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Berlin Brandenburg

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  • 1
    Language: English
    In: Journal of the American Chemical Society, 19 January 2011, Vol.133(2), pp.167-9
    ISSN: 00027863
    E-ISSN: 1520-5126
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  • 2
    Language: English
    In: Journal of the American Chemical Society, 03 April 2013, Vol.135(13), pp.5062-7
    Description: We investigated salt interactions with butyramide as a simple mimic of cation interactions with protein backbones. The experiments were performed in aqueous metal chloride solutions using two spectroscopic techniques. In the first, which provided information about contact pair formation, the response of the amide I band to the nature and concentration of salt was monitored in bulk aqueous solutions via attenuated total reflection Fourier transform infrared spectroscopy. It was found that molar concentrations of well-hydrated metal cations (Ca(2+), Mg(2+), Li(+)) led to the rise of a peak assigned to metal cation-bound amides (1645 cm(-1)) and a decrease in the peak associated with purely water-bound amides (1620 cm(-1)). In a complementary set of experiments, the effect of cation identity and concentration was investigated at the air/butyramide/water interface via vibrational sum frequency spectroscopy. In these studies, metal ion-amide binding led to the ordering of the adjacent water layer. Such experiments were sensitive to the interfacial partitioning of cations in either a contact pair with the amide or as a solvent separated pair. In both experiments, the ordering of the interactions of the cations was: Ca(2+) 〉 Mg(2+) 〉 Li(+) 〉 Na(+) ≈ K(+). This is a direct cationic Hofmeister series. Even for Ca(2+), however, the apparent equilibrium dissociation constant of the cation with the amide carbonyl oxygen was no tighter than ∼8.5 M. For Na(+) and K(+), no evidence was found for any binding. As such, the interactions of metal cations with amides are far weaker than the analogous binding of weakly hydrated anions.
    Keywords: Amides -- Chemistry ; Water -- Chemistry
    ISSN: 00027863
    E-ISSN: 1520-5126
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  • 3
    Language: English
    In: Analytical Chemistry, Nov 19, 2013, Vol.85(22), p.10803(9)
    Description: While electrophoresis in lipid bilayers has been performed since the 1970s, the technique has until now been unable to accurately measure the charge on lipids and proteins within the membrane based on drift velocity measurements. Part of the problem is caused by the use of the Einstein-Smoluchowski equation to estimate the electrophoretic mobility of such species. The source of the error arises from the fact that a lipid headgroup is typically smaller than the Debye length of the adjacent aqueous solution in most electrophoresis experiments. Instead, the Henry equation can more accurately predict the electrophoretic mobility at sufficient ionic strength. This was done for three dye-labeled lipids with different sized head groups and a charge on each lipid of -1. Also, the charge was measured as a function of pH for two titratable lipids that were fluorescently labeled. Finally, it was shown that the Henry equation also has difficulties measuring the correct lipid charge at salt concentrations below 5 mM, where electroosmotic forces are more significant.
    Keywords: Electrophoresis – Analysis ; Lipids – Analysis ; Fluorescence – Analysis
    ISSN: 0003-2700
    Source: Cengage Learning, Inc.
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  • 4
    Language: English
    In: Journal of the American Chemical Society, 20 June 2012, Vol.134(24), pp.10039-46
    Description: The specific binding sites of Hofmeister ions with an uncharged 600-residue elastin-like polypeptide, (VPGVG)(120), were elucidated using a combination of NMR and thermodynamic measurements along with molecular dynamics simulations. It was found that the large soft anions such as SCN(-) and I(-) interact with the polypeptide backbone via a hybrid binding site that consists of the amide nitrogen and the adjacent α-carbon. The hydrocarbon groups at these sites bear a slight positive charge, which enhances anion binding without disrupting specific hydrogen bonds to water molecules. The hydrophobic side chains do not contribute significantly to anion binding or the corresponding salting-in behavior of the biopolymer. Cl(-) binds far more weakly to the amide nitrogen/α-carbon binding site, while SO(4)(2-) is repelled from both the backbone and hydrophobic side chains of the polypeptide. The Na(+) counterions are also repelled from the polypeptide. The identification of these molecular-level binding sites provides new insights into the mechanism of peptide-anion interactions.
