterization, growth). Multivariable analysis was performed to assess associations with patient characteristics at both visits. Associations between BNP and neurodevelopmental variables were investigated at the 14 month visit as neurodevelopmental assessment was performed only at this visit. Results BNP was significantly higher before SCPC (n=173) than at 14 months (n=134); median [IQR] 80.8 pg/ml [35–187] v. 34.5 pg/ml [17–67], p<0.01. BNP > 100 pg/ml was present in 72 (42%) subjects pre-SCPC and 21 (16%) at 14 months. In the 117 patients who had BNP at both visits, the median BNP decreased 32 pg/mL [1–79 pg/mL], p<0.01. In longitudinal multivariable analysis, higher BNP were associated with a higher end-systolic volume z-score (p=0.01), greater degree of atrioventricular (AV) valve regurgitation (p<0.01), lower weight z-score (p<0.01), and lower length z-score (p=0.02) In multivariable analyses, higher BNP at 14 months was associated with presence of arrhythmia post-SCPC surgery (p<0.01), prior Norwood procedure (p<0.01), longer length of hospital stay post-SCPC surgery (p=0.04), and lower Bayley Psychomotor Developmental Index (p=0.02). Conclusion BNP decreases in infants with SV from the pre- SCPC visit to 14 months. Higher BNP is associated with increased ventricular dilation in systole, increased AV valve

  11. Mixtures of oppositely charged polypeptides as high-performance dispersing agents for single-wall carbon nanotubes.

    PubMed

    Lee, Gordon K-C; Sach, Clare; Green, Malcolm L H; Wong, Luet-Lok; Salzmann, Christoph G

    2010-10-07

    A new and simple strategy for the dispersion of single-wall carbon nanotubes in aqueous media is presented which does not rely on hydrophobic interactions between the polypeptidic dispersing agent and the nanotubes, and allows the surface charge of the resulting conjugate materials to be controlled.

  12. Single-step immobilization of cell adhesive peptides on a variety of biomaterial substrates via tyrosine oxidation with copper catalyst and hydrogen peroxide.

    PubMed

    Kakinoki, Sachiro; Yamaoka, Tetsuji

    2015-04-15

    Immobilization of biologically active peptides which were isolated from extracellular matrix proteins is a powerful strategy for the design and functionalization of biomaterial substrates. However, the method of peptide immobilization was restricted, that is, peptide is often immobilized through the reactive groups inherent in substrates with multistep reactions. Here, we report a single-step immobilization of fibronectin-derived cell adhesive peptide (Arg-Glu-Asp-Val; REDV) onto polymer materials by use of tyrosine oxidation with copper catalyst and hydrogen peroxide. REDV peptide was successfully immobilized on tissue culture polystyrene, poly(ethylene terephthalate), poly(vinyl chloride), expanded-poly(tetrafluoroethylene), and poly(l-lactic acid), resulting in enhanced adhesion of human umbilical vein endothelial cells. This method is a single-step reaction under very mild conditions and is available for the biological functionalization of various medical devices.

  13. Single photon emission at 1.55 μm from charged and neutral exciton confined in a single quantum dash

    SciTech Connect

    Dusanowski, Ł. Syperek, M.; Mrowiński, P.; Rudno-Rudziński, W.; Misiewicz, J.; Sęk, G.; Somers, A.; Kamp, M.; Höfling, S.; Reithmaier, J. P.

    2014-07-14

    We investigate charged and neutral exciton complexes confined in a single self-assembled InAs/InGaAlAs/InP quantum dash emitting at 1.55 μm. The emission characteristics have been probed by measuring high-spatial-resolution polarization-resolved photoluminescence and cross-correlations of photon emission statistics at T = 5 K. The photon auto-correlation histogram of the emission from both the neutral and charged exciton indicates a clear antibunching dip with as-measured g{sup (2)}(0) values of 0.18 and 0.31, respectively. It proves that these exciton complexes confined in single quantum dashes of InP-based material system can act as true single photon emitters being compatible with standard long-distance fiber communication technology.

  14. Accounting for changes in particle charge, dry mass and composition occurring during studies of single levitated particles.

    PubMed

    Haddrell, Allen E; Davies, James F; Yabushita, Akihiro; Reid, Jonathan P

    2012-10-11

    The most used instrument in single particle hygroscopic analysis over the past thirty years has been the electrodynamic balance (EDB). Two general assumptions are made in hygroscopic studies involving the EDB. First, it is assumed that the net charge on the droplet is invariant over the time scale required to record a hygroscopic growth cycle. Second, it is assumed that the composition of the droplet is constant (aside from the addition and removal of water). In this study, we demonstrate that these assumptions cannot always be made and may indeed prove incorrect. The presence of net charge in the humidified vapor phase reduces the total net charge retained by the droplet over prolonged levitation periods. The gradual reduction in charge limits the reproducibility of hygroscopicity measurements made on repeated RH cycles with a single particle, or prolonged experiments in which the particle is held at a high relative humidity. Further, two contrasting examples of the influence of changes in chemical composition changes are reported. In the first, simple acid-base chemistry in the droplet leads to the irreversible removal of gaseous ammonia from a droplet containing an ammonium salt on a time scale that is shorter than the hygroscopicity measurement. In the second example, the net charge on the droplet (<100 fC) is high enough to drive redox chemistry within the droplet. This is demonstrated by the reduction of iodic acid in a droplet made solely of iodic acid and water to form iodine and an iodate salt.

  15. Electron-induced dissociation of singly charged organic cations as a tool for structural characterization of pharmaceutical type molecules.

    PubMed

    Mosely, Jackie A; Smith, Michael J P; Prakash, Aruna S; Sims, Martin; Bristow, Anthony W T

    2011-06-01

    Collision-induced dissociation (CID) and electron-induced dissociation (EID) have been investigated for a selection of small, singly charged organic molecules of pharmaceutical interest. Comparison of these techniques has shown that EID carried out on an FTICR MS and CID performed on a linear ion trap MS produce complementary data. In a study of 33 molecule-cations, EID generated over 300 product ions compared to 190 product ions by CID with an average of only 3 product ions per precursor ion common to both tandem MS techniques. Even multiple stages of CID failed to generate many of the product ions observed following EID. The charge carrying species is also shown to have a very significant effect on the degree of fragmentation and types of product ion resulting from EID. Protonated species behave much like the ammonium adduct with suggestion of a hydrogen atom from the charge carrying species strongly affecting the fragmentation mechanism. Sodium and potassium are retained by nearly every product ion formed from [M + Na](+) or [M + K](+) and provide information to complement the EID of [M + H](+) or [M + NH(4)](+). In summary, EID is proven to be a fitting partner to CID in the structural elucidation of small singly charged ions and by studying EID of a molecule-ion holding different charge carrying species, an even greater depth of detail can be obtained for functional groups commonly used in synthetic chemistry.

  16. Active charge state control of single NV centres in diamond by in-plane Al-Schottky junctions

    NASA Astrophysics Data System (ADS)

    Schreyvogel, C.; Polyakov, V.; Wunderlich, R.; Meijer, J.; Nebel, C. E.

    2015-07-01

    In this paper, we demonstrate an active control of the charge state of a single nitrogen-vacancy (NV) centre by using in-plane Schottky-diode geometries with aluminium on hydrogen-terminated diamond surface. A switching between NV+, NV0 and NV- can be performed with the Al-gates which apply electric fields in the hole depletion region of the Schottky junction that induces a band bending modulation, thereby shifting the Fermi-level over NV charge transition levels. We simulated the in-plane band structure of the Schottky junction with the Software ATLAS by solving the drift-diffusion model and the Poisson-equation self-consistently. We simulated the IV-characteristics, calculated the width of the hole depletion region, the position of the Fermi-level intersection with the NV charge transition levels for different reverse bias voltages applied on the Al-gate. We can show that the field-induced band bending modulation in the depletion region causes a shifting of the Fermi-level over NV charge transition levels in such a way that the charge state of a single NV centre and thus its electrical and optical properties is tuned. In addition, the NV centre should be approx. 1-2 μm away from the Al-edge in order to be switched with moderate bias voltages.

  17. Taming the Wildness of "Trojan-Horse" Peptides by Charge-Guided Masking and Protease-Triggered Demasking for the Controlled Delivery of Antitumor Agents.

    PubMed

    Shi, Nian-Qiu; Qi, Xian-Rong

    2017-03-14

    Cell-penetrating peptide (CPP), also called "Trojan Horse" peptide, has become a successful approach to deliver various payloads into cells for achieving the intracellular access. However, the "Trojan Horse" peptide is too wild, not just to "Troy", but rather widely distributed in the body. Thus, there is an urgent need to tame the wildness of "Trojan Horse" peptide for targeted delivery of antineoplastic agents to the tumor site. To achieve this goal, we exploit a masked CPP-doxorubicin conjugate platform for targeted delivery of chemotherapeutic drugs using charge-guided masking and protease-triggered demasking strategies. In this platform, the cell-penetrating function of the positively CPP (d-form nonaarginine) is abrogated by a negatively shielding peptide (masked CPP), and between them is a cleavable substrate peptide by the protease (MMP-2/9). Protease-triggered demasking would occur when the masked CPP reached the MMP-2/9-riched tumor. The CPP-doxorubicin conjugate (CPP-Dox) and the masked CPP-Dox conjugate (mCPP-Dox) were used as models for the evaluation of masking and demasking processes. It was found that exogenous MMP-2/9 could effectively trigger the reversion of CPP-cargo in this conjugate, and this trigger adhered to the Michaelis-Menten kinetics profile. This conjugate was sensitive to the trigger of endogenous MMP-2/9 and could induce enhanced cytotoxicity toward MMP-2/9-rich tumor cells. In vivo antitumor efficacy revealed that this masked conjugate had considerable antitumor activity and could inhibit the tumor growth at a higher level relative to CPP-cargo. Low toxicity in vivo showed the noticeably decreased wildness of this conjugate toward normal tissues and more controllable entry of antitumor agents into "Troy". On the basis of analyses in vitro and in vivo, this mCPP-cargo conjugate delivery system held an improved selectivity toward MMP-2/9-rich tumors and would be a promising strategy for tumor-targeted treatment.

  18. Characterization of natural peptide ligands for HLA-B*4402 and -B*4403: implications for peptide involvement in allorecognition of a single amino acid change in the HLA-B44 heavy chain.

    PubMed

    Fleischhauer, K; Avila, D; Vilbois, F; Traversari, C; Bordignon, C; Wallny, H J

    1994-11-01

    This study describes the characterization of endogenous peptides associated with the two major subtypes of HLA-B44. The two subtypes differ for a single amino acid substitution from Asp (HLA-B*4402) to Leu (HLA-B*4403) in position 156 of the alpha 2 domain, causing strong alloreactivity in vivo. In order to study the involvement of peptides in this phenomenon, the peptide motifs of the two subtypes were determined from natural peptide pools using Edman degradation. The motif was found to be essentially identical for HLA-B*4402 and -B*4403, with a strong predominance for Glu at position 2, Tyr or Phe at positions 9 and 10 and hydrophobic residues, especially Met, at position 3. Two individual naturally processed ligands of HLA-B*4403 were sequenced and shown to be derived from intracellularly expressed proteins found in protein sequence databases. The sequence of these natural peptide ligands conform well to the determined motif. These data will allow the prediction of HLA-B44 restricted peptide epitopes from viral and tumor antigens of known amino acid sequences. Moreover, they indicate that the peptide repertoire presented by HLA-B*4402 and -B*4403 is very similar, suggesting that the strong alloresponse between these two subtypes is not due to presentation of a different set of self peptides.

  19. Molecular simulation of flavin adenine dinucleotide immobilized on charged single-walled carbon nanotubes for biosensor applications.

    PubMed

    Yang, Guang; Kang, Zhengzhong; Ye, Xuesong; Wu, Tao; Zhu, Qin

    2012-12-01

    The reconstitution of apo-glucose oxidase (apo-GOx) on single-walled carbon nanotubes (SWNTs) functionalized with the cofactor, flavin adenine dinucleotide (FAD), greatly improved electron transfer turnover rate of the redox reactions in glucose sensing with glucose sensors. The research reported here is aimed to better understand molecular details of affection of the charging SWNT to the conformational changes of FAD, in order to find a rational design and selection scheme of SWNT which is suitable for the FAD and apo-GOx to perform their reconstitution. In this report, molecular simulations of FAD functionalized differently charged SWNTs were carried outin an aqueous environment, with counterions to maintain total charge neutrality. The conformation and orientation changes were observed by both trajectory and quantitative analyses. The simulation results showed that in both uncharged and positively charged SWNT situations, FAD adsorbed onto SWNT at the end of the simulations, which increased the steric resistance of molecules and hindered the reconstitution of apo-GOx and FAD to some degree. By contrast, FAD functionalized negatively charged SWNT maintained its original conformation largely. In addition, negatively charged SWNT may be the best choice for electron transfer mediator for the reconstitution of apo-GOx on relay-cofactor units associated with electrodes. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Laserspray Ionization, a New Atmospheric Pressure MALDI Method for Producing Highly Charged Gas-phase Ions of Peptides and Proteins Directly from Solid Solutions*

    PubMed Central

    Trimpin, Sarah; Inutan, Ellen D.; Herath, Thushani N.; McEwen, Charles N.

    2010-01-01

    The first example of a matrix-assisted laser desorption/ionization (MALDI) process producing multiply charged mass spectra nearly identical to those observed with electrospray ionization (ESI) is presented. MALDI is noted for its ability to produce singly charged ions, but in the experiments described here multiply charged ions are produced by laser ablation of analyte incorporated into a common MALDI matrix, 2,5-dihydroxybenzoic acid, using standard solvent-based sample preparation protocols. Laser ablation is known to produce matrix clusters in MALDI provided a threshold energy is achieved. We propose that these clusters (liquid droplets) are highly charged, and under conditions that produce sufficient matrix evaporation, ions are field-evaporated from the droplets similarly to ESI. Because of the multiple charging, advanced mass spectrometers with limited mass-to-charge range can be used for protein characterization. Thus, using an Orbitrap mass spectrometer, low femtomole quantities of proteins produce full-range mass spectra at 100,000 mass resolution with <5-ppm mass accuracy and with 1-s acquisition. Furthermore, the first example of protein fragmentation using electron transfer dissociation with MALDI is presented. PMID:19955086

  1. Laserspray ionization, a new atmospheric pressure MALDI method for producing highly charged gas-phase ions of peptides and proteins directly from solid solutions.

    PubMed

    Trimpin, Sarah; Inutan, Ellen D; Herath, Thushani N; McEwen, Charles N

    2010-02-01

    The first example of a matrix-assisted laser desorption/ionization (MALDI) process producing multiply charged mass spectra nearly identical to those observed with electrospray ionization (ESI) is presented. MALDI is noted for its ability to produce singly charged ions, but in the experiments described here multiply charged ions are produced by laser ablation of analyte incorporated into a common MALDI matrix, 2,5-dihydroxybenzoic acid, using standard solvent-based sample preparation protocols. Laser ablation is known to produce matrix clusters in MALDI provided a threshold energy is achieved. We propose that these clusters (liquid droplets) are highly charged, and under conditions that produce sufficient matrix evaporation, ions are field-evaporated from the droplets similarly to ESI. Because of the multiple charging, advanced mass spectrometers with limited mass-to-charge range can be used for protein characterization. Thus, using an Orbitrap mass spectrometer, low femtomole quantities of proteins produce full-range mass spectra at 100,000 mass resolution with <5-ppm mass accuracy and with 1-s acquisition. Furthermore, the first example of protein fragmentation using electron transfer dissociation with MALDI is presented.

  2. Novel pH-sensitive charge-reversal cell penetrating peptide conjugated PEG-PLA micelles for docetaxel delivery: in vitro study.

