Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes

The time scale for ordering of the polypeptide backbone relative to the side chains is a critical issue in protein folding. The interplay between ordering of the backbone and ordering of the side chains is particularly important for the formation of β-sheet structures, as the polypeptide chain searches for the native stabilizing cross-strand interactions. We have studied these issues in the N-terminal domain of protein L9 (NTL9), a model protein with mixed α/β structure. We have developed a general approach for introducing site-specific IR probes for the side chains (azide) and backbone ((13)C═(18)O) using recombinant protein expression. Temperature-jump time-resolved IR spectroscopy combined with site-specific labeling enables independent measurement of the respective backbone and side-chain dynamics with single residue resolution. We have found that side-chain ordering in a key region of the β-sheet structure occurs on a slower time scale than ordering of the backbone during the folding of NTL9, likely as a result of the transient formation of non-native side-chain interactions.     

Using liquid crystals as a readout system in urinary albumin assays

Detecting human serum albumin (HSA) in urine samples is a standard procedure for the diagnosis of kidney problems and the prognosis of patients with chronic kidney diseases (CKDs). In this study, we developed a HSA assay by incorporating a thin layer of liquid crystals (LCs) as a readout system such that the presence of HSA in urine samples can be detected as optical signals. In combination with dilution protocols, this assay can be used to estimate the concentration range of HSA simply by counting the number of bright spots. Our results show that the assay can detect HSA at concentrations as low as 15 μg mL(-1). It is anticipated that this assay can provide a faster and simpler alternative for the diagnosis and prognosis of patients with kidney diseases.     

Aziridine-mediated ligation and site-specific modification of unprotected peptides

A synthesis of aziridine-containing peptides via the Cu(II)-promoted coupling of unprotected peptide thioacids and N-H aziridine-2-carbonyl peptides is reported. The unique reactivity of the resulting N-acylated aziridine-2-carbonyl peptides facilitates their subsequent regioselective and stereoselective nucleophilic ring-opening to give unprotected peptides that are specifically modified at the ligation site. The aziridine-mediated peptide ligation concept is exemplified using H(2)O as the nucleophile, producing a Xaa-Thr linkage (where Xaa can be an epimerizable and hindered amino acid). The overall process is compatible with a variety of unprotected amino acid functionality, most notably the N-terminal and Lys side chain amines.     

A review of the determination of organic compounds in Bayer process liquors

Bayer process liquors present a difficult and complex matrix to the analytical chemist, and the history of the application of modern analytical techniques to this problem is a case study in innovation. All Bayer process liquors contain organic compounds, in amounts varying from traces to several grams per litre. The total organic carbon content of Bayer liquors may be less than 5 g/L up to as much as 40 g/L. The presence of these organic impurities is of concern to Bayer technologists because they can have significant impacts on the economics of the process and the quality of the product. This review examines the history and current state-of-the-art of the analysis of organics in Bayer process liquors, and provides guidance on the applicable techniques matched to a comprehensive list of the compounds most likely to be present.     

A new application of scanning electrochemical microscopy for the label-free interrogation of antibody-antigen interactions

Within this work we present a ‘proof of principle’ study for the use of scanning electrochemical microscopy (SECM) to detect and image biomolecular interactions in a label-free assay as a potential alternative to current fluorescence techniques. Screen-printed carbon electrodes were used as the substrate for the deposition of a dotted array, where the dots consist of biotinylated polyethyleneimine. These were then further derivatised, first with neutravidin and then with a biotinylated antibody to the protein neuron specific enolase (NSE). SECM using a ferrocene carboxylic acid mediator showed clear differences between the array and the surrounding unmodified carbon. Imaging of the arrays before and following exposure to various concentrations of the antigen showed clear evidence for specific binding of the NSE antigen to the antibody derivatised dots. Non-specific binding was quantified. Control experiments with other proteins showed only non-specific binding across the whole of the substrate, thereby confirming that specific binding does occur between the antibody and antigen at the surface of the dots. Binding of the antigen was accompanied by a measured increase in current response, which may be explained in terms of protein electrostatic interaction and hydrophobic interactions to the mediator, thereby increasing the localised mediator flux. A calibration curve was obtained between 500 fg mL⁻¹ to 200 pg mL⁻¹ NSE which demonstrated a logarithmic relationship between the current change upon binding and antigen concentration without the need for any labelling of the substrate.     

