Eliminating positively charged lysine epsilon-NH3+ groups on the surface of carbonic anhydrase has no significant influence on its folding from sodium dodecyl sulfate

This study compares the folding of two polypeptides--bovine carbonic anhydrase (BCA) and peracetylated BCA (BCA-Ac(18))--having the same sequence of amino acids but differing by 18 formal units of charge, from a solution containing denaturing concentrations of sodium dodecyl sulfate (SDS). Acetylation of BCA with acetic anhydride converts all 18 lysine-epsilon-NH(3)(+) groups to lysine-epsilon-NHCOCH(3) groups and generates BCA-Ac(18). Both BCA and BCA-Ac(18) are catalytically active, and circular dichroism spectroscopy (CD) suggests that they have similar secondary and tertiary structures. SDS at concentrations above approximately 10 mM denatured both proteins. When the SDS was removed by dialysis, both proteins were regenerated in native form. This study suggests that large differences in the net charge of the polypeptide have no significant influence on the structure, the ability to refold, or the rate of refolding of this protein from solutions containing SDS. This study reinforces the idea that charged residues on the surface of BCA do not guide protein folding and raises the broader question of why proteins have charged residues on their surface, outside of the region of the active site.     

Uranium analysis in urine by inductively coupled plasma dynamic reaction cell mass spectrometry

Urine uranium concentrations are the best biological indicator for identifying exposure to depleted uranium (DU). Internal exposure to DU causes an increased amount of urine uranium and a decreased ratio of ²³⁵U/²³⁸U in urine samples, resulting in measurements that vary between 0.00725 and 0.002 (i.e., natural and depleted uraniums ²³⁵U/²³⁸U ratios, respectively). A method based on inductively coupled plasma dynamic reaction cell mass spectrometry (ICP-DRC-MS) was utilized to identify DU in urine by measuring the quantity of total U and the ²³⁵U/²³⁸U ratio. The quantitative analysis was achieved using ²³³U as an internal standard. The analysis was performed both with and without the reaction gas oxygen. The reaction gas converted ionized ²³⁵U⁺ and ²³⁸U⁺ into ²³⁵UO₂⁺ (m/z=267) and ²³⁸UO₂⁺ (m/z=270). This conversion was determined to be over 90% efficient. A polyatomic interference at m/z 234.8 was successfully removed from the ²³⁵U signal under either DRC operating conditions (with or without oxygen as a reaction gas). The method was validated with 15 urine samples of known uranium compositions. The method detection limit for quantification was determined to be 0.1 pg U mL^–1 urine and an average coefficient of variation (CV) of 1–2% within the sample measurements. The method detection limit for determining ²³⁵U/²³⁸U ratio was 3.0 pg U mL^–1 urine. An additional 21 patient samples were analyzed with no information about medical history. The measured ²³⁵U/²³⁸U ratio within the urine samples correctly identified the presence or absence of internal DU exposure in all 21 patients.The opinions and assertions expressed herein are those of the authors and are not to be construed as official or as representing the views of the Armed Forces Institute of Pathology, the Department of the Army, or the Department of Defense     

Conformational stability of helical peptides containing a thioamide linkage

[structure: see text] Thioxo peptide analogues of the alpha-helical peptide GCN4-p1 were synthesized and evaluated for helicity and oligomeric state. Sedimentation equilibrium and CD measurements indicate that the thioxo peptides fold into parallel alpha-helical coiled coil structures essentially identical to the native structure. This work marks the first incorporation of a thioamide linkage into the backbone of an alpha-helix and demonstrates that a thioamide linkage is compatible with positions within the helix as well as near the C-terminus.     

Quantitative measurements of recombinant HIV surface glycoprotein 120 binding to several glycosphingolipids expressed in planar supported lipid bilayers

The interaction of recombinant HIV-1 surface glycoprotein gp120 (rgp120) with natural isolates of lactosylceramide (LacCer), glucosylceramide (GlcCer), and galactosylceramide (GalCer) has been quantitatively measured under equilibrium conditions using total internal reflection fluorescence (TIRF) spectroscopy. The binding affinity (K(a)) of rgp120 to these glycosphingolipids (GSLs), reconstituted at 5 mol % in supported planar lipid bilayers composed of 95 mol % POPC, is ca. 10(6) M(-1) for dissolved rgp120 concentrations greater than 25 nM. In contrast, at concentrations of rgp120 between 0.2 and 15 nM, rgp120 does not bind significantly to LacCer and GlcCer, but has a high affinity for GalCer with a measured K(a) value of 1.6 x 10(9) M(-1). However, protein surface coverage measurements show that this strong binding process accounts for very little of the total protein adsorbed over the entire concentration range studied. At a protein concentration of ca. 20 nM, the surface coverage is only 3% of that achieved at apparent saturation (i.e., when the protein concentration is ca. 220 nM). Thus the "high affinity" binding sites comprise only a small fraction of the total number of binding sites. Several other variables were investigated. Rgp120 binding behavior at membranes doped with alpha-hydroxygalactosylceramide (alpha-GalCer) was very similar to that observed with GalCer, showing that the presence/absence of an alpha-hydroxy moiety does not significantly affect galactosylceramide recognition. Phase segregation of GalCer, which occurs when the mole fraction of this GSL in a POPC bilayer exceeds ca. 0.1, was also investigated and showed no effect on binding affinity at low rgp120 concentrations. To investigate the influence of fatty acid chain length, GSLs with monodisperse C(18) and C(24) chain lengths, both with and without an alpha-hydroxy moiety, were synthesized, and their binding affinity to rgp120 was examined. Relative to the natural isolates (which contain a mixture of chain lengths), minimal differences were observed; thus among the compounds tested, fatty acid chain length does not affect GSL recognition. The results of this work should aid efforts to design anti-HIV-1 agents based on membrane-tethered, carbohydrate-based receptors for rgp120.     