    PubMed

    Ouahab, Ammar; Cheraga, Nihad; Onoja, Vitus; Shen, Yan; Tu, Jiasheng

    2014-05-15

    In order to create a pH-sensitive charge-reversal system for cell penetrating peptides (CPP) to prevent non-specific internalization of the drug; and concomitantly enhance the physical stability and tumor targetability of poly(ethylene glycol)-poly(d,l-lactide) (PEG-PLA) micelles, two sets of novel PEG-PLA micelles were developed. Cell penetrating decapeptide arginine-glycine (RG)5 and a pH-sensitive masking decapeptide histidine-glutamic acid (HE)5 were conjugated at the PEG free end to produce pH sensitive with peptides outside micelles (PHPO), while the pH sensitive with peptides inside micelles (PHPI) are the micelles obtained with the two peptides conjugated to the free end of the PLA block. The polymers were successfully synthesized and characterized by (1)H NMR and GPC. The mixed micelles were prepared and characterized for their loading efficiency, particle size and zeta potential. The surface charge of PHPO was greatly affected by the pH of the solution and (RG)5:(HE)5 ratio at the surface. The pH value of the solution at which the surface charge of PHPO reversed could be manipulated by the feed ratio of (RG)5-PEG-PLA (RGO) and (HE)5-PEG-PLA (HEO), hence, HEO:RGO molar ratio of 45:55 was selected for tumor targeting. Docetaxel (DTX) was sufficiently solubilized by DTX-PHPO with a loading efficiency of 90.18 ± 1.65%. At pH 7.4, DTX loaded mPEG-PLA (DTX-PM) (41.2 ± 0.3 nm), DTX-PHPO (195.3 ± 1.9 nm) and DTX-PHPI (190.9 ± 4.5 nm) showed sustained DTX release of less than 55% within 48 h. However, at pH 6.8 DTX-PHPI released 87.29 ± 0.24%, while DTX-PHPO released 70.49 ± 0.39% of the initial DTX amount within 48 h. Moreover, the physical stability of DTX-PHPO was increased due to the electrostatic interaction of the two peptides. The cellular uptake of DTX-PHPO in SGC-7901 cells and the cell killing effect tested on MCF-7 cells were enhanced by 2 folds at pH 6.8 compared to pH 7.4. Hence, DTX-PHPO is highly pH-sensitive in mildly acidic pH and exhibited

  3. Fast detection of single-charge tunneling to a graphene quantum dot in a multi-level regime

    NASA Astrophysics Data System (ADS)

    Müller, T.; Güttinger, J.; Bischoff, D.; Hellmüller, S.; Ensslin, K.; Ihn, T.

    2012-07-01

    In situ-tunable radio-frequency reflectometry is used for fast charge-detection measurements on a graphene single quantum dot. The variable capacitance of our special matching network both grants tunability and compensates for the large stray capacitance between the charge sensor's contacts and the doped silicon oxide backgate. To demonstrate the high detection bandwidth thus achieved, the rates for tunneling into and out of the dot through the same barrier are determined. Finally, an analytical model for calculating these rates in the multi-level tunneling regime is presented and found to correspond very well to our experimental observations.

  4. Anderson Insulators in Self-Assembled Gold Nanoparticles Thin Films: Single Electron Hopping between Charge Puddles Originated from Disorder.

    PubMed

    Jiang, Cheng-Wei; Ni, I-Chih; Hsieh, Yun-Lien; Tzeng, Shien-Der; Wu, Cen-Shawn; Kuo, Watson

    2017-06-12

    The Anderson insulating states in Au nanoparticle assembly are identified and studied under the application of magnetic fields and gate voltages. When the inter-nanoparticle tunneling resistance is smaller than the quantum resistance, the system showing zero Mott gap can be insulating at very low temperature. In contrast to Mott insulators, Anderson insulators exhibit great negative magnetoresistance, inferring charge delocalization in a strong magnetic field. When probed by the electrodes spaced by ~200 nm, they also exhibit interesting gate-modulated current similar to the multi-dot single electron transistors. These results reveal the formation of charge puddles due to the interplay of disorder and quantum interference at low temperatures.

  5. Twisted intra-molecular charge transfer investigations of semiorganic triglycine phosphate single crystal for non linear optical applications

    NASA Astrophysics Data System (ADS)

    Meera, M. R.; Joselin Beaula, T.; Rayar, S. L.; Bena Jothy, V.

    2017-09-01

    NLO materials are gaining importance in technologies such as optical communication, optical computing and dynamic image processing. Many NLO crystals grown by mixing amino acids with various organic and inorganic acids have been reported in the literature. Hence, glycine mixed semi-organic material will be of special interest as a fundamental building block to develop many complex crystals with improved NLO properties. A semi organic Single crystal of Triglycine Phosphate (TGP) which was grown and spectral analysis have been using FTIR and Raman spectral analysis. Natural Bond Orbital Analysis and the atomic natural charges are also predicted. HOMO LUMO energy gap value suggests the possibility of charge transfer within the molecule.

  6. Back-action-induced excitation of electrons in a silicon quantum dot with a single-electron transistor charge sensor

    SciTech Connect

    Horibe, Kosuke; Oda, Shunri; Kodera, Tetsuo

    2015-02-02

    Back-action in the readout of quantum bits is an area that requires a great deal of attention in electron spin based-quantum bit architecture. We report here back-action measurements in a silicon device with quantum dots and a single-electron transistor (SET) charge sensor. We observe the back-action-induced excitation of electrons from the ground state to an excited state in a quantum dot. Our measurements and theoretical fitting to the data reveal conditions under which both suitable SET charge sensor sensitivity for qubit readout and low back-action-induced transition rates (less than 1 kHz) can be achieved.

  7. Characteristics control of room-temperature operating single electron transistor with floating gate by charge pump circuit

    NASA Astrophysics Data System (ADS)

    Nozue, Motoki; Suzuki, Ryota; Nomura, Hirotoshi; Saraya, Takuya; Hiramoto, Toshiro

    2013-10-01

    A single electron transistor (SET) with floating gate, which has a non-volatile memory effect, is successfully integrated with a charge pump circuit that consists of conventional MOS circuits on the same chip. By applying high voltage generated by the charge pump circuit to SET with floating gate, characteristics control of the Coulomb blockade oscillation is demonstrated at room temperature for the first time. This attempt will open a new path of adding new functionality to conventional MOS circuits by integration with so-called "Beyond CMOS" devices.

  8. Charge integration successive approximation analog-to-digital converter for focal plane applications using a single amplifier

    NASA Technical Reports Server (NTRS)

    Zhou, Zhimin (Inventor); Pain, Bedabrata (Inventor)

    1999-01-01

    An analog-to-digital converter for on-chip focal-plane image sensor applications. The analog-to-digital converter utilizes a single charge integrating amplifier in a charge balancing architecture to implement successive approximation analog-to-digital conversion. This design requires minimal chip area and has high speed and low power dissipation for operation in the 2-10 bit range. The invention is particularly well suited to CMOS on-chip applications requiring many analog-to-digital converters, such as column-parallel focal-plane architectures.

  9. Measurement of Muon Neutrino Charged Current Single $\\pi^0$ Production on Hydrocarbon using MINERvA

    SciTech Connect

    Altinok, Ozgur

    2017-01-01

    A sample of charged-current single pion production events for the semi- exclusive channel νµ + CH → µ-π0 + nucleon(s) has been obtained using neutrino exposures of the MINERvA detector. Differential cross sections for muon momentum, muon production angle, pion momentum, pion production angle, and four-momentum transfer square Q2 are reported and are compared to a GENIE-based simulation. The cross section versus neutrino energy is also re- ported. The effects of pion final-state interactions on these cross sections are investigated. The effect of baryon resonance suppression at low Q2 is examined and an event re-weight used by two previous experiments is shown to improve the data versus simulation agreement. The differential cross sections for Q2 for Eν < 4.0 GeV and Eν ≥ 4.0 GeV are examined and the shapes of these distributions are compared to those from the experiment’s $\\bar{v}$µ-CC (π0) measurement. The polarization of the pπ0 system is measured and compared to the simulation predictions. The hadronic invariant mass W distribution is examined for evidence of resonance content, and a search is reported for evidence of a two-particle two-hole (2p2h) contribution. All of the differential cross-section measurements of this Thesis are compared with published MINERvA measurements for νµ-CC (π+) and \\bar{v}$µ-CC (π0) processes.

  10. Anisotropy, phonon modes, and free charge carrier parameters in monoclinic β -gallium oxide single crystals

    NASA Astrophysics Data System (ADS)

    Schubert, M.; Korlacki, R.; Knight, S.; Hofmann, T.; Schöche, S.; Darakchieva, V.; Janzén, E.; Monemar, B.; Gogova, D.; Thieu, Q.-T.; Togashi, R.; Murakami, H.; Kumagai, Y.; Goto, K.; Kuramata, A.; Yamakoshi, S.; Higashiwaki, M.

    2016-03-01

    We derive a dielectric function tensor model approach to render the optical response of monoclinic and triclinic symmetry materials with multiple uncoupled infrared and far-infrared active modes. We apply our model approach to monoclinic β -Ga2O3 single-crystal samples. Surfaces cut under different angles from a bulk crystal, (010) and (2 ¯01 ), are investigated by generalized spectroscopic ellipsometry within infrared and far-infrared spectral regions. We determine the frequency dependence of 4 independent β -Ga2O3 Cartesian dielectric function tensor elements by matching large sets of experimental data using a point-by-point data inversion approach. From matching our monoclinic model to the obtained 4 dielectric function tensor components, we determine all infrared and far-infrared active transverse optic phonon modes with Au and Bu symmetry, and their eigenvectors within the monoclinic lattice. We find excellent agreement between our model results and results of density functional theory calculations. We derive and discuss the frequencies of longitudinal optical phonons in β -Ga2O3 . We derive and report density and anisotropic mobility parameters of the free charge carriers within the tin-doped crystals. We discuss the occurrence of longitudinal phonon plasmon coupled modes in β -Ga2O3 and provide their frequencies and eigenvectors. We also discuss and present monoclinic dielectric constants for static electric fields and frequencies above the reststrahlen range, and we provide a generalization of the Lyddane-Sachs-Teller relation for monoclinic lattices with infrared and far-infrared active modes. We find that the generalized Lyddane-Sachs-Teller relation is fulfilled excellently for β -Ga2O3 .

  11. Fullerene-Assisted Photoinduced Charge Transfer of Single-Walled Carbon Nanotubes through a Flavin Helix.

    PubMed

    Mollahosseini, Mehdi; Karunaratne, Erandika; Gibson, George N; Gascón, Jose A; Papadimitrakopoulos, Fotios

    2016-05-11

    One of the greatest challenges with single-walled carbon nanotube (SWNT) photovoltaics and nanostructured devices is maintaining the nanotubes in their pristine state (i.e., devoid of aggregation and inhomogeneous doping) so that their unique spectroscopic and transport characteristics are preserved. To this effect, we report on the synthesis and self-assembly of a C60-functionalized flavin (FC60), composed of PCBM and isoalloxazine moieties attached on either ends of a linear, C-12 aliphatic spacer. Small amounts of FC60 (up to 3 molar %) were shown to coassembly with an organic soluble derivative of flavin (FC12) around SWNTs and impart effective dispersion and individualization. A key annealing step was necessary to perfect the isoalloxazine helix and expel the C60 moiety away from the nanotubes. Steady-state and transient absorption spectroscopy illustrate that 1% or higher incorporation of FC60 allows for an effective photoinduced charge transfer quenching of the encased SWNTs through the seamless helical encase. This is enabled via the direct π-π overlap between the graphene sidewalls, isoalloxazine helix, and the C60 cage that facilitates SWNT exciton dissociation and electron transfer to the PCBM moiety. Atomistic molecular simulations indicate that the stability of the complex originates from enhanced van der Waals interactions of the flexible spacer wrapped around the fullerene that brings the C60 in π-π overlap with the isoalloxazine helix. The remarkable spectral purity (in terms of narrow E(S)ii line widths) for the resulting ground-state complex signals a new class of highly organized supramolecular nanotube architecture with profound importance for advanced nanostructured devices.

  12. Air charged and microtip catheters cannot be used interchangeably for urethral pressure measurement: a prospective, single-blind, randomized trial.

    PubMed

    Zehnder, Pascal; Roth, Beat; Burkhard, Fiona C; Kessler, Thomas M

    2008-09-01

    We determined and compared urethral pressure measurements using air charged and microtip catheters in a prospective, single-blind, randomized trial. A consecutive series of 64 women referred for urodynamic investigation underwent sequential urethral pressure measurements using an air charged and a microtip catheter in randomized order. Patients were blinded to the type and sequence of catheter used. Agreement between the 2 catheter systems was assessed using the Bland and Altman 95% limits of agreement method. Intraclass correlation coefficients of air charged and microtip catheters for maximum urethral closure pressure at rest were 0.97 and 0.93, and for functional profile length they were 0.9 and 0.78, respectively. Pearson's correlation coefficients and Lin's concordance coefficients of air charged and microtip catheters were r = 0.82 and rho = 0.79 for maximum urethral closure pressure at rest, and r = 0.73 and rho = 0.7 for functional profile length, respectively. When applying the Bland and Altman method, air charged catheters gave higher readings than microtip catheters for maximum urethral closure pressure at rest (mean difference 7.5 cm H(2)O) and functional profile length (mean difference 1.8 mm). There were wide 95% limits of agreement for differences in maximum urethral closure pressure at rest (-24.1 to 39 cm H(2)O) and functional profile length (-7.7 to 11.3 mm). For urethral pressure measurement the air charged catheter is at least as reliable as the microtip catheter and it generally gives higher readings. However, air charged and microtip catheters cannot be used interchangeably for clinical purposes because of insufficient agreement. Hence, clinicians should be aware that air charged and microtip catheters may yield completely different results, and these differences should be acknowledged during clinical decision making.

  13. Thermal and single frequency counter-current ultrasound pretreatments of sodium caseinate: enzymolysis kinetics and thermodynamics, amino acids composition, molecular weight distribution and antioxidant peptides.

    PubMed

    Abdualrahman, Mohammed Adam Y; Ma, Haile; Zhou, Cunshan; Yagoub, Abu ElGasim A; Hu, Jiali; Yang, Xue

    2016-12-01

    Due to the disadvantages of traditional enzymolysis, pretreatments are crucial to enhance protein enzymolysis. Enzymolysis kinetics and thermodynamics, amino acids composition, molecular weight distribution, fluorescence spectroscopy and antioxidant activity of thermal (HT) and single frequency counter-current ultrasound (SCFU) pretreated sodium caseinate (NaCas) were studied. Enzymolysis of untreated NaCas (control) improved significantly (P < 0.05) by SFCU and followed by HT. Values of the Michaelis-Menten constant (KM ) of SFCU and HT were 0.0212 and 0.0250, respectively. HT and SFCU increased (P < 0.05) the reaction rate constant (k) by 38.64 and 90.91%, respectively at 298 K. k values decreased with increasing temperature. The initial activation energy (46.39 kJ mol(-1) ) reduced (P < 0.05) by HT (39.66 kJ mol(-1) ) and further by SFCU (33.42 kJ mol(-1) ). SFCU-pretreated NaCas hydrolysates had the highest contents of hydrophobic, aromatic, positively and negatively charged amino acids. Medium-sized peptides (5000-1000 Da) are higher in SFCU (78.11%) than HT and the control. SFCU induced molecular unfolding of NaCas proteins. Accordingly, SFCU-pretreated NaCas hydrolysate exhibited the highest scavenging activity on DPPH and hydroxyl radicals, reducing power, and iron chelating ability. SFCU pretreatment would be a useful tool for production of bioactive peptides from NaCas hydrolysate. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  14. Proton magnetic resonance studies on peptide fragments of troponin-C containing single calcium-binding sites.

    PubMed

    Leavis, P C; Evans, J S; Levine, B A

    1982-07-01

    Proton magnetic resonance spectroscopy has been employed to study the solution conformation of three cleavage fragments of troponin-C, each containing a single Ca(II)-binding site and corresponding to different regions in the primary sequence; viz. CB8 (residues 46-77), CB9 (residues 85-134) and TH2 (residues 121-159). Although all three peptides lack a well-defined tertiary fold in the absence of metal ions, several spectral features indicate the presence of local conformational constraints in each apo-peptide. Ca(II) binding led to spectral changes consistent with increased restriction of backbone motility and the adoption of a more compact conformation. Studies using paramagnetic ions as conformational probes support current views concerning the nature of the ligands at the metal binding sites. The nature and kinetics of the structural influence of metal binding suggest that the conformational constraints existing in the CB8 apo-peptide provide an adequate Ca(II)-binding configuration. In contrast, the CB9 and TH2 peptides exhibit spectral changes consistent with an increased local structure in the region of helix E (residues 94-102) in the case of CB9 and helix H (residues 148-159) in the case of TH2. In CB9, conformation changes also appear to be transmitted to a portion of the sequence (residues 87-93) preceding helix E, a putative site of interaction between troponin-C and troponin-I. These data are discussed with reference to the contribution of long-range (interdomain) interactions within troponin-C and the modulation of troponin subunit protein-protein interactions by Ca(II) binding.

  15. Stochastic heating of a single Brownian particle by charge fluctuations in a radio-frequency produced plasma sheath.

    PubMed

    Schmidt, Christian; Piel, Alexander

    2015-10-01

    The Brownian motion of a single particle in the plasma sheath is studied to separate the effect of stochastic heating by charge fluctuations from heating by collective effects. By measuring the particle velocities in the ballistic regime and by carefully determining the particle mass from the Epstein drag it is shown that for a pressure of 10 Pa, which is typical of many experiments, the proper kinetic temperature of the Brownian particle remains close to the gas temperature and rises only slightly with particle size. This weak effect is confirmed by a detailed model for charging and charge fluctuations in the sheath. A substantial temperature rise is found for decreasing pressure, which approximately shows the expected scaling with p(-2). The system under study is an example for non-equilibrium Brownian motion under the influence of white noise without corresponding dissipation.