    Keywords: Ions -- Chemistry ; Peptides -- Chemistry
    ISSN: 00027863
    E-ISSN: 1520-5126
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  • 5
    Language: English
    In: Journal of the American Chemical Society, 09 May 2012, Vol.134(18), pp.7773-9
    Description: Phosphatidylserine (PS) embedded within supported lipid bilayers was found to bind Cu(2+) from solution with extraordinarily high affinity. In fact, the equilibrium dissociation constant was in the femtomolar range. The resulting complex formed in a 1:2 Cu(2+)-to-PS ratio and quenches a broad spectrum of lipid-bound fluorophores in a reversible and pH-dependent fashion. At acidic pH values, the fluorophores were almost completely unquenched, while at basic pH values significant quenching (85-90%) was observed. The pH at which the transition occurred was dependent on the PS concentration and ranged from approximately pH 5 to 8. The quenching kinetics was slow at low Cu(2+) concentrations and basic pH values (up to several hours), while the unquenching reaction was orders of magnitude more rapid upon lowering the pH. This was consistent with diffusion-limited complex formation at basic pH but rapid dissociation under acidic conditions. The tight binding of Cu(2+) to PS may have physiological consequences under certain circumstances.
    Keywords: Copper -- Metabolism ; Lipid Bilayers -- Metabolism ; Phosphatidylserines -- Metabolism
    ISSN: 00027863
    E-ISSN: 1520-5126
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  • 6
    Language: English
    In: Analytical chemistry, 21 July 2015, Vol.87(14), pp.7163-70
    Description: Herein, we developed a new separation-based detection method that is capable of simultaneously identifying multiple competitively binding proteins for the same ligand on supported lipid bilayers (SLBs). This strategy used unlabeled target analyte proteins that bind to fluorescently tagged, lipid-conjugated ligands within the SLB. The protein-ligand binding complexes were then focused under an applied potential to different locations within the SLB based on each protein's size and charge. Both protein identity and relative surface concentration information could be obtained, simultaneously. Specifically, the competitive binding of streptavidin and goat anti-biotin for biotin-conjugated lipids was explored. It was found that streptavidin could inhibit the binding of goat anti-biotin antibodies for biotin-cap-1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl)(biotin-cap-NBD-PE) lipids and that streptavidin more effectively outcompeted the anti-biotin antibody at lower protein concentrations. Also, modulating the chemical composition of the membrane helped control the ultimate focusing position and separation of the streptavidin-bound biotin, anti-biotin-bound biotin, and free biotin-conjugated lipid bands. The assay developed herein provides a simple and convenient strategy for simultaneously monitoring target analytes that bind to the identical ligand and may ultimately be useful in developing assays that help overcome problems associated with cross-reactivity.
    Keywords: Binding, Competitive ; Antibodies -- Analysis ; Lipid Bilayers -- Chemistry ; Streptavidin -- Analysis
    ISSN: 00032700
    E-ISSN: 1520-6882
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  • 7
    Language: English
    In: The journal of physical chemistry. B, 28 June 2012, Vol.116(25), pp.7389-97
    Description: Thermodynamic and surface-specific spectroscopic investigations were carried with an elastin-like polypeptide (ELP) containing 16 aspartic acid residues. The goal was to explore the role of the carboxylate moieties in hydrophobic collapse and related Hofmeister effects. Experiments were conducted with a series of monovalent and divalent metal chloride salts. Both phase transition temperature and spectroscopic data demonstrated that the divalent cations showed relatively strong association to the carboxylate sites on the biopolymer with K(d) values in the range of 1 to 10 mM. The ordering of the divalent series was: Zn(2+) 〉 Ca(2+) 〉 Ba(2+) 〉 Sr(2+) 〉 Mg(2+). Monovalent cations displayed weaker binding which ranged from 78 mM for NH(4)(+) to 345 mM for Cs(+). The order for this series was: NH(4)(+) 〉 Li(+) 〉 Na(+) 〉 NMe(4)(+) 〉 K(+) 〉 Rb(+) ≥ Cs(+). These results are in general agreement with the notion that strongly hydrated cations bind more tightly to carboxylate groups than do weakly hydrated cations. Moreover, the data for the monovalent series was partially consistent with the law of matching water affinity, although Li(+) and NH(4)(+) did not follow the model. The series for the divalent cations did not appear to obey the law of matching water affinity at all.