Molecular recognition probes of solvation thermodynamics in solvent mixtures

High-throughput UV-Vis experiments using four molecular recognition-based probes, made by the combination of two hydrogen bond acceptors, tri-n-butylphosphine oxide and N,N'-bis(2-ethylhexyl)acetamide, and two hydrogen bond donors, 4-phenylazophenol and 4-nitrophenol, were performed. The association constants for the 1 : 1 H-bond interaction involved in each probe system were measured in mixtures of a polar and non-polar solvent, di-n-hexyl ether and n-octane, respectively. Similar behaviour was observed for all four systems. When the concentration of the polar solvent was low, the association constant was identical to that observed in pure n-octane. However, once the concentration of the polar solvent exceeded a threshold, the association constant decreased linearly with the concentration of di-n-hexyl ether. Selective solvation in mixtures can be understood based on the competition between the multiple competing equilibria in the system. In this case, solvation thermodynamics are dominated by competition of the ether for solvation of H-bond donors. For the more polar solute, 4-nitrophenol, the selective solvation starts at lower concentrations of the polar solvent compared with the less polar solute, 4-phenylazophenol. Thus the speciation and hence the properties of systems containing multiple solutes and multiple solvents can be estimated from the H-bond properties and the concentrations of the individual functional groups.     

Alkenylphosphonates: unexpected products from reactions of methyl 2-[(diethoxyphosphoryl)methyl]benzoate under Horner-Wadsworth-Emmons conditions

Methyl 2-[(diethoxyphosphoryl)methyl]benzoate reacts with several aldehydes to produce an alkenylphosphonate as the major product, together with varying amounts of the expected Horner-Wadsworth-Emmons product, a 1,2-disubstituted E-alkene. Use of a bulky aldehyde or the tert-butyl ester favours the normal HWE product.     

Development and applications of whole cell biosensors for ecotoxicity testing

Whole cell biosensors are the focus of considerable and increasing interest worldwide as methods for detecting and quantifying environmental toxicity, including biochemical oxygen demand (BOD), heavy metals, antibiotics, pesticides and herbicides. This review follows the development of whole cell biosensors from attempts to utilise changes in cellular metabolism to determine BOD and general toxicity, through the exploitation of unique metabolic pathways to detect specific toxicants, to the increasingly widespread use of genetic engineering to build new, and modify existing, sensing pathways.     

Experimental studies and thermal modelling of 1064- and 532-nm Nd:YVO4 micro-laser ablation of polyimide

Experiments and thermal modelling of polyimide ablation using the fundamental 1064-nm emission from a 20-kHz nanosecond diode-pumped solid-state Nd:YVO₄ micro-laser are described and compared with findings for the 532-nm doubled output. For exposures restricted to short pulse trains, it is found that micron-scale-size ablation features can be defined with this laser, even though polyimide films have weak absorption at 1064 nm and relatively weak absorption at 532 nm. There is evidence at both wavelengths of an incubation effect, driven by thermal modification of the polymer and, with long-term exposure at 1064 nm, Raman micro-spectroscopy reveals a progressive growth of predominantly amorphous carbon in the ablation site. Calculations of the temperature rise produced in the polymer by exposure to a high-repetition-rate pulse train are described that aid an understanding of the thermal aspects of the interaction at the two wavelengths. PACS 42.55.Xi; 44.10.+i; 52.38.Mf     

Randomly coloring sparse random graphs with fewer colors than the maximum degree

We analyze Markov chains for generating a random k‐coloring of a random graph G_n,d/n. When the average degree d is constant, a random graph has maximum degree Θ(log n/log log n), with high probability. We show that, with high probability, an efficient procedure can generate an almost uniformly random k‐coloring when k = Θ(log log n/log log log n), i.e., with many fewer colors than the maximum degree. Previous results hold for a more general class of graphs, but always require more colors than the maximum degree. © 2006 Wiley Periodicals, Inc. Random Struct. Alg., 2006