  16. Effective Control of the Charge and Magnetic States of Transition-Metal Atoms on Single-Layer Boron Nitride

    NASA Astrophysics Data System (ADS)

    Huang, Bing; Xiang, Hongjun; Yu, Jaejun; Wei, Su-Huai

    2012-05-01

    Developing approaches to effectively control the charge and magnetic states is critical to the use of magnetic nanostructures in quantum information devices but is still challenging. Here we suggest that the magnetic and charge states of transition-metal (TM) doped single-layer boron-nitride (SLBN) systems can be easily controlled by the (internal) defect engineering and (external) electric fields (Eext). The relative positions and symmetries of the in-gap levels induced by defect engineering and the TM d-orbital energy levels effectively determine the charge states and magnetic properties of the TM/SLBN system. Remarkably, the application of an Eext can easily control the size of the crystal field splitting of the TM d orbitals and thus, leading to the spin crossover in TM/SLBN, which could be used as Eext-driven nonvolatile memory devices. Our conclusion obtained from TM/SLBN is valid generally in other TM adsorbed layered semiconductors.

  17. Construction of a single polypeptide that matures and exports the lasso peptide microcin J25.

    PubMed

    Pan, Si Jia; Rajniak, Jakub; Cheung, Wai Ling; Link, A James

    2012-02-13

    Roped in: The lasso peptide microcin J25 (MccJ25) is matured by two enzymes and is exported by a putative ABC transporter. We probed the function of the maturation enzymes using mutagenesis. We demonstrate that fusions of the enzymes with intervening linkers can produce MccJ25. Even a 151 kDa tripartite fusion between the ABC transporter and the two enzymes is capable of producing and exporting MccJ25.

  18. Performance of single photon-counting X-ray charge coupled devices

    NASA Technical Reports Server (NTRS)

    Riegler, G. R.; Stern, R. A.; Liewer, K.; Vescelus, F.; Nousek, J. A.; Garmire, G. P.

    1981-01-01

    Results of intial performance tests on X-ray sensing properties of charge-coupled devices (CCDs) are presented. CCDs have demonstrated excellent spatial resolution and good spectral resolution, superior to that of non-imaging proportional counters.

  19. Pion single- and double-charge-exchange reactions at low energies

    SciTech Connect

    Baer, H.W.

    1987-01-01

    The general features of pion charge-exchange reactions at energies of 20 to 80 MeV leading to nuclear isobaric-analog states (IAS) and double-isobaric-analog states (DIAS) are reviewed. The recent progress achieved in understanding the role of short-range N-N correlations in the double-charge-exchange reactions is presented. 36 refs., 21 figs., 2 tabs.

  20. A surface charge-switchable and folate modified system for co-delivery of proapoptosis peptide and p53 plasmid in cancer therapy.

    PubMed

    Chen, Si; Rong, Lei; Lei, Qi; Cao, Peng-Xi; Qin, Si-Yong; Zheng, Di-Wei; Jia, Hui-Zhen; Zhu, Jing-Yi; Cheng, Si-Xue; Zhuo, Ren-Xi; Zhang, Xian-Zheng

    2016-01-01

    To improve the tumor therapeutic efficiency and reduce undesirable side effects, ternary FK/p53/PEG-PLL(DA) complexes with a detachable surface shielding layer were designed. The FK/p53/PEG-PLL(DA) complexes were fabricated by coating the folate incorporated positively charged FK/p53 complexes with charge-switchable PEG-shield (PEG-PLL(DA)) through electrostatic interaction. At the physiological pH 7.4 in the bloodstream, PEG-PLL(DA) could extend the circulating time by shielding the positively charged FK/p53 complexes. After the accumulation of the FK/p53/PEG-PLL(DA) complexes in tumor sites, tumor-acidity-triggered charge switch led to the detachment of PEG-PLL(DA) from the FK/p53 complexes, and resulted in efficient tumor cell entry by folate-mediated uptake and electrostatic attraction. Stimulated by the high content glutathione (GSH) in cytoplasm, the cleavage of disulfide bond resulted in the liberation of proapoptosis peptide C-KLA(TPP) and the p53 gene, which exerted the combined tumor therapy by regulating both intrinsic and extrinsic apoptotic pathways. Both in vitro and in vivo studies confirmed that the ternary detachable complexes FK/p53/PEG-PLL(DA) could enhance antitumor efficacy and reduce adverse effects to normal cells. These findings indicate that the tumor-triggered decomplexation of FK/p53/PEG-PLL(DA) supplies a useful strategy for targeting delivery of different therapeutic agents in synergetic anticancer therapy. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Chemically assembled double-dot single-electron transistor analyzed by the orthodox model considering offset charge

    SciTech Connect

    Kano, Shinya; Maeda, Kosuke; Majima, Yutaka; Tanaka, Daisuke; Sakamoto, Masanori; Teranishi, Toshiharu

    2015-10-07

    We present the analysis of chemically assembled double-dot single-electron transistors using orthodox model considering offset charges. First, we fabricate chemically assembled single-electron transistors (SETs) consisting of two Au nanoparticles between electroless Au-plated nanogap electrodes. Then, extraordinary stable Coulomb diamonds in the double-dot SETs are analyzed using the orthodox model, by considering offset charges on the respective quantum dots. We determine the equivalent circuit parameters from Coulomb diamonds and drain current vs. drain voltage curves of the SETs. The accuracies of the capacitances and offset charges on the quantum dots are within ±10%, and ±0.04e (where e is the elementary charge), respectively. The parameters can be explained by the geometrical structures of the SETs observed using scanning electron microscopy images. Using this approach, we are able to understand the spatial characteristics of the double quantum dots, such as the relative distance from the gate electrode and the conditions for adsorption between the nanogap electrodes.

  2. Effect of body biasing on single-event induced charge collection in deep N-well technology

    NASA Astrophysics Data System (ADS)

    Ding, Yi; Hu, Jian-Guo; Qin, Jun-Rui; Tan, Hong-Zhou

    2015-07-01

    As the device size decreases, the soft error induced by space ions is becoming a great concern for the reliability of integrated circuits (ICs). At present, the body biasing technique is widely used in highly scaled technologies. In the paper, using the three-dimensional technology computer-aided design (TCAD) simulation, we analyze the effect of the body biasing on the single-event charge collection in deep N-well technology. Our simulation results show that the body biasing mainly affects the behavior of the source, and the effect of body biasing on the charge collection for the nMOSFET and pMOSFET is quite different. For the nMOSFET, the RBB will increase the charge collection, while the FBB will reduce the charge collection. For the pMOSFET, the effect of RBB on the SET pulse width is small, while the FBB has an adverse effect. Moreover, the differenceof the effect of body biasing on the charge collection is compared in deep N-well and twin well.

  3. Single-stranded DNA detection by solvent-induced assemblies of a metallo-peptide-based complex

    NASA Astrophysics Data System (ADS)

    Das, Priyadip; Reches, Meital

    2016-05-01

    DNA detection is highly important for the sensitive sensing of different pathogenic bacteria and viruses. The major challenge is to create a sensor that can selectively detect very small concentrations of DNA without the need for amplification or complicated equipment. Different technologies such as optical, electrochemical and microgravimetric approaches can detect DNA fragments. Here we show, for the first time, the use of self-assembled nanostructures generated by a metallo-peptide as an optical sensing platform for DNA detection. The system can selectively detect single stranded DNA fragments by fluorescence measurements as it can discriminate even one base mismatch and can perform in the presence of other interfering proteins. This system may be useful in lab-on-a-chip applications.DNA detection is highly important for the sensitive sensing of different pathogenic bacteria and viruses. The major challenge is to create a sensor that can selectively detect very small concentrations of DNA without the need for amplification or complicated equipment. Different technologies such as optical, electrochemical and microgravimetric approaches can detect DNA fragments. Here we show, for the first time, the use of self-assembled nanostructures generated by a metallo-peptide as an optical sensing platform for DNA detection. The system can selectively detect single stranded DNA fragments by fluorescence measurements as it can discriminate even one base mismatch and can perform in the presence of other interfering proteins. This system may be useful in lab-on-a-chip applications. Electronic supplementary information (ESI) available: Peptide and receptor synthesis, characterization of the final and intermediate products, experimental details and additional figures including SEM, TEM, DLS, XRD, UV analysis and AFM topographic analysis. See DOI: 10.1039/c5nr07714a

  4. Characterization of nanoprobe uptake in single cells: spatial and temporal tracking via SERS labeling and modulation of surface charge

    PubMed Central

    Gregas, Molly K.; Yan, Fei; Scaffidi, Jonathan; Wang, Hsin-Neng; Vo-Dinh, Tuan

    2014-01-01

    A critical aspect for use of nanoprobes in biomedical research and clinical applications involves fundamental spatial and temporal characterization of their uptake and distribution in cells. Raman spectroscopy and two-dimensional Raman imaging were used to identify and locate nanoprobes in single cells using surface-enhanced Raman scattering detection. To study the efficiency of cellular uptake, silver nanoparticles functionalized with three different positive-, negative-, and neutrally charged Raman labels were co-incubated with cell cultures and internalized via normal cellular processes. The surface charge on the nanoparticles was observed to modulate uptake efficiency, demonstrating a dual function of the surface modifications as tracking labels and as modulators of cell uptake. These results indicate that the functionalized nanoparticle construct has potential for sensing and delivery in single living cells and that use of surface-enhanced Raman scattering for tracking and detection is a practical and advantageous alternative to traditional fluorescence methods. PMID:20817123

  5. Direct Measurement of Pore Dynamics and Leakage Induced by a Model Antimicrobial Peptide in Single Vesicles and Cells.

    PubMed

    Burton, Matthew G; Huang, Qi M; Hossain, Mohammed A; Wade, John D; Palombo, Enzo A; Gee, Michelle L; Clayton, Andrew H A

    2016-06-28

    Antimicrobial peptides are promising therapeutic alternatives to counter growing antimicrobial resistance. Their precise mechanism of action remains elusive, however, particularly with respect to live bacterial cells. We investigated the interaction of a fluorescent melittin analogue with single giant unilamellar vesicles, giant multilamellar vesicles, and bilamellar Gram-negative Escherichia coli (E. coli) bacteria. Time-lapse fluorescence lifetime imaging microscopy was employed to determine the population distribution of the fluorescent melittin analogue between pore state and membrane surface state, and simultaneously measure the leakage of entrapped fluorescent species from the vesicle (or bacterium) interior. In giant unilamellar vesicles, leakage from vesicle interior was correlated with an increase in level of pore states, consistent with a stable pore formation mechanism. In giant multilamellar vesicles, vesicle leakage occurred more gradually and did not appear to correlate with increased pore states. Instead pore levels remained at a low steady-state level, which is more in line with coupled equilibria. Finally, in single bacterial cells, significant increases in pore levels were observed over time, which were correlated with only partial loss of cytosolic contents. These observations suggested that pore formation, as opposed to complete dissolution of membrane, was responsible for the leakage of contents in these systems, and that the bacterial membrane has an adaptive capacity that resists peptide attack. We interpret the three distinct pore dynamics regimes in the context of the increasing physical and biological complexity of the membranes.

  6. Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy.

    PubMed

    Das, Priyadip; Duanias-Assaf, Tal; Reches, Meital

    2017-03-06

    The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

  7. Effect of Copper and Zinc on the Single Molecule Self-Affinity of Alzheimer's Amyloid-β Peptides.

    PubMed

    Hane, Francis T; Hayes, Reid; Lee, Brenda Y; Leonenko, Zoya

    2016-01-01

    The presence of trace concentrations of metallic ions, such as copper and zinc, has previously been shown to drastically increase the aggregation rate and neurotoxicity of amyloid-β (Aβ), the peptide implicated in Alzheimer's disease (AD). The mechanism of why copper and zinc accelerate Aβ aggregation is poorly understood. In this work, we use single molecule force spectroscopy (SMFS) to probe the kinetic and thermodynamic parameters (dissociation constant, Kd, kinetic dissociation rate, koff, and free energy, ΔG) of the dissociation of an Aβ dimer, the amyloid species which initiates the amyloid cascade. Our results show that nanomolar concentrations of copper do not change the single molecule affinity of Aβ to another Aβ peptide in a statistically significant way, while nanomolar concentrations of zinc decrease the affinity of Aβ-Aβ by an order of magnitude. This suggests that the binding of zinc ion to Aβ may interfere with the binding of Aβ-Aβ, leading to a lower self-affinity.

  8. Effect of Copper and Zinc on the Single Molecule Self-Affinity of Alzheimer’s Amyloid-β Peptides

    PubMed Central

    Hane, Francis T.; Hayes, Reid; Lee, Brenda Y.; Leonenko, Zoya

    2016-01-01

    The presence of trace concentrations of metallic ions, such as copper and zinc, has previously been shown to drastically increase the aggregation rate and neurotoxicity of amyloid-β (Aβ), the peptide implicated in Alzheimer’s disease (AD). The mechanism of why copper and zinc accelerate Aβ aggregation is poorly understood. In this work, we use single molecule force spectroscopy (SMFS) to probe the kinetic and thermodynamic parameters (dissociation constant, Kd, kinetic dissociation rate, koff, and free energy, ΔG) of the dissociation of an Aβ dimer, the amyloid species which initiates the amyloid cascade. Our results show that nanomolar concentrations of copper do not change the single molecule affinity of Aβ to another Aβ peptide in a statistically significant way, while nanomolar concentrations of zinc decrease the affinity of Aβ-Aβ by an order of magnitude. This suggests that the binding of zinc ion to Aβ may interfere with the binding of Aβ-Aβ, leading to a lower self-affinity. PMID:26808970

  9. Measurement of differential cross sections for single neutral pion produced by charged-current interactions in MINERvA

    NASA Astrophysics Data System (ADS)

    Le, Trung; Minerva Collaboration

    2014-09-01

    MINERvA is a neutrino scattering experiment which uses the intense neutrino beam from the NuMI beam line at FNAL. The detector employs high spatial resolution, is fully active, and designed to study interactions of neutrinos using different nuclei. We present the differential cross sections for single neutral pion produced by charged-current interactions of anti-neutrinos in plastic scintillator. We also compare the differential cross sections to predictions by the GENIE event generator.

  10. Electropositive charge in alpha-defensin bactericidal activity: functional effects of Lys-for-Arg substitutions vary with the peptide primary structure.

    PubMed

    Llenado, R Alan; Weeks, Colby S; Cocco, Melanie J; Ouellette, André J

    2009-11-01

    Cationic amino acids contribute to alpha-defensin bactericidal activity. Curiously, although Arg and Lys have equivalent electropositive charges at neutral pH, alpha-defensins contain an average of nine Arg residues per Lys residue. To investigate the role of high alpha-defensin Arg content, all Arg residues in mouse Paneth cell alpha-defensin cryptdin 4 (Crp4) and rhesus myeloid alpha-defensin 4 (RMAD-4) were replaced with Lys to prepare (R/K)-Crp4 and (R/K)-RMAD-4, respectively. Lys-for-Arg replacements in Crp4 attenuated bactericidal activity and slowed the kinetics of Escherichia coli ML35 cell permeabilization, and (R/K)-Crp4 required longer exposure times to reduce E. coli cell survival. In marked contrast, Lys substitutions in RMAD-4 improved microbicidal activity against certain bacteria and permeabilized E. coli more effectively. Therefore, Arg-->Lys substitutions attenuated activity in Crp4 but not in RMAD-4, and the functional consequences of Arg-->Lys replacements in alpha-defensins are dependent on the peptide primary structure. In addition, the bactericidal effects of (R/K)-Crp4 and (R/K)-RMAD-4 were more sensitive to inhibition by NaCl than those of the native peptides, suggesting that the high Arg content of alpha-defensins may be under selection to confer superior microbicidal function under physiologic conditions.

  11. PH dependent adhesive peptides

    DOEpatents

    Tomich, John; Iwamoto, Takeo; Shen, Xinchun; Sun, Xiuzhi Susan

    2010-06-29

    A novel peptide adhesive motif is described that requires no receptor or cross-links to achieve maximal adhesive strength. Several peptides with different degrees of adhesive strength have been designed and synthesized using solid phase chemistries. All peptides contain a common hydrophobic core sequence flanked by positively or negatively charged amino acids sequences.

