Improved curve fitting procedures to determine equilibrium binding constants

For ligand-biomacromolecule titration experiments it has been traditional practice to extract parameters such as the equilibrium binding constant K and the number of bases per ligand binding site n with relatively labour intensive methods, usually based on single wavelength data, such as the difference method by Rodger and Nordén coupled together with a Scatchard plot. Presented in this paper are both the theory and a least squares fitting method to derive parameters such as K and n more directly from all spectral non-linear experimental data. Both the case of non competitive binding of a metal complex ligand to DNA and the case of displacement by a metal complex ligand of an ethidium marker attached to the DNA are considered. This work may be applied directly to reduce experimental data produced by a spectropolarimeter (for circular or linear dichroism) or a spectrophotometer (for fluorescence or UV-Vis spectroscopy).     

Photoreactivity of iron(III)-aerobactin: photoproduct structure and iron(III) coordination

UV photolysis of the ferric aerobactin complex results in decarboxylation of the alpha-hydroxy carboxylic acid group of the central citrate moiety of aerobactin. The structure determination of the photooxidized ligand shows that decarboxylation occurs at the citrate moiety forming a 3-ketoglutarate moiety. Proton and carbon-13 NMR establish the presence of keto and enol tautomers of the apo-photoproduct, with the enol form prevailing in water. The photoproduct retains the ability to coordinate iron(III). The values of the ligand protonation constants, the pKa of the Fe(III)-ligand complex, and the Fe(III) stability constant of the photoproduct of aerobactin are all close to those of aerobactin. CD spectroscopy suggests that the chirality of the ferric complexes of aerobactin and its photoproduct are similar. Like aerobactin, the photoproduct promotes iron acquisition by the source bacterium, Vibrio sp. DS40M5.     

Microwave‐accelerated synthesis of benzyl 3,5‐dimethyl‐pyrrole‐2‐carboxylate

Benzyl 3,5‐dimethyl‐pyrrole‐2‐carboxylate, a very useful pyrrole in porphyrin and dipyrromethene synthesis, can be synthesized via the Knorr‐type reaction, but in low yield. Alternative routes to benzyl 3,5‐dimethyl‐pyrrole‐2‐carboxylate have been developed involving the trans‐esterification of ethyl 3,5‐dimethyl‐pyrrole‐2‐carboxylate and the de‐acetylation of benzyl 4‐acetyl‐3,5‐dimethyl‐2‐carboxylate, both precursors being easily obtained using the Knorr reaction. These traditional methods involve treatment of the known products with a strong basic solution or heating for extended periods which often lead to decomposition. The use of microwave energy to promote these two reactions proves to be an extremely efficient way to obtain benzyl 3,5‐dimethyl‐pyrrole‐2‐carboxylate quickly, in high yield, and in excellent purity with no need for recrystallization. Of particular note is the use of catalytic sodium methoxide in benzyl alcohol, rather than stoichiometric amounts of sodium benzoxide, to effect benzylation.     

Single-isomer tetrasubstituted olefins from regioselective and stereospecific palladium-catalyzed coupling of beta-chloro-alpha-iodo-alpha,beta-unsaturated esters

The efficient regioselective and stereospecific synthesis of tetrasubstituted olefins using a mild and convenient method is disclosed. 2-Alkynyl esters are selectively converted to E-beta-chloro-alpha-iodo-alpha,beta-unsaturated esters by exposure to Bu4NI in refluxing dichloroethane. These products are produced cleanly, regio- and stereoselectively, and in high yields. Single-isomer tetrasubstituted olefins bearing four different carbon substituents are then synthesized by sequential palladium-catalyzed coupling reactions. Selectivity results from reactivity differences in the intermediate substrates.     

Water-soluble porphyrin detection in a pure-silica photonic crystal fiber

Aqueous solutions of the water-soluble porphyrin 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrinatomanganese(III) acetate were inserted into the holes of a photonic crystal fiber, and the porphyrin absorption bands were identified. Results were obtained for three concentrations. The porphyrins in water show no surface interactions with the silica walls of the capillary channels. We discuss the implications for future hybrid electronic and photonic fiber devices.     