Diastereoselective ring-closing metathesis: synthesis of P-stereogenic phosphinates from prochiral phosphinic acid derivatives

[reaction: see text] The preparation of phosphorus-containing trienes featuring two diastereotopic vinyl moieties followed by a diastereoselective ring-closing metathesis is described. This methodology allowed for the synthesis of novel highly functionalized P-stereogenic heterocycles featuring both an exo- and an endocyclic double bond. An investigation into the factors influencing the diastereochemical outcome of the ring-closing metathesis is also presented, revealing that the geometry of the double bonds conjugated to phosphorus is important and that 1,3-stereoinduction is superior to 1,4-stereoinduction for these reactions.     

Comparison of micro- and mesoporous inorganic materials in the uptake and release of the drug model fluorescein and its analogues

The uptake of the three species of the drug model fluorescein (fluorescein sodium salt (FNa), fluorescein free acid (F), and fluorescein diacetate (FDA)) by zeolite NaX and the mesoporous zeotype MCM-41 was investigated as well as their release rates into solutions at pH 7 and pH 4.5. UV/Vis analysis was carried out at a wavelength of 490 nm. Uptakes of the sodium salt of 9 % for zeolite X and 14 % for MCM suggest little penetration of the pores. The use of ethanol as the loading solvent for F resulted in little uptake for both zeolitic materials due to the successful competition of the ethanol for binding sites. Use of acetone (weaker proton acceptor) as loading solvent significantly improved the uptake of F to 17 % and 12 % for zeolite X and MCM, respectively, whilst the uptake of FDA in acetone increased still further to 22 % and 17 % for zeolite X and MCM, respectively. Generally there was a large initial release of the fluorescein analogues from the surface of the zeolites with very little further increase over time. The prescence of an esterase enzyme in the release medium of FDA tripled the release from MCM to 15 % but left the release from zeolite X unaffected at 6 %. The results obtained show that uptake of fluorescein and its analogues is dependent on the loading solvent used, the amount released is influenced by not only the solvent but the pH and the presence of enzymes in the release medium.     

Interaction of atrazine with Laurentian fulvic acid: binding and hydrolysis

Ultrafiltration fractionation and liquid chromatography (LC) have been applied to the study of the binding and hydrolysis of the polar herbicide atrazine on a stoichiometrically well characterized fulvic acid. Binding requires extensive carboxylate site protonation but the binding sites represent a very small fraction of total carboxylate. The data show that binding of atrazine is not competitive with binding of the hydrolytic product hydroxyatrazine. However, smaller molecular weight fractions of the fulvic acid mixture compete with atrazine for sites on the larger molecular weight fraction. Binding equilibrium is not rapid. A model of binding involving hydrogen bonding and/or charge-transfer complexing to specific sites created dynamically by the conformational equilibria of the higher molecular weight polymeric fulvic acid fractions is proposed as the best accommodation of the variety of observed facts.     

Size-selected (2-10 nm) gold nanoparticles for matrix assisted laser desorption ionization of peptides

In this report, first use of size-selected gold nanoparticles (AuNPs) as matrixes for matrix assisted laser desorption/ionization (MALDI) is described for peptides and proteins. In comparison with conventional organic acid MALDI matrixes, the optimum matrix-to-analyte ratio with AuNP matrixes is reduced by 10-14 orders of magnitude. Significant differences in the relative abundances of the ions observed in positive and negative mode MALDI-time-of-flight mass spectrometry (TOFMS) are revealed as the AuNP size distribution is decreased from 10 to 2 nm, whereby 2-nm AuNPs exhibit quantum confinement effects prevalent in quantum dots. AuNP matrixes allow for selective analyte ionization, as demonstrated in the selective MALDI-TOFMS of phosphotyrosine in a background of phosphoserine and phosphothreonine peptides.     

The Bohlmann-Rahtz route to functionalised pyridine scaffolds and their use in library synthesis

The Bohlmann-Rahtz reaction has been used to prepare 2,3,6-trisubstituted pyridines suitable for use in library synthesis. The synthesis of piperidine substituted nicotinic acid derivative 9 has been optimised and carried out on a large scale to give ca. 500 g of scaffold which was used in the generation of the pyridine library 11.     

Cyclodextrin catalysis of the smiles rearrangement of 4-nitrophenyl salicylate

α- and β-Cyclodextrins accelerate the Smiles rearrangement of 4-nitrophenyl salicylate which proceeds through the mechanism of intramolecular aromatic nucleophilic substitution. The binding and catalytic rate constants were calculated from the dependences of the observed pseudo-first-order rate constants of the rearrangement reaction on cyclodextrin concentration obtained at various pH values. The catalysis was interpreted in terms of a tighter binding of the anionic, highly delocalized δ-complex intermediate than that of the substrate to cyclodextrins.