  12. Single-molecule investigation of the interactions between reconstituted planar lipid membranes and an analogue of the HP(2-20) antimicrobial peptide

    SciTech Connect

    Mereuta, Loredana; Luchian, Tudor Park, Yoonkyung; Hahm, Kyung-Soo

    2008-09-05

    In this study, we employed electrophysiology experiments carried out at the single-molecule level to study the mechanism of action of the HPA3 peptide, an analogue of the linear antimicrobial peptide, HP(2-20), isolated from the N-terminal region of the Helicobacter pylori ribosomal protein. Amplitude analysis of currents fluctuations induced by HPA3 peptide at various potentials in zwitterionic lipid membranes reveal the existence of reproducible conductive states in the stochastic behavior of such events, which directly supports the existence of transmembrane pores induced the peptide. From our data recorded both at the single-pore and macroscopic levels, we propose that the HPA3 pore formation is electrophoretically facilitated by trans-negative transmembrane potentials, and HPA3 peptides translocate into the trans monolayers after forming the pores. We present evidence according to which the decrease in the membrane dipole potential of a reconstituted lipid membranes leads to an augmentation of the membrane activity of HPA3 peptides, and propose that a lower electric dipole field of the interfacial region of the membrane caused by phloretin facilitates the surface-bound HPA3 peptides to break free from one leaflet of the membrane, insert into the membrane and contribute to pore formation spanning the entire thickness of the membrane.

  13. Single-molecule investigation of the interactions between reconstituted planar lipid membranes and an analogue of the HP(2-20) antimicrobial peptide.

    PubMed

    Mereuta, Loredana; Luchian, Tudor; Park, Yoonkyung; Hahm, Kyung-Soo

    2008-09-05

    In this study, we employed electrophysiology experiments carried out at the single-molecule level to study the mechanism of action of the HPA3 peptide, an analogue of the linear antimicrobial peptide, HP(2-20), isolated from the N-terminal region of the Helicobacter pylori ribosomal protein. Amplitude analysis of currents fluctuations induced by HPA3 peptide at various potentials in zwitterionic lipid membranes reveal the existence of reproducible conductive states in the stochastic behavior of such events, which directly supports the existence of transmembrane pores induced the peptide. From our data recorded both at the single-pore and macroscopic levels, we propose that the HPA3 pore formation is electrophoretically facilitated by trans-negative transmembrane potentials, and HPA3 peptides translocate into the trans monolayers after forming the pores. We present evidence according to which the decrease in the membrane dipole potential of a reconstituted lipid membranes leads to an augmentation of the membrane activity of HPA3 peptides, and propose that a lower electric dipole field of the interfacial region of the membrane caused by phloretin facilitates the surface-bound HPA3 peptides to break free from one leaflet of the membrane, insert into the membrane and contribute to pore formation spanning the entire thickness of the membrane.

  14. Growth of single crystal with a gradient of concentration of impurities by the Czochralski method using additional liquid charging

    NASA Astrophysics Data System (ADS)

    Galutskiy, V. V.; Vatlina, M. I.; Stroganova, E. V.

    2009-02-01

    Er- and Yb-doped congruent LiNbO 3 (CLN) single crystals and Cr 3+- and Mg 2+-doped stoichiometric LiNbO 3 (SLN) single crystals were grown by the Czochralski method using additional liquid charging. Changes in the absorption spectra of the transitions 2F 7/2→ 2F 5/2 in Yb 3+ ions and 4I 15/2→ 2H 11/2 in Er 3+ ions along the length of a single-crystal plate correlate with a specific gradient of concentration of Yb 3+ and Er 3+ ions in the crystal. The correlation of the absorption spectra of the optical centers of Cr 3+ ions in stoichiometric LiNbO 3 single crystals with the content of magnesium along the length of the crystal is reported.

  15. Multi-Hierarchical Self-Assembly of Collagen Mimetic Peptides into AAB Type Heterotrimers, Nanofibers and Hydrogels Driven by Charged Pair Interactions

    NASA Astrophysics Data System (ADS)

    O'Leary, Lesley Russell

    2011-12-01

    Replicating the multi-hierarchical self-assembly of collagen (peptide chain to triple helix to nanofiber and, finally, to a hydrogel) has long attracted scientists, both from the fundamental science perspective of supramolecular chemistry and for the potential biomedical applications perceived in tissue engineering. In terms of triple helical formation, collagen is the most abundant protein in the human body with at least 28 types, yet research involving collagen mimetic systems has only recently began to consider the innate ability of collagen to control helix composition and register. Collagen triple helices can be homotrimeric or heterotrimeric and while some types of natural collagen form only one specific composition of helix, others can form multiple. It is critical to fully understand and, if possible, reproduce the control that native collagen has on helix composition and register. In terms of nanofiber formation, many approaches to drive the self-assembly of synthetic systems through the same steps as natural collagen have been partially successful, but none have simultaneously demonstrated all levels of structural assembly. In this work, advancements in the ability to control helix composition and replicate the multi-hierarchical assembly of collagen are described. Both positive and negative design for the assembly of AAB type collagen heterotrimers were utilized by promoting heterotrimer formation though the use of charged amino acids to form intra-helix electrostatic interactions, while simultaneously discouraging homotrimers, resulting in the identification of multiple peptide systems with full control over the composition of the resulting triple helix. Similar salt-bridged hydrogen bonds between charged residues were incorporated into nanofiber forming peptides, one of which successfully assembled into sticky-ended triple helices, nanofibers with characteristic triple helical packing visible in the solution state, and strong hydrogels that are

  16. Measuring the Charge of a Single Dielectric Nanoparticle Using a High-Q Optical Microresonator

    NASA Astrophysics Data System (ADS)

    Chen, You-Ling; Jin, Wei-Liang; Xiao, Yun-Feng; Zhang, Xuming

    2016-10-01

    Measuring the charge of a nanoparticle is of great importance in many fields including optics, astronomy, biochemistry, atmospheric science, environmental engineering, and dusty plasma. Here, we propose to use a high-Q whispering-gallery-mode (WGM) optical microresonator to detect the surface and bulk charge of a dielectric nanoparticle. Because of the modification of nanoparticle conductivity induced by the surplus electrons, both the coupling strength between the nanoparticle and the WGM and the dissipation changes compared with the case of a neutral nanoparticle. The charge density can be inferred from the transmission spectrum of the WGM microresonator. By monitoring the mode splitting, the linewidth broadening or the resonance dip value of the transmission spectrum, surface (bulk) electron density as low as 0.007 nm-2 (0.001 nm-3) can be detected for nanoparticles with negative (positive) electron affinity. The high sensitivity is attributed to the ultranarrow resonance linewidth and small mode volume of the microresonator.

  17. Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer

    PubMed Central

    Gardner, Myles W.; Smith, Suncerae I.; Ledvina, Aaron R.; Madsen, James A.; Coon, Joshua J.; Schwartz, Jae C.; Stafford, George C.; Brodbelt, Jennifer S.

    2009-01-01

    A dual pressure linear ion trap mass spectrometer was modified to permit infrared multiphoton dissociation (IRMPD) in each of the two cells - the first a high pressure cell operated at nominally 5 × 10-3 Torr and the second a low pressure cell operated at nominally 3 × 10-4 Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photodissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y1 fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of ~100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than 90% of the product ion current in the IRMPD mass spectra of doubly charged peptide ions was composed of singly charged product ions compared to the CID mass spectra in which the abundances of the multiply and singly charged product ions were equally divided. Highly charged primary product ions also underwent efficient photodissociation to yield singly charged secondary product ions, thus simplifying the IRMPD product ion mass spectra. PMID:19739654

  18. Infrared multiphoton dissociation of peptide cations in a dual pressure linear ion trap mass spectrometer.

    PubMed

    Gardner, Myles W; Smith, Suncerae I; Ledvina, Aaron R; Madsen, James A; Coon, Joshua J; Schwartz, Jae C; Stafford, George C; Brodbelt, Jennifer S

    2009-10-01

    A dual pressure linear ion trap mass spectrometer was modified to permit infrared multiphoton dissociation (IRMPD) in each of the two cells-the first a high pressure cell operated at nominally 5 x 10(-3) Torr and the second a low pressure cell operated at nominally 3 x 10(-4) Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photodissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y(1) fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of approximately 100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than 90% of the product ion current in the IRMPD mass spectra of doubly charged peptide ions was composed of singly charged product ions compared to the CID mass spectra in which the abundances of the multiply and singly charged product ions were equally divided. Highly charged primary product ions also underwent efficient photodissociation to yield singly charged secondary product ions, thus simplifying the IRMPD product ion mass spectra.

  19. Multiplexed hybridizations of positively charge-tagged peptide nucleic acids detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

    PubMed

    Bauer, Oliver; Guerasimova, Anna; Sauer, Sascha; Thamm, Sabine; Steinfath, Matthias; Herwig, Ralf; Janitz, Michal; Lehrach, Hans; Radelof, Uwe

    2004-01-01

    Peptide nucleic acid (PNA) is a novel class of DNA analogues in which the entire sugar-phosphate backbone is replaced by a pseudopeptide counterpart. Owing to its neutral character and the consequent lack of electrostatic repulsion, PNA exhibits very stable heteroduplex formation with complementary nucleic acid that is essentially ionic strength independent and enables hybridization under minimum salt conditions. This feature as well as its superior ion stability and easy ionization compared to DNA renders PNA very attractive for hybridization-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) applications. We have developed an approach to DNA characterization that takes advantage of multiplexed PNA hybridizations analyzed by MALDI-TOFMS. Our motivation was the further development of oligonucleotide fingerprinting, an efficient technique for cDNA and genomic DNA library characterization. Through positive 'charge-tagging' of PNA the efficiency of detection in MALDI-TOFMS was considerably enhanced permitting an unparalleled degree of multiplexing. Results from the simultaneous hybridization of 21 charge-tagged PNA hexamer oligonucleotides showed that genomic DNA and cDNA clones are successfully characterized on the basis of their hybridization profiles. The degree of multiplexing achieved may render a significant increase in throughput and hence efficiency of oligonucleotide fingerprinting possible.

  20. Use of a Spreadsheet to Calculate the Net Charge of Peptides and Proteins as a Function of pH: An Alternative to Using "Canned" Programs to Estimate the Isoelectric Point of These Important Biomolecules

    ERIC Educational Resources Information Center

    Sims, Paul A.

    2010-01-01

    An approach is presented that utilizes a spreadsheet to allow students to explore different means of calculating and visualizing how the charge on peptides and proteins varies as a function of pH. In particular, the concept of isoelectric point is developed to allow students to compare the results of their spreadsheet calculations with those of…

  1. Use of a Spreadsheet to Calculate the Net Charge of Peptides and Proteins as a Function of pH: An Alternative to Using "Canned" Programs to Estimate the Isoelectric Point of These Important Biomolecules

    ERIC Educational Resources Information Center

    Sims, Paul A.

    2010-01-01

    An approach is presented that utilizes a spreadsheet to allow students to explore different means of calculating and visualizing how the charge on peptides and proteins varies as a function of pH. In particular, the concept of isoelectric point is developed to allow students to compare the results of their spreadsheet calculations with those of…

  2. Detection of singly- and doubly-charged quaternary ammonium drugs in equine urine by liquid chromatography/tandem mass spectrometry.

    PubMed

    Ho, Emmie N M; Kwok, W H; Wong, April S Y; Wan, Terence S M

    2012-01-13

    Quaternary ammonium drugs (QADs) are anticholinergic agents some of which are known to have been abused or misused in equine sports. A recent review of literature shows that the screening methods reported thus far for QADs mainly cover singly-charged QADs. Doubly-charged QADs are extremely polar substances which are difficult to be extracted and poorly retained on reversed-phase columns. It would be ideal if a comprehensive method can be developed which can detect both singly- and doubly-charged QADs. This paper describes an efficient liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the simultaneous detection and confirmation of 38 singly- and doubly-charged QADs at sub-parts-per-billion (ppb) to low-ppb levels in equine urine after solid-phase extraction. Quaternary ammonium drugs were extracted from equine urine by solid-phase extraction (SPE) using an ISOLUTE(®) CBA SPE column and analysed by LC/MS/MS in the positive electrospray ionisation mode. Separation of the 38 QADs was achieved on a polar group embedded C18 LC column with a mixture of aqueous ammonium formate (pH 3.0, 10 mM) and acetonitrile as the mobile phase. Detection and confirmation of the 38 QADs at sub-ppb to low-ppb levels in equine urine could be achieved within 16 min using selected reaction monitoring (SRM). Matrix interference of the target transitions at the expected retention times was not observed. Other method validation data, including precision and recovery, were acceptable. The method was successfully applied to the analyses of drug-administration samples.

  3. Single-conformation and diastereomer specific ultraviolet and infrared spectroscopy of model synthetic foldamers: alpha/beta-peptides.

    PubMed

    James, William H; Baquero, Esteban E; Shubert, V Alvin; Choi, Soo Hyuk; Gellman, Samuel H; Zwier, Timothy S

    2009-05-13

    Resonant two-photon ionization (R2PI), UV hole-burning (UVHB), and resonant ion-dip infrared (RIDIR) spectroscopies have been used to record single-conformation infrared and ultraviolet spectra of three model synthetic foldamers with heterogeneous backbones, alpha/beta-peptides Ac-beta(3)-hAla-L-Phe-NHMe (betaalphaL), Ac-beta(3)-hAla-D-Phe-NHMe (betaalphaD), and Ac-L-Phe-beta(3)-hAla-NHMe (alphabetaL), isolated and cooled in a supersonic expansion. BetaalphaL and betaalphaD are diastereomers, differing only in the configuration of the alpha-amino acid residue; betaalphaL and alphabetaL contain the same residues, but differ in residue order. In all three alpha/beta-peptides the beta(3)-residue has S absolute configuration. UVHB spectroscopy is used to determine that there are six conformers of each molecule and to locate and characterize their S(0)-S(1) transitions in the origin region. RIDIR spectra in the amide NH stretch region reflect the number and strength of intramolecular H-bonds present. Comparison of the RIDIR spectra with scaled, harmonic vibrational frequencies and infrared intensities leads to definite assignments for the conformational families involved. C8/C7(eq) double-ring structures are responsible for three conformers of betaalphaL and four of betaalphaD, including those with the most intense transitions in the R2PI spectra. This preference for C8/C7(eq) double rings appears to be dictated by the C7(eq) ring of the alpha-peptide subunit. Three of the conformers of betaalphaL and betaalphaD form diastereomeric pairs (A/A', C/C', and G/G') that have nearly identical S(0)-S(1) origin positions in the UV and belong to the same conformational family, indicating no significant change associated with the change in chirality of the alpha-peptide subunit. However, betaalphaL favors formation of a C6/C5 conformer over C11, while the reverse preference holds in betaalphaD. Calculations indicate that the selective stabilization of the lowest-energy C11(g

  4. Realization of a Cascaded Quantum System: Heralded Absorption of a Single Photon Qubit by a Single-Electron Charged Quantum Dot.

    PubMed

    Delteil, Aymeric; Sun, Zhe; Fält, Stefan; Imamoğlu, Atac

    2017-04-28

    Photonic losses pose a major limitation for the implementation of a quantum state transfer between nodes of a quantum network. A measurement that heralds a successful transfer without revealing any information about the qubit may alleviate this limitation. Here, we demonstrate the heralded absorption of a single photonic qubit, generated by a single neutral quantum dot, by a single-electron charged quantum dot that is located 5 m away. The transfer of quantum information to the spin degree of freedom takes place upon the emission of a photon; for a properly chosen or prepared quantum dot, the detection of this photon yields no information about the qubit. We show that this process can be combined with local operations optically performed on the destination node by measuring classical correlations between the absorbed photon color and the final state of the electron spin. Our work suggests alternative avenues for the realization of quantum information protocols based on cascaded quantum systems.

  5. Realization of a Cascaded Quantum System: Heralded Absorption of a Single Photon Qubit by a Single-Electron Charged Quantum Dot

    NASA Astrophysics Data System (ADS)

    Delteil, Aymeric; Sun, Zhe; Fält, Stefan; Imamoǧlu, Atac

    2017-04-01

    Photonic losses pose a major limitation for the implementation of a quantum state transfer between nodes of a quantum network. A measurement that heralds a successful transfer without revealing any information about the qubit may alleviate this limitation. Here, we demonstrate the heralded absorption of a single photonic qubit, generated by a single neutral quantum dot, by a single-electron charged quantum dot that is located 5 m away. The transfer of quantum information to the spin degree of freedom takes place upon the emission of a photon; for a properly chosen or prepared quantum dot, the detection of this photon yields no information about the qubit. We show that this process can be combined with local operations optically performed on the destination node by measuring classical correlations between the absorbed photon color and the final state of the electron spin. Our work suggests alternative avenues for the realization of quantum information protocols based on cascaded quantum systems.