“Wet” Versus “Dry” Folding of Polyproline

When the all-cis polyproline-I helix (PPI, favored in 1-propanol) of polyproline-13 is introduced into water, it folds into the all-trans polyproline-II (PPII) helix through at least six intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702–12711 (2014)]. Here, we show that the solvent-free intermediates refold into the all-cis PPI helix with high (>90%) efficiency. Moreover, in the absence of solvent, each intermediate appears to utilize the same small set of pathways observed for the solution-phase PPII → PPI transition upon immersion of PPII_aq in 1-propanol. That folding in solution (under conditions where water is displaced by propanol) and folding in vacuo (where energy required for folding is provided by collisional activation) occur along the same pathway is remarkable. Implicit in this statement is that 1-propanol mimics a “dry” environment, similar to the gas phase. We note that intermediates with structures that are similar to PPII_aq can form PPII under the most gentle activation conditions—indicating that some transitions observed in water (i.e., “wet” folding, are accessible (albeit inefficient) in vacuo. Lastly, these “dry” folding experiments show that PPI (all cis) is favored under “dry” conditions, which underscores the role of water as the major factor promoting preference for trans proline.

Open image in new window

Graphical Abstract ?

     

Ultrasonically induced phthalocyanine degradation: decolouration vs. metal release

The ultrasonically induced degradations of nickel(II) 2,9,16,23-tetraphenoxy-29H, 31H-phthalocyanine and vanadyl 2,9,16,23-tetraphenoxy-29H, 31H-phthalocyanine in a biphasic system consisting of chloroform and water are investigated. Decolourisation of the organic phase containing the metallo-phthalocyanines is found to occur rapidly (approximately minutes for 8 ml of ca. 5 microM solution). Analysis of the aqueous solute via ICP-OES, reveals significant amounts of the released nickel ultimately transfers into the aqueous phase but at a rate much slower than that of decolourisation, whereas the vanadium remains within the organic phase suggesting only partial degradation despite efficient decolourisation.     

Atomic force microscopy analysis of wool fibre surfaces in air and under water

Wool fibre surfaces have been treated by solvent cleaning which leaves the native covalently bound surface lipid layer intact, and by alcoholic alkali which removes the lipid layer. The resultant surfaces have been analysed by atomic force microscopy (AFM), with particular emphasis on force–distance (F–d) methods. Methodologies were developed for investigation in situ in water of both the surface topography and the characteristics of the lipid layer. Longitudinal surface texturing was resolved in images of wool fibre surfaces in air; the texturing remained prominent after exposure to water. High resolution F–d curves revealed features associated with the lipid layer. A simple formalism was used to show that the layer had a thickness of a few nm, and an effective stiffness of some 0.12±0.01 N/m. Strong adhesive interactions, equivalent to a pressure of 0.1 MPa, acted on the tip at the tip-to-substrate interface. The methodology and formalism are likely to be relevant in the broad field of thin-film analysis and for fibre technology.     

Single-cell FRET imaging of transferrin receptor trafficking dynamics by Sfp-catalyzed, site-specific protein labeling

Fluorescence imaging of living cells depends on an efficient and specific method for labeling the target cellular protein with fluorophores. Here we show that Sfp phosphopantetheinyl transferase-catalyzed protein labeling is suitable for fluorescence imaging of membrane proteins that spend at least part of their membrane trafficking cycle at the cell surface. In this study, transferrin receptor 1 (TfR1) was fused to peptide carrier protein (PCP), and the TfR1-PCP fusion protein was specifically labeled with fluorophore Alexa 488 by Sfp. The trafficking of transferrin-TfR1-PCP complex during the process of transferrin-mediated iron uptake was imaged by fluorescence resonance energy transfer between the fluorescently labeled transferrin ligand and TfR1 receptor. We thus demonstrated that Sfp-catalyzed small molecule labeling of the PCP tag represents a practical and efficient tool for molecular imaging studies in living cells.     

A macrocyclic β-iodoallenolate intermediate is key: synthesis of the ABD core of phomactin A

An enantioselective strategy for the synthesis of phomactin natural products is described. The Lewis acid triggered cyclization of a β-iodoallenolate embedded in a 12-membered macrocycle was used to obtain a highly functionalized bicyclo[9.3.1]pentadecane in good yield and high diastereoselectivity. This iodoenone contains the substituents of the AD ring system of the phomactin family of natural products, appropriate for further functionalization. Synthesis of the oxadecalin core of phomactin A from the AD iodoenone intermediate was achieved. In this unusual strategy, rings A and B are both fashioned within a macrocyclic precursor.