    Keywords: Carboxylic Acids -- Metabolism ; Cations -- Metabolism ; Chlorides -- Metabolism ; Elastin -- Metabolism
    ISSN: 15206106
    E-ISSN: 1520-5207
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  • 8
    Language: English
    In: Journal of the American Chemical Society, 26 September 2012, Vol.134(38), pp.15832-9
    Description: Single-particle tracking experiments were carried out with gold nanoparticle-labeled solid supported lipid bilayers (SLBs) containing increasing concentrations of ganglioside (GM(1)). The negatively charged nanoparticles electrostatically associate with a small percentage of positively charged lipids (ethyl phosphatidylcholine) in the bilayers. The samples containing no GM(1) show random diffusion in 92% of the particles examined with a diffusion constant of 4.3(±4.5) × 10(-9) cm(2)/s. In contrast, samples containing 14% GM(1) showed a mixture of particles displaying both random and confined diffusion, with the majority of particles, 62%, showing confined diffusion. Control experiments support the notion that the nanoparticles are not associating with the GM(1) moieties but instead most likely confined to regions in between the GM(1) clusters. Analysis of the root-mean-squared displacement plots for all of the data reveals decreasing trends in the confined diffusion constant and diameter of the confining region versus increasing GM(1) concentration. In addition, a linearly decreasing trend is observed for the percentage of randomly diffusing particles versus GM(1) concentration, which offers a simple, direct way to measure the percolation threshold for this system, which has not previously been measured. The percolation threshold is found to be 22% GM(1) and the confining diameter at the percolation threshold only ∼50 nm.
    Keywords: Lipid Bilayers ; Nanoparticles ; Gangliosides -- Chemistry
    ISSN: 00027863
    E-ISSN: 1520-5126
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  • 9
    Language: English
    In: Analytical chemistry, 15 March 2011, Vol.83(6), pp.2090-6
    Description: A pH controlled flow cell device was constructed to allow electrophoretic movement of charged lipids and membrane associated proteins in supported phospholipid bilayers. The device isolated electrolysis products near the electrodes from the electrophoresis process within the bilayer. This allowed the pH over the bilayer region to remain within ±0.2 pH units or better over many hours at salt concentrations up to 10 mM. Using this setup, it was found that the electrophoretic mobility of a dye conjugated lipid (Texas Red 1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (TR-DHPE)) was essentially constant between pH 3.3 and 9.3. In contrast, streptavidin, which was bound to biotinylated lipids, shifted from migrating cathodically at acidic pH values to migrating anodically under basic conditions. This shift was due to the modulation of the net charge on the protein, which changed the electrophoretic forces experienced by the macromolecule. The addition of a polyethylene glycol (PEG) cushion beneath the bilayer or the increase in the ionic strength of the buffer solution resulted in a decrease of the electroosmotic force experienced by the streptavidin with little effect on the Texas Red-DHPE. As such, it was possible in part to control the electrophoretic and electroosmotic contributions to streptavidin independently of one another.
    Keywords: Electrophoresis -- Methods ; Lipid Bilayers -- Chemistry
    ISSN: 00032700
    E-ISSN: 1520-6882
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  • 10
    Language: English
    In: Biosensors and Bioelectronics, October 2012, Vol.38(1), pp.74-78
    Description: We have developed a technique for sensing protein–small molecule and protein–ion interactions in bulk aqueous solution by utilizing a pH sensitive dye, 5-(and-6)-carboxyfluorescein, conjugated to free lysine residues on the surfaces of designated capture proteins. The fluorescein intensity was found to change by about 6% and 15% for small molecule and ion binding, respectively. The assay works by modulating the local electric fields around a pH sensitive dye. This, in turn, alters the dye's apparent pK value. Such changes may result directly from the charge on the analyte, occur through allosteric effects related to the binding process, or result from a combination of both. The assay was used to follow the binding of Ca to calmodulin (CaM) and thiamine monophosphate (ThMP) to thiamine binding protein A (TbpA). The results demonstrate a binding constant of 1.1 μM for the Ca /CaM pair and 3.2 nM for ThMP/TbpA pair, which are in excellent agreement with literature values. These assays demonstrate the generality of this method for observing the interactions of small molecules and ions with capture proteins. In fact, the assay should work as a biosensor platform for most proteins containing a specific ligand binding site, which would be useful as a simple and rapid preliminary screen of protein–ligand interactions. ► pH modulation sensing detects the binding of small molecules and ions to proteins. ► The optical biosensor developed is a rapid method for screening ligand–receptor binding. ► The method developed is general and can be used with most proteins containing a binding site.
    Keywords: Biosensor ; Fluorescein ; Protein ; Small Molecule ; Ph Sensitive ; Labeling ; Engineering ; Biology
    ISSN: 0956-5663
    E-ISSN: 1873-4235
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