  6. Peptidic determinants and structural model of human NDP kinase B (Nm23-H2) bound to single-stranded DNA.

    PubMed

    Raveh, S; Vinh, J; Rossier, J; Agou, F; Véron, M

    2001-05-22

    Isoform B of human NDP kinase (NDPK-B) was previously identified as a transcription factor stimulating in vitro and ex vivo the transcription of the c-myc oncogene, which involves this enzyme in carcinogenesis. We have studied the enzymatic properties of NDPK-B in the presence of several single-stranded oligonucleotides. We show that the oligonucleotides are competitive inhibitors of the catalytic activity, indicating that the active site acts as a binding template for the anchorage of the oligonucleotide. Furthermore, the presence of a guanine at the 3'-end of several different aptamers increases its affinity 10-fold. To define the surface of the protein contacting the DNA within the nucleoprotein complex, we used single nanosecond laser pulses as the cross-linking reagent and MALDI-TOF mass spectrometry to identify cross-linked peptides purified from proteolytic digests of the cross-linked complex. Using 11-mer and 30-mer single-stranded oligonucleotides, the same three different nucleopeptides were identified after irradiation of the complexes, indicating a common binding mode for these two aptamers. Taken together, these results allowed us to propose a structural model of NDPK-B bound to single-stranded DNA.

  7. Electrode configuration and signal subtraction technique for single polarity charge carrier sensing in ionization detectors

    DOEpatents

    Luke, P.

    1996-06-25

    An ionization detector electrode and signal subtraction apparatus and method provide at least one first conductive trace formed onto the first surface of an ionization detector. The first surface opposes a second surface of the ionization detector. At least one second conductive trace is also formed on the first surface of the ionization detector in a substantially interlaced and symmetrical pattern with the at least one first conductive trace. Both of the traces are held at a voltage potential of a first polarity type. By forming the traces in a substantially interlaced and symmetric pattern, signals generated by a charge carrier are substantially of equal strength with respect to both of the traces. The only significant difference in measured signal strength occurs when the charge carrier moves to within close proximity of the traces and is received at the collecting trace. The measured signals are then subtracted and compared to quantitatively measure the magnitude of the charge and to determine the position at which the charge carrier originated within the ionization detector. 9 figs.

  8. Electrode configuration and signal subtraction technique for single polarity charge carrier sensing in ionization detectors

    DOEpatents

    Luke, Paul

    1996-01-01

    An ionization detector electrode and signal subtraction apparatus and method provides at least one first conductive trace formed onto the first surface of an ionization detector. The first surface opposes a second surface of the ionization detector. At least one second conductive trace is also formed on the first surface of the ionization detector in a substantially interlaced and symmetrical pattern with the at least one first conductive trace. Both of the traces are held at a voltage potential of a first polarity type. By forming the traces in a substantially interlaced and symmetric pattern, signals generated by a charge carrier are substantially of equal strength with respect to both of the traces. The only significant difference in measured signal strength occurs when the charge carrier moves to within close proximity of the traces and is received at the collecting trace. The measured signals are then subtracted and compared to quantitatively measure the magnitude of the charge and to determine the position at which the charge carrier originated within the ionization detector.

  9. Sustained Release of Mitomycin C from Its Conjugate with Single-Walled Carbon Nanotubes Associated by Pegylated Peptide.

    PubMed

    Ohta, Takahisa; Hashida, Yasuhiko; Yamashita, Fumiyoshi; Hashida, Mitsuru

    2016-01-01

    A novel sustained release formulation of mitomycin C (MMC) was developed by employing single-walled carbon nanotubes (SWCNTs) wrapped by designed peptide with polyethylene glycol (PEG) modification (pegylation) as a nano-scale molecular platform. The amino groups of polycationic and amphiphilic H-(-Cys-Trp-Lys-Gly-)(-Lys-Trp-Lys-Gly-)6-OH [CWKG(KWKG)6] peptide associated with SWCNTs were modified using PEG with 12 units (PEG12) to improve the dispersion stability of the composite. Then thiol groups of peptide were conjugated with MMC using N-ε-maleimidocaproic acid (EMCA) as a linker via transformation of aziridine group of MMC. The obtained SWCNTs-CWKG(KWKG)6-(PEG)12-C6-MMC composites particularly that with 13.6% PEG modification extent of amino groups, showed good dispersion stability both in water and in a cell culture medium for 24 h. The release of MMC from SWCNTs-CWKG(KWKG)6-(PEG)12-C6-MMC was confirmed to follow first-order kinetics being accelerated by the pH increase in good agreement with the results observed for MMC-dextran conjugate with the same conjugation structure. The SWCNTs-CWKG(KWKG)6-(PEG)12 composite exhibited a considerably low cytotoxicity against cultured human lung adenocarcinoma epithelial cell line (A549). In contrast, SWCNTs-CWKG(KWKG)6-(PEG)12-C6-MMC demonstrated delayed but relatively corresponding antitumor activity with free MMC at the same concentration. The results suggested the potential role of SWCNTs-CWKG(KWKG)6-(PEG)12 as a carrier for a controlled release drug delivery system (DDS).

  10. Quantification of Steady-State Ion Transport through Single Conical Nanopores and a Nonuniform Distribution of Surface Charges

    SciTech Connect

    Liu, Juan; Wang, Dengchao; Kvetny, Maksim; Brown, Warren; Liu, Yan; Wang, Gangli

    2013-07-09

    Electrostatic interactions of mobile charges in solution with the fixed surface charges are known to strongly affect stochastic sensing and electrochemical energy conversion processes at nanodevices or devices with nanostructured interfaces. The key parameter to describe this interaction, surface charge density (SCD), is not directly accessible at nanometer scale and often extrapolated from ensemble values. In this report, the steady-state current–voltage (i–V) curves measured using single conical glass nanopores in different electrolyte solutions are fitted by solving Poisson and Nernst–Planck equations through finite element approach. Both high and low conductivity state currents of the rectified i–V curve are quantitatively fitted in simulation at less than 5% error. The overestimation of low conductivity state current using existing models is overcome by the introduction of an exponential SCD distribution inside the conical nanopore. A maximum SCD value at the pore orifice is determined from the fitting of the high conductivity state current, while the distribution length of the exponential SCD gradient is determined by fitting the low conductivity state current. Quantitative fitting of the rectified i–V responses and the efficacy of the proposed model are further validated by the comparison of electrolytes with different types of cations (K+ and Li+). In conclusion, the gradient distribution of surface charges is proposed to be dependent on the local electric field distribution inside the conical nanopore.

  11. Hydride formation and thermal desorption spectra of hydrogen of cathodically charged single-phase gamma titanium aluminide

    SciTech Connect

    Takasaki, Akito; Furuya, Yoshio

    1999-02-05

    The authors have previously reported thermal desorption spectra of hydrogen obtained from cathodically charged two-phase (Ti{sub 3}Al ({alpha}{sub 2}) + TiAl ({gamma})) titanium aluminides by means of thermal desorption spectroscopy (TDS), in which hydrogen ion current (H{sub 2}{sup +}) corresponding to hydrogen evolution rate during heating was measured by a quadrupole mass spectrometer in an ultra-high vacuum condition. Several accelerated hydrogen evolutions (TDS peak temperatures) have been observed in a series of TDS measurement, and then the authors have suggested that these peaks were dependent on the microstructures ({alpha}{sub 2} and {gamma} phases) as well as dissociation of the hydride phase which formed during cathodic charging. A comparison with the TDS spectra from other series of titanium aluminides, such as a single-phase {gamma} alloy, might give clearer views of the microstructural dependence on hydrogen evolution kinetics. In this paper, hydride formation, hydrogen uptake and hydrogen evolution kinetic of a cathodically charged single-phase {gamma} titanium aluminide are investigated, and these results are compared with the previous ones obtained in two-phase ({alpha}{sub 2} + {gamma}) titanium aluminides.

  12. Large-Scale Single Particle and Cell Trapping based on Rotating Electric Field Induced-Charge Electroosmosis.

    PubMed

    Wu, Yupan; Ren, Yukun; Tao, Ye; Hou, Likai; Jiang, Hongyuan

    2016-12-06

    We propose a simple, inexpensive microfluidic chip for large-scale trapping of single particles and cells based on induced-charge electroosmosis in a rotating electric field (ROT-ICEO). A central floating electrode array, was placed in the center of the gap between four driving electrodes with a quadrature configuration and used to immobilize single particles or cells. Cells were trapped on the electrode array by the interaction between ROT-ICEO flow and buoyancy flow. We experimentally optimized the efficiency of trapping single particles by investigating important parameters like particle or cell density and electric potential. Experimental and numerical results showed good agreement. The operation of the chip was verified by trapping single polystyrene (PS) microspheres with diameters of 5 and 20 μm and single yeast cells. The highest single particle occupancy of 73% was obtained using a floating electrode array with a diameter of 20 μm with an amplitude voltage of 5 V and frequency of 10 kHz for PS microbeads with a 5-μm diameter and density of 800 particles/μL. The ROT-ICEO flow could hold cells against fluid flows with a rate of less than 0.45 μL/min. This novel, simple, robust method to trap single cells has enormous potential in genetic and metabolic engineering.

  13. A novel peptide delivers plasmids across blood-brain barrier into neuronal cells as a single-component transfer vector.

    PubMed

    Fu, Ailing; Zhang, Miaomiao; Gao, Feiyan; Xu, Xingran; Chen, Zhangbao

    2013-01-01

    There is no data up to now to show that peptide can deliver plasmid into brain as a single-component transfer vector. Here we show that a novel peptide, RDP (consisted of 39 amino acids), can be exploited as an efficient plasmid vector for brain-targeting delivery. The plasmids containing Lac Z reporter gene (pVAX-Lac Z) and BDNF gene (pVAX-BDNF) are complexed with RDP and intravenously injected into mice. The results of gel retardation assay show that RDP enables to bind DNA in a dose-dependent manner, and the X-Gal staining identity that Lac Z is specifically expressed in the brain. Also, the results of Western blot and immunofluorescence staining of BDNF indicate that pVAX-BDNF complexed with RDP can be delivered into brain, and show neuroprotective properties in experimental Parkinson's disease (PD) model. The results demonstrate that RDP enables to bind and deliver DNA into the brain, resulting in specific gene expression in the neuronal cells. This strategy provides a novel, simple and effective approach for non-viral gene therapy of brain diseases.

  14. Single nucleotide polymorphisms of the haptoglobin gene in non-small cell lung cancer treated with personalized peptide vaccination

    PubMed Central

    Waki, Kayoko; Yamada, Teppei; Yoshiyama, Koichi; Terazaki, Yasuhiro; Sakamoto, Shinjiro; Sugawara, Shunichi; Takamori, Shinzo; Itoh, Kyogo; Yamada, Akira

    2017-01-01

    The present study analyzed polymorphisms of the 5′ flanking region (from nt −840 to +151) of the haptoglobin gene in 120 patients with advanced non-small cell lung cancer (NSCLC) receiving personalized peptide vaccinations. In the region, six single nucleotide polymorphisms (SNPs) were confirmed, of which two, rs5472 and rs9927981, were completely linked to each other. The minor allele frequencies of rs5472/rs9927981 and rs4788458 were higher than those of the other three SNPs. The genotype frequencies of rs5472 or rs9927981 were A/A or C/C (42.5%, n=51), A/G or C/T (40.8%, n=49), and G/G or T/T (16.7%, n=20), respectively; and those of rs4788458 were T/T (34.2%, n=41), T/C (40.0%, n=48), and C/C (25.8%, n=31). The association between polymorphism rs5472/rs9927981 and prognosis, or between rs4788458 and prognosis, was analyzed further. However, no correlation was found between these SNPs and overall survival, regardless of subgroup analysis of gender, histology or concurrent therapy. These results suggest that the polymorphisms rs5472/rs9927981 and rs4788458 are not useful prognostic tools for patients with NSCLC treated with personalized peptide vaccination. PMID:28356990

  15. Investigating the Neuroprotective Effects of Turmeric Extract: Structural Interactions of β-Amyloid Peptide with Single Curcuminoids

    PubMed Central

    Randino, Rosario; Grimaldi, Manuela; Persico, Marco; De Santis, Augusta; Cini, Elena; Cabri, Walter; Riva, Antonella; D’Errico, Gerardino; Fattorusso, Caterina; D’Ursi, Anna Maria; Rodriquez, Manuela

    2016-01-01

    A broad biophysical analysis was performed to investigate the molecular basis of the neuroprotective action of Curcuma longa extracts in Alzheimer’s disease. By combining circular dichroism and electron paramagnetic resonance experiments with molecular modeling calculations, the minor components of Curcuma longa extracts, such as demethoxycurcumin (2, DMC), bisdemethoxycurcumin (3, BDMC) and cyclocurcumin (4, CYC), were analyzed in a membrane environment mimicking the phospholipid bilayer. Our study provides the first evidence on the relative role of single curcuminoids interacting with Aβ-peptide. When the CYC and curcumin metabolite tetrahydrocurcumin (5, THC) were inserted into an anionic lipid solution, a significant modification of the Aβ CD curves was detected. These data were implemented by EPR experiments, demonstrating that CYC reaches the inner part of the bilayer, while the other curcuminoids are localized close to the membrane interface. Computational studies provided a model for the curcuminoid-Aβ interaction, highlighting the importance of a constrained “semi-folded” conformation to interact with Aβ analogously to the pattern observed in α-helical coiled-coil peptide structures. This combined approach led to a better understanding of the intriguing in vitro and in vivo activity of curcuminoids as anti-Alzheimer agents, paving a new path for the rational design of optimized druggable analogues. PMID:28004737

  16. Single Charge Current in a Normal Mesoscopic Region Attached to Superconductor Leads via a Coupled Poisson Nonequilibrium Green Function Formalism

    PubMed Central

    Marin, F. P.

    2014-01-01

    We study the I-V characteristic of mesoscopic systems or quantum dot (QD) attached to a pair of superconducting leads. Interaction effects in the QD are considered through the charging energy of the QD; that is, the treatment of current transport under a voltage bias is performed within a coupled Poisson nonequilibrium Green function (PNEGF) formalism. We derive the expression for the current in full generality but consider only the regime where transport occurs only via a single particle current. We show for this case and for various charging energies values U 0 and associated capacitances of the QD the effect on the I-V characteristic. Also the influence of the coupling constants on the I-V characteristic is investigated. Our approach puts forward a novel interpretation of experiments in the strong Coulomb regime. PMID:24977220

  17. Visualization of single-wall carbon nanotube (SWNT) networks in conductive polystyrene nanocomposites by charge contrast imaging.

    PubMed

    Loos, Joachim; Alexeev, Alexander; Grossiord, Nadia; Koning, Cor E; Regev, Oren

    2005-09-01

    The morphology of conductive nanocomposites consisting of low concentration of single-wall carbon nanotubes (SWNT) and polystyrene (PS) has been studied using atomic force microscopy (AFM), transmission electron microscopy (TEM) and, in particular, scanning electron microscopy (SEM). Application of charge contrast imaging in SEM allows visualization of the overall SWNT dispersion within the polymer matrix as well as the identification of individual or bundled SWNTs at high resolution. The contrast mechanism involved will be discussed. In conductive nanocomposites the SWNTs are homogeneously dispersed within the polymer matrix and form a network. Beside fairly straight SWNTs, strongly bended SWNTs have been observed. However, for samples with SWNT concentrations below the percolation threshold, the common overall charging behavior of an insulating material is observed preventing the detailed morphological investigation of the sample.

  18. The recent single-tag two-photon experiments at petra and the issue of quark charges

    NASA Astrophysics Data System (ADS)

    Godbole, R. M.; Pati, J. C.; Rindani, S. D.; Jayaraman, T.; Rajasekaran, G.

    1984-07-01

    The data of recent single-tag two-photon experiments indicating noticeable excess in ( overlineRγγ ) jet over fractionally charged quark-parton model-predictions is studied from the point of view of its implications on the gauge integer charge quark model. Focusing attention on the region of pT exceeding about 3 GeV, where higher order QCD and non-perturbative effects might be expected to be small, it is noted that this excess and its Q2 dependence can be attributed to the presence of a colour component in the electromagnetic current provided the effective mass of the gluon lies between about 150 to 350 MeV. Accurate measurements of overlineRγγ in the high pT region ( p T ⪆ 5 GeV) are crucial for an unambiguous distinction between fcq and gauge-icq models.

  19. Transparent Flash Memory Using Single Ta2O5 Layer for Both Charge-Trapping and Tunneling Dielectrics.

    PubMed

    Hota, Mrinal K; Alshammari, Fwzah H; Salama, Khaled N; Alshareef, Husam N

    2017-07-05

    We report reproducible multibit transparent flash memory in which a single solution-derived Ta2O5 layer is used simultaneously as a charge-trapping layer and a tunneling layer. This is different from conventional flash memory cells where two different dielectric layers are typically used. Under optimized programming/erasing operations, the memory device shows excellent programmable memory characteristics with a maximum memory window of ∼10.7 V. Moreover, the flash memory device shows a stable 2-bit memory performance and good reliability, including data retention for more than 10(4) s and endurance performance for more than 100 cycles. The use of a common charge-trapping and tunneling layer can simplify the fabrication of advanced flash memories.

  20. Fractionally Charged Zero-Energy Single-Particle Excitations in a Driven Fermi Sea

    NASA Astrophysics Data System (ADS)

    Moskalets, Michael

    2016-07-01

    A voltage pulse of a Lorentzian shape carrying half of the flux quantum excites out of a zero-temperature Fermi sea an electron in a mixed state, which looks like a quasiparticle with an effectively fractional charge e /2 . A prominent feature of such an excitation is a narrow peak in the energy distribution function lying exactly at the Fermi energy μ . Another spectacular feature is that the distribution function has symmetric tails around μ , which results in a zero-energy excitation. This sounds improbable since at zero temperature all available states below μ are fully occupied. The resolution lies in the fact that such a voltage pulse also excites electron-hole pairs, which free some space below μ and thus allow a zero-energy quasiparticle to exist. I discuss also how to address separately electron-hole pairs and a fractionally charged zero-energy excitation in an experiment.

  1. Single-Step Affinity Purification of ERK Signaling Complexes Using the Streptavidin-Binding Peptide (SBP) Tag.

    PubMed

    Yang, Liu; Veraksa, Alexey

    2017-01-01

    Elucidation of biological functions of signaling proteins is facilitated by studying their protein-protein interaction networks. Affinity purification combined with mass spectrometry (AP-MS) has become a favorite method to study protein complexes. Here we describe a procedure for single-step purification of ERK (Rolled) and associated proteins from Drosophila cultured cells. The use of the streptavidin-binding peptide (SBP) tag allows for a highly efficient isolation of native ERK signaling complexes, which are suitable for subsequent analysis by mass spectrometry. Our analysis of the ERK interactome has identified both known and novel signaling components. This method can be easily adapted for SBP-based purification of protein complexes in any expression system.

  2. Design of Accumulators and Liquid/Gas Charging of Single Phase Mechanically Pumped Fluid Loop Heat Rejection Systems

    NASA Technical Reports Server (NTRS)

    Bhandari, Pradeep; Dudik, Brenda; Birur, Gajanana; Karlmann, Paul; Bame, David; Mastropietro, A. J.

    2012-01-01

    For single phase mechanically pumped fluid loops used for thermal control of spacecraft, a gas charged accumulator is typically used to modulate pressures within the loop. This is needed to accommodate changes in the working fluid volume due to changes in the operating temperatures as the spacecraft encounters varying thermal environments during its mission. Overall, the three key requirements on the accumulator to maintain an appropriate pressure range throughout the mission are: accommodation of the volume change of the fluid due to temperature changes, avoidance of pump cavitation and prevention of boiling in the liquid. The sizing and design of such an accumulator requires very careful and accurate accounting of temperature distribution within each element of the working fluid for the entire range of conditions expected, accurate knowledge of volume of each fluid element, assessment of corresponding pressures needed to avoid boiling in the liquid, as well as the pressures needed to avoid cavitation in the pump. The appropriate liquid and accumulator strokes required to accommodate the liquid volume change, as well as the appropriate gas volumes, require proper sizing to ensure that the correct pressure range is maintained during the mission. Additionally, a very careful assessment of the process for charging both the gas side and the liquid side of the accumulator is required to properly position the bellows and pressurize the system to a level commensurate with requirements. To achieve the accurate sizing of the accumulator and the charging of the system, sophisticated EXCEL based spreadsheets were developed to rapidly come up with an accumulator design and the corresponding charging parameters. These spreadsheets have proven to be computationally fast and accurate tools for this purpose. This paper will describe the entire process of designing and charging the system, using a case study of the Mars Science Laboratory (MSL) fluid loops, which is en route to

  3. Design of Accumulators and Liquid/Gas Charging of Single Phase Mechanically Pumped Fluid Loop Heat Rejection Systems

    NASA Technical Reports Server (NTRS)

    Bhandari, Pradeep; Dudik, Brenda; Birur, Gajanana; Karlmann, Paul; Bame, David; Mastropietro, A. J.

    2012-01-01

    For single phase mechanically pumped fluid loops used for thermal control of spacecraft, a gas charged accumulator is typically used to modulate pressures within the loop. This is needed to accommodate changes in the working fluid volume due to changes in the operating temperatures as the spacecraft encounters varying thermal environments during its mission. Overall, the three key requirements on the accumulator to maintain an appropriate pressure range throughout the mission are: accommodation of the volume change of the fluid due to temperature changes, avoidance of pump cavitation and prevention of boiling in the liquid. The sizing and design of such an accumulator requires very careful and accurate accounting of temperature distribution within each element of the working fluid for the entire range of conditions expected, accurate knowledge of volume of each fluid element, assessment of corresponding pressures needed to avoid boiling in the liquid, as well as the pressures needed to avoid cavitation in the pump. The appropriate liquid and accumulator strokes required to accommodate the liquid volume change, as well as the appropriate gas volumes, require proper sizing to ensure that the correct pressure range is maintained during the mission. Additionally, a very careful assessment of the process for charging both the gas side and the liquid side of the accumulator is required to properly position the bellows and pressurize the system to a level commensurate with requirements. To achieve the accurate sizing of the accumulator and the charging of the system, sophisticated EXCEL based spreadsheets were developed to rapidly come up with an accumulator design and the corresponding charging parameters. These spreadsheets have proven to be computationally fast and accurate tools for this purpose. This paper will describe the entire process of designing and charging the system, using a case study of the Mars Science Laboratory (MSL) fluid loops, which is en route to

  4. Single ion induced surface nanostructures: a comparison between slow highly charged and swift heavy ions.

    PubMed

    Aumayr, Friedrich; Facsko, Stefan; El-Said, Ayman S; Trautmann, Christina; Schleberger, Marika

    2011-10-05

    This topical review focuses on recent advances in the understanding of the formation of surface nanostructures, an intriguing phenomenon in ion-surface interaction due to the impact of individual ions. In many solid targets, swift heavy ions produce narrow cylindrical tracks accompanied by the formation of a surface nanostructure. More recently, a similar nanometric surface effect has been revealed for the impact of individual, very slow but highly charged ions. While swift ions transfer their large kinetic energy to the target via ionization and electronic excitation processes (electronic stopping), slow highly charged ions produce surface structures due to potential energy deposited at the top surface layers. Despite the differences in primary excitation, the similarity between the nanostructures is striking and strongly points to a common mechanism related to the energy transfer from the electronic to the lattice system of the target. A comparison of surface structures induced by swift heavy ions and slow highly charged ions provides a valuable insight to better understand the formation mechanisms.

  5. Spectroscopic Studies of Doping and Charge Transfer in Single Walled Carbon Nanotubes and Lead Sulfide Quantum Dots

    NASA Astrophysics Data System (ADS)

    Haugen, Neale O.

    The use of single wall carbon nanotubes (SW-CNTs) in solar photovoltaic (PV) devices is a relatively new, but quickly growing field. SW-CNTs have found application as transparent front contacts, and high work function back contacts in thin film solar PV. For the utility of SW-CNTs to be fully realized, however, controllable and stable doping as well as long term protection from doping must be achieved. Spectroscopic techniques facilitate detailed investigations of the intrinsic and variable properties of semiconductor materials without the issues of contact deposition and the possibility of sample contamination. Detailed spectroscopic analysis of the doping induced changes in the optical properties of SW-CNTs has revealed normally hidden excited state transitions in large diameter single walled carbon nanotubes for the first time. Spectroscopic monitoring of the degree of doping in SW-CNTs made possible studies of the dopant complex desorption and readsorption energies and kinetics. The long term protection from doping of SW-CNTs exposed to ambient laboratory conditions was achieved as a result of the more detailed understanding of the doping processes and mechanisms yielded by these spectroscopic studies. The application of SW-CNTs to other roles in solar PV devices was another goal of this research. Efficient collection of photogenerated charge carriers in semiconductor quantum dot (QD) based solar photovoltaic devices has been limited primarily by the poor transport properties and high density of recombination sites in the QD films. Coupling semiconductor QDs to nanomaterials with better transport properties is one potential solution to the poor transport within the QD films. This portion of the work investigated the possibility of charge transfer occurring in nano-heterostructures (NHSs) of PbS QDs and SW-CNTs produced through spontaneous self-assembly in solution. Electronic coupling in the form of charge transfer from the QDs to the SW-CNTs is unambiguously

  6. Gas-phase synthesis of singly and multiply charged polyoxovanadate anions employing electrospray ionization and collision induced dissociation.

    PubMed

    Al Hasan, Naila M; Johnson, Grant E; Laskin, Julia

    2013-09-01

    Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy(n-) and VxOyCl(n-) ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N(+), tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCl(n-) and VxOyCl(L)((n-1)-) clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl((1-2)-) and VxOy ((1-2)-) anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top

  7. Gas-Phase Synthesis of Singly and Multiply Charged Polyoxovanadate Anions Employing Electrospray Ionization and Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Al Hasan, Naila M.; Johnson, Grant E.; Laskin, Julia

    2013-09-01

    Electrospray ionization mass spectrometry (ESI-MS) combined with in-source fragmentation and tandem mass spectrometry (MS/MS) experiments were used to generate a wide range of singly and multiply charged vanadium oxide cluster anions including VxOy n- and VxOyCln- ions (x = 1-14, y = 2-36, n = 1-3), protonated clusters, and ligand-bound polyoxovanadate anions. The cluster anions were produced by electrospraying a solution of tetradecavanadate, V14O36Cl(L)5 (L = Et4N+, tetraethylammonium), in acetonitrile. Under mild source conditions, ESI-MS generates a distribution of doubly and triply charged VxOyCln- and VxOyCl(L)(n-1)- clusters predominantly containing 14 vanadium atoms as well as their protonated analogs. Accurate mass measurement using a high-resolution LTQ/Orbitrap mass spectrometer (m/Δm = 60,000 at m/z 410) enabled unambiguous assignment of the elemental composition of the majority of peaks in the ESI-MS spectrum. In addition, high-sensitivity mass spectrometry allowed the charge state of the cluster ions to be assigned based on the separation of the major from the much less abundant minor isotope of vanadium. In-source fragmentation resulted in facile formation of smaller VxOyCl(1-2)- and VxOy (1-2)- anions. Collision-induced dissociation (CID) experiments enabled systematic study of the gas-phase fragmentation pathways of the cluster anions originating from solution and from in-source CID. Surprisingly simple fragmentation patterns were obtained for all singly and doubly charged VxOyCl and VxOy species generated through multiple MS/MS experiments. In contrast, cluster anions originating directly from solution produced comparatively complex CID spectra. These results are consistent with the formation of more stable structures of VxOyCl and VxOy anions through low-energy CID. Furthermore, our results demonstrate that solution-phase synthesis of one precursor cluster anion combined with gas-phase CID is an efficient approach for the top-down synthesis of a

  8. Spin, charge, and single-particle spectral functions of the one-dimensional quarter filled Holstein model

    NASA Astrophysics Data System (ADS)

    Assaad, F. F.

    2008-10-01

    We use a recently developed extension of the weak-coupling diagrammatic determinantal quantum Monte Carlo method to investigate the spin, charge, and single-particle spectral functions of the one-dimensional quarter filled Holstein model with phonon frequency ω0=0.1t . As a function of the dimensionless electron-phonon coupling we observe a transition from a Luttinger to a Luther-Emery liquid with dominant 2kf charge fluctuations. Emphasis is placed on the temperature dependence of the single-particle spectral function. At high temperatures and in both phases it is well accounted for within a self-consistent Born approximation. In the low-temperature Luttinger liquid phase we observe features that compare favorably with a bosonization approach retaining only forward scattering. In the Luther-Emery phase, the spectral function at low temperatures shows a quasiparticle gap that matches half the spin gap, whereas at temperatures above which this quasiparticle gap closes characteristic features of the Luttinger liquid model are apparent. Our results are based on lattice simulations on chains up to L=20 for two-particle properties and on cluster dynamical mean-field theory calculations with clusters up to 12 sites for the single-particle spectral function.

  9. Charge Dependence and Electric Quadrupole Effects on Single-Nucleon Removal in Relativistic and Intermediate Energy Nuclear Collisions

    NASA Technical Reports Server (NTRS)

    Norbury, John W.

    1992-01-01

    Single nucleon removal in relativistic and intermediate energy nucleus-nucleus collisions is studied using a generalization of Weizsacker-Williams theory that treats each electromagnetic multipole separately. Calculations are presented for electric dipole and quadrupole excitations and incorporate a realistic minimum impact parameter, Coulomb recoil corrections, and the uncertainties in the input photonuclear data. Discrepancies are discussed. The maximum quadrupole effect to be observed in future experiments is estimated and also an analysis of the charge dependence of the electromagnetic cross sections down to energies as low as 100 MeV/nucleon is made.

  10. Charge dependence and electric quadrupole effects on single-nucleon removal in relativistic and intermediate energy nuclear collisions

    NASA Technical Reports Server (NTRS)

    Norbury, J. W.; Townsend, L. W. (Principal Investigator)

    1990-01-01

    Single-nucleon removal in relativistic and intermediate energy nucleus-nucleus collisions is studied using a generalization of Weizsacker-Williams theory that treats each electromagnetic multipole separately. Calculations are presented for electric dipole and quadrupole excitations and incorporate a realistic minimum impact parameter, Coulomb recoil corrections, and the uncertainties in the input photonuclear data. Discrepancies are discussed. The maximum quadrupole effect to be observed in future experiments is estimated and also an analysis of the charge dependence of the electromagnetic cross sections down to energies as low as 100 MeV/nucleon is made.

  11. Peptide-Directed Assembly of Single-Helical Gold Nanoparticle Superstructures Exhibiting Intense Chiroptical Activity.

    PubMed

    Merg, Andrea D; Boatz, Jennifer C; Mandal, Abhishek; Zhao, Gongpu; Mokashi-Punekar, Soumitra; Liu, Chong; Wang, Xianting; Zhang, Peijun; van der Wel, Patrick C A; Rosi, Nathaniel L

    2016-10-11

    Chiral nanoparticle assemblies are an interesting class of materials whose chiroptical properties make them attractive for a variety of applications. Here, C18-(PEPAu(M-ox))2 (PEPAu(M-ox) = AYSSGAPPM(ox)PPF) is shown to direct the assembly of single-helical gold nanoparticle superstructures that exhibit exceptionally strong chiroptical activity at the plasmon frequency with absolute g-factor values up to 0.04. Transmission electron microscopy (TEM) and cryogenic electron tomography (cryo-ET) results indicate that the single helices have a periodic pitch of approximately 100 nm and consist of oblong gold nanoparticles. The morphology and assembled structure of C18-(PEPAu(M-ox))2 are studied using TEM, atomic force microscopy (AFM), Fourier transform infrared (FTIR) spectroscopy, circular dichroism (CD) spectroscopy, X-ray diffraction (XRD), and solid-state nuclear magnetic resonance (ssNMR) spectroscopy. TEM and AFM reveal that C18-(PEPAu(M-ox))2 assembles into linear amyloid-like 1D helical ribbons having structural parameters that correlate to those of the single-helical gold nanoparticle superstructures. FTIR, CD, XRD, and ssNMR indicate the presence of cross-β and polyproline II secondary structures. A molecular assembly model is presented that takes into account all experimental observations and that supports the single-helical nanoparticle assembly architecture. This model provides the basis for the design of future nanoparticle assemblies having programmable structures and properties.

  12. Minimizing the energy spread within a single bunch by shaping its charge distribution

    SciTech Connect

    Loew, G.A.; Wang, J.W.

    1985-03-01

    It has been known for some time that partial compensation of the longitudinal wake field effects can be obtained for any bunch by placing it ahead of the accelerating crest (in space), thereby letting the positive rising sinusoidal field offset the negative beam loading field. The work presented in this paper shows that it is possible to obtain complete compensation, i.e., to reduce the energy spread essentially to zero by properly shaping the longitudinal charge distribution of the bunch and by placing it at the correct position on the wave. 3 refs., 5 figs., 3 tabs.

  13. Single-charge-exchange reactions and the neutron density at the surface of the nucleus

    NASA Astrophysics Data System (ADS)

    Loc, Bui Minh; Auerbach, Naftali; Khoa, Dao T.

    2017-07-01

    In this paper, we study the charge-exchange reaction to the isobaric analog state using two types of transition densities. One transition density is equal to the difference of the total neutron density minus the total proton density and the other one is the density of the excess neutrons only. We show that for projectiles that do not probe the interior of the nucleus but mostly the surface of this nucleus, distinct differences in the cross section arise when two types of transition densities are employed. We demonstrate this by considering the (3He,t ) reaction.

  14. Single-hole spectral function and spin-charge separation in the t-J model

    NASA Astrophysics Data System (ADS)

    Mishchenko, A. S.; Prokof'ev, N. V.; Svistunov, B. V.

    2001-07-01

    Worm algorithm Monte Carlo simulations of the hole Green function with subsequent spectral analysis were performed for 0.1<=J/t<=0.4 on lattices with up to L×L=32×32 sites at a temperature as low as T=J/40, and present, apparently, the hole spectral function in the thermodynamic limit. Spectral analysis reveals a δ-function-sharp quasiparticle peak at the lower edge of the spectrum that is incompatible with the power-law singularity and thus rules out the possibility of spin-charge separation in this parameter range. Spectral continuum features two peaks separated by a gap ~4÷5 t.

  15. Light-particle single ionization of argon: Influence of the projectile charge sign

    SciTech Connect

    Otranto, S.; Olson, R. E.

    2009-07-15

    The ionization of the 3p orbital of argon by incident electrons and positrons is studied by means of the post version of the continuum distorted wave-eikonal initial-state model. Results are presented at both 200 and 500 eV impact energies for conditions amenable to present experiments. Differences in the fully differential cross sections (FDCSs) are analyzed and the influence of the projectile charge sign on the emission dynamics is discussed. The FDCSs are found to display the classic binary plus recoil peak structure at 500 eV, but transition to a more complicated four-lobed structure at the lower impact energy.

  16. Synthetic surfactant based on analogues of SP-B and SP-C is superior to single-peptide surfactants in ventilated premature rabbits.

    PubMed

    Almlén, Andreas; Walther, Frans J; Waring, Alan J; Robertson, Bengt; Johansson, Jan; Curstedt, Tore

    2010-06-01

    Respiratory distress syndrome (RDS) is currently treated with surfactant preparations obtained from natural sources and attempts to develop equally active synthetic surfactants have been unsuccessful. One difference in composition is that naturally derived surfactants contain the two hydrophobic proteins SP-B and SP-C while synthetic preparations contain analogues of either SP-B or SP-C. It was recently shown that both SP-B and SP-C (or SP-C33, an SP-C analogue) are necessary to establish alveolar stability at end-expiration in a rabbit RDS model, as reflected by high lung gas volumes without application of positive end-expiratory pressure. To study the efficacy of fully synthetic surfactants containing analogues of both SP-B and SP-C compared to surfactants with only one protein analogue. Premature newborn rabbits, treated with synthetic surfactants, were ventilated for 30 min without positive end-expiratory pressure. Tidal volumes as well as lung gas volumes at end-expiration were determined. Treatment with 2% Mini-B (a short-cut version of SP-B) and 2% SP-C33, or its C-terminally truncated form SP-C30, in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 68:31 (w/w) resulted in median lung gas volumes of 8-9 ml/kg body weight, while animals treated with 2% Mini-B surfactant or 2% SP-C33/SP-C30 surfactant had lung gas volumes of 3-4 ml/kg, and those treated with Curosurf, a porcine surfactant, 15-17 ml/kg. In contrast, mixing SP-C33 with peptides with different distributions of positively charged and hydrophobic residues did not improve lung gas volumes. The data indicate that synthetic surfactants containing analogues of both SP-B and SP-C might be superior to single-peptide surfactants in the treatment of RDS.

  17. Synthetic Surfactant Based on Analogues of SP-B and SP-C Is Superior to Single-Peptide Surfactants in Ventilated Premature Rabbits

    PubMed Central

    Almlén, Andreas; Walther, Frans J.; Waring, Alan J.; Robertson, Bengt; Johansson, Jan; Curstedt, Tore

    2010-01-01

    Background Respiratory distress syndrome (RDS) is currently treated with surfactant preparations obtained from natural sources and attempts to develop equally active synthetic surfactants have been unsuccessful. One difference in composition is that naturally derived surfactants contain the two hydrophobic proteins SP-B and SP-C while synthetic preparations contain analogues of either SP-B or SP-C. It was recently shown that both SP-B and SP-C (or SP-C33, an SP-C analogue) are necessary to establish alveolar stability at end-expiration in a rabbit RDS model, as reflected by high lung gas volumes without application of positive end-expiratory pressure. Objectives: To study the efficacy of fully synthetic surfactants containing analogues of both SP-B and SP-C compared to surfactants with only one protein analogue. Methods Premature newborn rabbits, treated with synthetic surfactants, were ventilated for 30 min without positive end-expiratory pressure. Tidal volumes as well as lung gas volumes at end-expiration were determined. Results Treatment with 2% Mini-B (a short-cut version of SP-B) and 2% SP-C33, or its C-terminally truncated form SP-C30, in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 68:31 (w/w) resulted in median lung gas volumes of 8–9 ml/kg body weight, while animals treated with 2% Mini-B surfactant or 2% SP-C33/SP-C30 surfactant had lung gas volumes of 3–4 ml/kg, and those treated with Curosurf, a porcine surfactant, 15–17 ml/kg. In contrast, mixing SP-C33 with peptides with different distributions of positively charged and hydrophobic residues did not improve lung gas volumes. Conclusions The data indicate that synthetic surfactants containing analogues of both SP-B and SP-C might be superior to single-peptide surfactants in the treatment of RDS. PMID:20110733

  18. Phytosulfokine, sulfated peptides that induce the proliferation of single mesophyll cells of Asparagus officinalis L.

    PubMed Central

    Matsubayashi, Y; Sakagami, Y

    1996-01-01

    Proliferation of dispersed plant cells in culture is strictly dependent on cell density, and cells in a low-density culture can only grow in the presence of conditioned medium (CM). No known plant hormones have been able to substitute for CM. To quantify the mitogenic activity of CM, we examined conditions for the assay system using mechanically dispersed mesophyll cells of Asparagus officinalis L. and established a highly sensitive bioassay method. By use of this method, the mitogenic activity of CM prepared from asparagus cells was characterized: it was heat-stable, susceptible to pronase digestion, and resistant to glycosidase treatment. On the basis of these results, the mitogenic activity in CM was purified 10(7)-fold by column chromatography, and two factors named phytosulfokine-alpha and -beta (PSK-alpha and PSK-beta) were obtained. By amino acid sequence analysis and mass spectrometry, the structures of these two factors were determined to be sulfated pentapeptide (H-Tyr(SO3H)-Ile-Tyr(SO3H)-Thr-Gln-OH) and sulfated tetrapeptide (H-Tyr(SO3H)-Ile-Tyr(SO3H)-Thr-OH). PSK-alpha and PSK-beta were prepared by chemical synthesis and enzymatic sulfation. The synthetic peptides exhibited the same activity as the natural factors, confirming the structure for PSK-alpha and PSK-beta mentioned above. This is the first elucidation of the structure of a conditioned medium factor required for the growth of low-density plant cell cultures. Images Fig. 3 Fig. 4 Fig. 5 PMID:8755525

  19. Biocatalytic self-assembly of supramolecular charge-transfer nanostructures based on n-type semiconductor-appended peptides.

    PubMed

    Nalluri, Siva Krishna Mohan; Berdugo, Cristina; Javid, Nadeem; Frederix, Pim W J M; Ulijn, Rein V

    2014-06-02

    The reversible in situ formation of a self-assembly building block (naphthalenediimide (NDI)-dipeptide conjugate) by enzymatic condensation of NDI-functionalized tyrosine (NDI-Y) and phenylalanine-amide (F-NH2) to form NDI-YF-NH2 is described. This coupled biocatalytic condensation/assembly approach is thermodynamically driven and gives rise to nanostructures with optimized supramolecular interactions as evidenced by substantial aggregation induced emission upon assembly. Furthermore, in the presence of di-hydroxy/alkoxy naphthalene donors, efficient charge-transfer complexes are produced. The dynamic formation of NDI-YF-NH2 and electronic and H-bonding interactions are analyzed and characterized by different methods. Microscopy (TEM and AFM) and rheology are used to characterize the formed nanostructures. Dynamic nanostructures, whose formation and function are driven by free-energy minimization, are inherently self-healing and provide opportunities for the development of aqueous adaptive nanotechnology. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Ultrasensitive Charge Detection Using a Cavity Embedded Single Cooper Pair Transistor

    DTIC Science & Technology

    2014-08-01

    Blais, R.-S. Huang, A. Wallraff, S. M. Girvin, and R. J. Schoelkopf, “Cavity Quantum Electrodynamics for Superconducting Electrical Circuits: An...R. J. Schoelkopf, “Strong Coupling of a Single Photon to a Superconducting Qubit Using Circuit Quantum Electrodynamics ,” Nature 431, 162 (2004... quantum dots Dsbased on the radio- frequency single electron transistor (RF-SET) or quantum point contact (RF-QPC). Our approach should be more

  1. Physical reasons for the unusual α-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides

    PubMed Central

    Vila, Jorge A.; Ripoll, Daniel R.; Scheraga, H. A.

    2000-01-01

    We have carried out conformational energy calculations on alanine-based copolymers with the sequence Ac-AAAAAXAAAA-NH2 in water, where X stands for lysine or glutamine, to identify the underlying source of stability of alanine-based polypeptides containing charged or highly soluble polar residues in the absence of charge–charge interactions. The results indicate that ionizable or neutral polar residues introduced into the sequence to make them soluble sequester the water away from the CO and NH groups of the backbone, thereby enabling them to form internal hydrogen bonds. This solvation effect dictates the conformational preference and, hence, modifies the conformational propensity of alanine residues. Even though we carried out simulations for specific amino acid sequences, our results provide an understanding of some of the basic principles that govern the process of folding of these short sequences independently of the kind of residues introduced to make them soluble. In addition, we have investigated through simulations the effect of the bulk dielectric constant on the conformational preferences of these peptides. Extensive conformational Monte Carlo searches on terminally blocked 10-mer and 16-mer homopolymers of alanine in the absence of salt were carried out assuming values for the dielectric constant of the solvent ɛ of 80, 40, and 2. Our simulations show a clear tendency of these oligopeptides to augment the α-helix content as the bulk dielectric constant of the solvent is lowered. This behavior is due mainly to a loss of exposure of the CO and NH groups to the aqueous solvent. Experimental evidence indicates that the helical propensity of the amino acids in water shows a dramatic increase on addition of certain alcohols, such us trifluoroethanol. Our results provide a possible explanation of the mechanism by which alcohol/water mixtures affect the free energy of helical alanine oligopeptides relative to nonhelical ones. PMID:11078529

  2. Charge transfer of single laser crystallized intrinsic and phosphorus-doped Si-nanocrystals visualized by Kelvin probe force microscopy

    SciTech Connect

    Xu, Jie; Xu, Jun Lu, Peng; Shan, Dan; Li, Wei; Chen, Kunji

    2014-10-07

    Isolated intrinsic and phosphorus doped (P-doped) Si-nanocrystals (Si-NCs) on n- and p-Si substrates are fabricated by excimer laser crystallization techniques. The formation of Si-NCs is confirmed by atomic force microscopy (AFM) and conductive AFM measurements. Kelvin probe force microscopy (KPFM) is then carried out to visualize the trapped charges in a single Si-NC dot which derives from the charge transfer between Si-NCs and Si substrates due to their different Fermi levels. The laser crystallized P-doped Si-NCs have a similar Fermi level around the mid-gap to the intrinsic counterparts, which might be caused by the inactivated impurity atoms or the surface states-related Fermi level pinning. A clear rise of the Fermi level in P-doped Si-NCs is observed after a short time thermal annealing treatment, indicating the activation of dopants in Si-NCs. Moreover, the surface charge quantity can be estimated using a simple parallel plate capacitor model for a quantitative understanding of the KPFM results at the nanoscale.

  3. Semi-empirical scaling for ion-atom single charge exchange cross sections in the intermediate velocity regime

    NASA Astrophysics Data System (ADS)

    Friedman, B.; DuCharme, G.

    2017-06-01

    We present a semi-empirical scaling law for non-resonant ion-atom single charge exchange cross sections for collisions with velocities from {10}7 {{t}}{{o}} {10}9 {cm} {{{s}}}-1 and ions with positive charge q< 8. Non-resonant cross sections tend to have a velocity peak at collision velocities v≲ 1 {{a}}{{u}} with exponential decay around this peak. We construct a scaling formula for the location of this peak then choose a functional form for the cross section curve and scale it. The velocity at which the cross section peaks, v m, is proportional to the energy defect of the collision, {{Δ }}E, which we predict with the decay approximation. The value of the cross section maximum is proportional to the charge state q, inversely proportional to the target ionization energy I T, and inversely proportional to v m. For the shape of the cross section curve, we use a function that decays exponentially asymptotically at high and low velocities. We scale this function with parameters {v}{{m}},{I}{{T}},{Z}{{T}},{and} {Z}{{P}}, where the {Z}{{T},{{P}}} are the target and projectile atomic numbers. For the more than 100 cross section curves that we use to find the scaling rules, the scaling law predicts cross sections within a little over a factor of 2 on average.

  4. Experimental study of the stochastic heating of a single Brownian particle by charge fluctuations

    NASA Astrophysics Data System (ADS)

    Schmidt, Christian; Piel, Alexander

    2016-08-01

    The Brownian motion of a micro-particle, which is suspended in the sheath of a radio-frequency discharge, is studied by high-speed video microscopy. In this environment, stochastic heating by charge fluctuations is expected, which should lead to an anisotropic kinetic temperature of the particle with a preferential heating in the direction of the mean electric field in the sheath. The stochastic heating should become more effective at low gas pressures where cooling by the neutral gas becomes ineffective. Our refined experiments confirm the anisotropic heating and the temperature rise for diminishing pressure. Particle-in-cell simulations have guided us in modifying the gap width of the discharge and to specify the dependence of the plasma density on gas pressure as n i ∝ p 1 / 2 . Since the stochastic heating rate also depends on the life-time of charge fluctuations, a temperature scaling T kin ∝ p 3 / 2 results, which is in agreement with the experimental data. The experimental procedure to eliminate other spurious heating mechanisms is described in detail.

  5. Charging effects in single InP/GaInP baby dots

    NASA Astrophysics Data System (ADS)

    Persson, Jonas

    2001-03-01

    It has recently been demonstrated that the matrix material plays a major role for the physical behavior of self-assembled InP/GaInP quantum dots. As the "intrinsically" n-type GaInP matrix fills the quantum dot with electrons the spectral behavior of the dot dramatically changes. For the larger, fully developed dots, the charging gives rise to several broad lines. With an external bias it is possible to reduce the electron population of the dot. For smaller dots, baby dots, we show the possibility of dramatically changing the appearance of the dot spectrum by a precise tuning of the size of the quantum dot. When the dot is small enough it is uncharged and the spectrum is very similar to other material systems, whereas a slightly larger dot is charged and the number of lines is dramatically increased. We present high spectral resolution photoluminescence measurements of individual InP/GaInP baby-dots and k\\cdotp calculations including direct and exchange interactions.

  6. Accumulative charge separation for solar fuels production: coupling light-induced single electron transfer to multielectron catalysis.

    PubMed

    Hammarström, Leif

    2015-03-17

    The conversion and storage of solar energy into a fuel holds promise to provide a significant part of the future renewable energy demand of our societies. Solar energy technologies today generate heat or electricity, while the large majority of our energy is used in the form of fuels. Direct conversion of solar energy to a fuel would satisfy our needs for storable energy on a large scale. Solar fuels can be generated by absorbing light and converting its energy to chemical energy by electron transfer leading to separation of electrons and holes. The electrons are used in the catalytic reduction of a cheap substrate with low energy content into a high-energy fuel. The holes are filled by oxidation of water, which is the only electron source available for large scale solar fuel production. Absorption of a single photon typically leads to separation of a single electron-hole pair. In contrast, fuel production and water oxidation are multielectron, multiproton reactions. Therefore, a system for direct solar fuel production must be able to accumulate the electrons and holes provided by the sequential absorption of several photons in order to complete the catalytic reactions. In this Account, the process is termed accumulative charge separation. This is considerably more complicated than charge separation on a single electron level and needs particular attention. Semiconductor materials and molecular dyes have for a long time been optimized for use in photovoltaic devices. Efforts are made to develop new systems for light harvesting and charge separation that are better optimized for solar fuel production than those used in the early devices presented so far. Significant progress has recently been made in the discovery and design of better homogeneous and heterogeneous catalysts for solar fuels and water oxidation. While the heterogeneous ones perform better today, molecular catalysts based on transition metal complexes offer much greater tunability of electronic and

  7. Detection of single-electron charging in an individual InAs quantum dot by noncontact atomic-force microscopy.

    PubMed

    Stomp, Romain; Miyahara, Yoichi; Schaer, Sacha; Sun, Qingfeng; Guo, Hong; Grutter, Peter; Studenikin, Sergei; Poole, Philip; Sachrajda, Andy

    2005-02-11

    Single-electron charging in an individual InAs quantum dot was observed by electrostatic force measurements with an atomic-force microscope (AFM). The resonant frequency shift and the dissipated energy of an oscillating AFM cantilever were measured as a function of the tip-back electrode voltage, and the resulting spectra show distinct jumps when the tip was positioned above the dot. The observed jumps in the frequency shift, with corresponding peaks in dissipation, are attributed to a single-electron tunneling between the dot and the back electrode governed by the Coulomb blockade effect, and are consistent with a model based on the free energy of the system. The observed phenomenon may be regarded as the "force version" of the Coulomb blockade effect.

  8. In Vitro Cellular Gene Delivery Employing a Novel Composite Material of Single-Walled Carbon Nanotubes Associated With Designed Peptides With Pegylation.

    PubMed

    Ohta, Takahisa; Hashida, Yasuhiko; Higuchi, Yuriko; Yamashita, Fumiyoshi; Hashida, Mitsuru

    2017-03-01

    Single-walled carbon nanotubes (SWCNTs) attract great interest in biomedical fields including application for drug delivery system. In this study, we developed a novel gene delivery system employing SWCNTs associated with polycationic and amphiphilic H-(-Lys-Trp-Lys-Gly-)7-OH [(KWKG)7] peptides having pegylation. SWCNTs wrapped with (KWKG)7 formed a complex with plasmid DNA (pDNA) in aqueous solution based on polyionic interaction but later underwent aggregation. On the other hand, a complex of pDNA and SWCNT-(KWKG)7 modified with polyethylene glycol (PEG) chains of 12 units [SWCNT-(KWKG)7-(PEG)12] afforded good dispersion stability for 24 h even in a cell culture medium. The in vitro cellular uptake of SWCNT-(KWKG)7-(PEG)12/pDNA complex prepared with fluorescence-labeled pDNA was evaluated with fluorescent microscopic observation and flow cytometry. The uptake by A549 human lung adenocarcinoma epithelial cells increased along with the extent of pegylation, suggesting the importance of dispersion stability in addition to the cationic charge which facilitates ionic cellular interaction. The expression of pDNA encoding the monomeric Kusabira-Orange 2 fluorescent protein in the form of the SWCNT-(KWKG)7-(PEG)12/pDNA complex demonstrated remarkable enhancement of transfection depending also on the extent of pegylation and the N/P ratio. The potential of the SWCNT composite wrapped with polycationic and amphiphilic (KWKG)7 with pegylation as a carrier for gene delivery was demonstrated.

  9. Frequency and Distribution of Single-Nucleotide Polymorphisms within mprF in Methicillin-Resistant Staphylococcus aureus Clinical Isolates and Their Role in Cross-Resistance to Daptomycin and Host Defense Antimicrobial Peptides

    PubMed Central

    Bayer, Arnold S.; Mishra, Nagendra N.; Chen, Liang; Kreiswirth, Barry N.; Rubio, Aileen

    2015-01-01

    MprF is responsible for the lysinylation of phosphatidylglycerol (PG) to synthesize the positively charged phospholipid (PL) species, lysyl-PG (L-PG). It has been proposed that the single-nucleotide polymorphisms (SNPs) within the mprF open reading frame (ORF) are associated with a gain-in-function phenotype in terms of daptomycin resistance in Staphylococcus aureus. (Note that although the official term is daptomycin nonsusceptibility, we use the term daptomycin resistance in this paper for ease of presentation.) Using 22 daptomycin-susceptible (DAPs)/daptomycin-resistant (DAPr) clinical methicillin-resistant S. aureus (MRSA) strain pairs, we assessed (i) the frequencies and distribution of putative mprF gain-in-function SNPs, (ii) the relationships of the SNPs to both daptomycin resistance and cross-resistance to the prototypical endovascular host defense peptide (HDP) thrombin-induced platelet microbicidal protein (tPMP), and (iii) the impact of mprF SNPs on positive surface charge phenotype and modifications of membrane PL profiles. Most of the mprF SNPs identified in our DAPr strains were clustered within the two MprF loci, (i) the central bifunctional domain and (ii) the C-terminal synthase domain. Moreover, we were able to correlate the presence and location of mprF SNPs in DAPr strains with HDP cross-resistance, positive surface charge, and L-PG profiles. Although DAPr strains with mprF SNPs in the bifunctional domain showed higher resistance to tPMPs than DAPr strains with SNPs in the synthase domain, this relationship was not observed in positive surface charge assays. These results demonstrated that both charge-mediated and -unrelated mechanisms are involved in DAP resistance and HDP cross-resistance in S. aureus. PMID:26055370

  10. Frequency and Distribution of Single-Nucleotide Polymorphisms within mprF in Methicillin-Resistant Staphylococcus aureus Clinical Isolates and Their Role in Cross-Resistance to Daptomycin and Host Defense Antimicrobial Peptides.

    PubMed

    Bayer, Arnold S; Mishra, Nagendra N; Chen, Liang; Kreiswirth, Barry N; Rubio, Aileen; Yang, Soo-Jin

    2015-08-01

    MprF is responsible for the lysinylation of phosphatidylglycerol (PG) to synthesize the positively charged phospholipid (PL) species, lysyl-PG (L-PG). It has been proposed that the single-nucleotide polymorphisms (SNPs) within the mprF open reading frame (ORF) are associated with a gain-in-function phenotype in terms of daptomycin resistance in Staphylococcus aureus. (Note that although the official term is daptomycin nonsusceptibility, we use the term daptomycin resistance in this paper for ease of presentation.) Using 22 daptomycin-susceptible (DAP(s))/daptomycin-resistant (DAP(r)) clinical methicillin-resistant S. aureus (MRSA) strain pairs, we assessed (i) the frequencies and distribution of putative mprF gain-in-function SNPs, (ii) the relationships of the SNPs to both daptomycin resistance and cross-resistance to the prototypical endovascular host defense peptide (HDP) thrombin-induced platelet microbicidal protein (tPMP), and (iii) the impact of mprF SNPs on positive surface charge phenotype and modifications of membrane PL profiles. Most of the mprF SNPs identified in our DAP(r) strains were clustered within the two MprF loci, (i) the central bifunctional domain and (ii) the C-terminal synthase domain. Moreover, we were able to correlate the presence and location of mprF SNPs in DAP(r) strains with HDP cross-resistance, positive surface charge, and L-PG profiles. Although DAP(r) strains with mprF SNPs in the bifunctional domain showed higher resistance to tPMPs than DAP(r) strains with SNPs in the synthase domain, this relationship was not observed in positive surface charge assays. These results demonstrated that both charge-mediated and -unrelated mechanisms are involved in DAP resistance and HDP cross-resistance in S. aureus.

  11. Probing single-charge fluctuations at a GaAs/AlAs interface using laser spectroscopy on a nearby InGaAs quantum dot.

    PubMed

    Houel, J; Kuhlmann, A V; Greuter, L; Xue, F; Poggio, M; Gerardot, B D; Dalgarno, P A; Badolato, A; Petroff, P M; Ludwig, A; Reuter, D; Wieck, A D; Warburton, R J

    2012-03-09

    We probe local charge fluctuations in a semiconductor via laser spectroscopy on a nearby self-assembled quantum dot. We demonstrate that the quantum dot is sensitive to changes in the local environment at the single-charge level. By controlling the charge state of localized defects, we are able to infer the distance of the defects from the quantum dot with ±5  nm resolution. The results identify and quantify the main source of charge noise in the commonly used optical field-effect devices.

  12. Immunoreactive prohormone atrial natriuretic peptides 1-30 and 31-67 - Existence of a single circulating amino-terminal peptide

    NASA Technical Reports Server (NTRS)

    Chen, Yu-Ming; Whitson, Peggy A.; Cintron, Nitza M.

    1990-01-01

    Sep-Pak C18 extraction of human plasma and radioimmunoassay using antibodies which recognize atrial natriuretic peptide (99-128) and the prohormone sequences 1-30 and 31-67 resulted in mean values from 20 normal subjects of 26.2 (+/- 9.2), 362 (+/- 173) and 368 (+/- 160) pg/ml, respectively. A high correlation coefficient between values obtained using antibodies recognizing prohormone sequences 1-30 and 31-67 was observed (R = 0.84). Extracted plasma immunoreactivity of 1-30 and 31-67 both eluted at 46 percent acetonitrile. In contrast, chromatographic elution of synthetic peptides 1-30 and 31-67 was observed at 48 and 39 percent acetonitrile, respectively. Data suggest that the radioimmunoassay of plasma using antibodies recognizing prohormone sequences 1-30 and 31-67 may represent the measurement of a unique larger amino-terminal peptide fragment containing antigenic sites recognized by both antisera.

  13. Effects of Voluntary Locomotion and Calcitonin Gene-Related Peptide on the Dynamics of Single Dural Vessels in Awake Mice

    PubMed Central

    Gao, Yu-Rong

    2016-01-01

    The dura mater is a vascularized membrane surrounding the brain and is heavily innervated by sensory nerves. Our knowledge of the dural vasculature has been limited to pathological conditions, such as headaches, but little is known about the dural blood flow regulation during behavior. To better understand the dynamics of dural vessels during behavior, we used two-photon laser scanning microscopy (2PLSM) to measure the diameter changes of single dural and pial vessels in the awake mouse during voluntary locomotion. Surprisingly, we found that voluntary locomotion drove the constriction of dural vessels, and the dynamics of these constrictions could be captured with a linear convolution model. Dural vessel constrictions did not mirror the large increases in intracranial pressure (ICP) during locomotion, indicating that dural vessel constriction was not caused passively by compression. To study how behaviorally driven dynamics of dural vessels might be altered in pathological states, we injected the vasodilator calcitonin gene-related peptide (CGRP), which induces headache in humans. CGRP dilated dural, but not pial, vessels and significantly reduced spontaneous locomotion but did not block locomotion-induced constrictions in dural vessels. Sumatriptan, a drug commonly used to treat headaches, blocked the vascular and behavioral the effects of CGRP. These findings suggest that, in the awake animal, the diameters of dural vessels are regulated dynamically during behavior and during drug-induced pathological states. SIGNIFICANT STATEMENT The vasculature of the dura has been implicated in the pathophysiology of headaches, but how individual dural vessels respond during behavior, both under normal conditions and after treatment with the headache-inducing peptide calcitonin gene-related peptide (CGRP), is poorly understood. To address these issues, we imaged individual dural vessels in awake mice and found that dural vessels constricted during voluntary locomotion, and

  14. Observation of charge transport through CdSe/ZnS quantum dots in a single-electron transistor structure

    NASA Astrophysics Data System (ADS)

    Kobo, Masanori; Yamamoto, Makoto; Ishii, Hisao; Noguchi, Yutaka

    2016-10-01

    We fabricated single-electron transistors (SETs) having CdSe/ZnS core-shell-type quantum dots (CdSe/ZnS-QDs) as a Coulomb island using a wet chemistry technique. The CdSe/ZnS-QDs were deposited onto Au electrodes with or without the assistance of a self-assembled monolayer of octane(di)thiols. The CdSe/ZnS-QDs were adsorbed onto the Au electrodes even without the interlayer of thiol molecules depending on the concentration of the CdSe/ZnS-QD solution. The electron-transport characteristics through the CdSe/ZnS-QDs were examined in an SET structure at 13 K. Coulomb blockade behavior with typical gate voltage dependence was clearly observed. The estimated charge addition energies of a CdSe/ZnS-QD ranged from 70 to 280 meV. Moreover, additional structures, including negative differential conductance, appeared in the stability diagram in the source-drain bias region beyond 100 mV; these structures are specific to single-charge transport through the discrete energy levels in the Coulomb island.

  15. Fabrication of single cylindrical Au-coated nanopores with non-homogeneous fixed charge distribution exhibiting high current rectifications.

    PubMed

    Nasir, Saima; Ali, Mubarak; Ramirez, Patricio; Gómez, Vicente; Oschmann, Bernd; Muench, Falk; Tahir, Muhammad Nawaz; Zentel, Rudolf; Mafe, Salvador; Ensinger, Wolfgang

    2014-08-13

    We designed and characterized a cylindrical nanopore that exhibits high electrochemical current rectification ratios at low and intermediate electrolyte concentrations. For this purpose, the track-etched single cylindrical nanopore in polymer membrane was coated with a gold (Au) layer via electroless plating technique. Then, a non-homogeneous fixed charge distribution inside the Au-coated nanopore was obtained by incorporating thiol-terminated uncharged poly(N-isopropylacrylamide) chains in series to poly(4-vinylpyridine) chains, which were positively charged at acidic pH values. The functionalization reaction was checked by measuring the current-voltage curves prior to and after the chemisorption of polymer chains. The experimental nanopore characterization included the effects of temperature, adsorption of chloride ions, electrolyte concentration, and pH of the external solutions. The results obtained are further explained in terms of a theoretical continuous model. The combination of well-established chemical procedures (thiol and self-assembled monolayer formation chemistry, electroless plating, ion track etching) and physical models (two-region pore and Nernst-Planck equations) permits the obtainment of a new nanopore with high current rectification ratios. The single pore could be scaled up to multipore membranes of potential interest for pH sensing and chemical actuators.

  16. Negative Ion MALDI Mass Spectrometry of Polyoxometalates (POMs): Mechanism of Singly Charged Anion Formation and Chemical Properties Evaluation

    NASA Astrophysics Data System (ADS)

    Boulicault, Jean E.; Alves, Sandra; Cole, Richard B.

    2016-08-01

    MALDI-MS has been developed for the negative ion mode analysis of polyoxometalates (POMs). Matrix optimization was performed using a variety of matrix compounds. A first group of matrixes offers MALDI mass spectra containing abundant intact singly charged anionic adduct ions, as well as abundant in-source fragmentations at elevated laser powers. A relative ranking of the ability to induce POM fragmentation is found to be: DAN > CHCA > CNA > DIT> HABA > DCTB > IAA. Matrixes of a second group provide poorer quality MALDI mass spectra without observable fragments. Sample preparation, including the testing of salt additives, was performed to optimize signals for a model POM, POMc12, the core structure of which bears four negative charges. The matrix 9-cyanoanthracene (CNA) provided the best signals corresponding to singly charged intact POMc12 anions. Decompositions of these intact anionic species were examined in detail, and it was concluded that hydrogen radical-induced mechanisms were not prevalent, but rather that the observed prompt fragments originate from transferred energy derived from initial electronic excitation of the CNA matrix. Moreover, in obtained MALDI mass spectra, clear evidence of electron transfer to analyte POM species was found: a manifestation of the POMs ability to readily capture electrons. The affinity of polyanionic POMc12 toward a variety of cations was evaluated and the following affinity ranking was established: Fe3+ > Al3+ > Li+ > Ga3+ > Co2+ > Cr3+ > Cu2+ > [Mn2+, Mg2+] > [Na+, K+]. Thus, from the available cationic species, specific adducts are preferentially formed, and evidence is given that these higher affinity POM complexes are formed in the gas phase during the early stages of plume expansion.

  17. Negative Ion MALDI Mass Spectrometry of Polyoxometalates (POMs): Mechanism of Singly Charged Anion Formation and Chemical Properties Evaluation.

    PubMed

    Boulicault, Jean E; Alves, Sandra; Cole, Richard B

    2016-08-01

    MALDI-MS has been developed for the negative ion mode analysis of polyoxometalates (POMs). Matrix optimization was performed using a variety of matrix compounds. A first group of matrixes offers MALDI mass spectra containing abundant intact singly charged anionic adduct ions, as well as abundant in-source fragmentations at elevated laser powers. A relative ranking of the ability to induce POM fragmentation is found to be: DAN > CHCA > CNA > DIT> HABA > DCTB > IAA. Matrixes of a second group provide poorer quality MALDI mass spectra without observable fragments. Sample preparation, including the testing of salt additives, was performed to optimize signals for a model POM, POMc12, the core structure of which bears four negative charges. The matrix 9-cyanoanthracene (CNA) provided the best signals corresponding to singly charged intact POMc12 anions. Decompositions of these intact anionic species were examined in detail, and it was concluded that hydrogen radical-induced mechanisms were not prevalent, but rather that the observed prompt fragments originate from transferred energy derived from initial electronic excitation of the CNA matrix. Moreover, in obtained MALDI mass spectra, clear evidence of electron transfer to analyte POM s