A review of methods for the calculation of solution free energies and the modelling of systems in solution.

Over the past decade, pharmaceutical companies have seen a decline in the number of drug candidates successfully passing through clinical trials, though billions are still spent on drug development. Poor aqueous solubility leads to low bio-availability, reducing pharmaceutical effectiveness. The human cost of inefficient drug candidate testing is of great medical concern, with fewer drugs making it to the production line, slowing the development of new treatments. In biochemistry and biophysics, water mediated reactions and interactions within active sites and protein pockets are an active area of research, in which methods for modelling solvated systems are continually pushed to their limits. Here, we discuss a multitude of methods aimed towards solvent modelling and solubility prediction, aiming to inform the reader of the options available, and outlining the various advantages and disadvantages of each approach.

Detection of explosives and their degradation products in soil environments.

Polynitro organic explosives [hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and 2,4,6-trinitrotoluene (TNT)] are typical labile environmental pollutants that can biotransform with soil indigenous microorganisms, photodegrade by sunlight and migrate through subsurface soil to cause groundwater contamination. To be able to determine the type and concentration of explosives and their (bio)transformation products in different soil environments, a comprehensive analytical methodology of sample preparation, separation and detection is thus required. The present paper describes the use of supercritical carbon dioxide (SC-CO2), acetonitrile (MeCN) (US Environmental Protection Agency Method 8330) and solid-phase microextraction (SPME) for the extraction of explosives and their degradation products from various water, soil and plant tissue samples for subsequent analysis by either HPLC-UV, capillary electrophoresis (CE-UV) or GC-MS. Contaminated surface and subsurface soil and groundwater were collected from either a TNT manufacturing facility or an anti-tank firing range. Plant tissue samples were taken fromplants grown in anti-tank firing range soil in a greenhouse experiment. All tested soil and groundwater samples from the former TNT manufacturing plant were found to contain TNT and some of its amino reduced and partially denitrated products. Their concentrations as determined by SPME-GC-MS and LC-UV depended on the location of sampling at the site. In the case of plant tissues, SC-CO2 extraction followed by CE-UV analysis showed only the presence of HMX. The concentrations of HMX (<200 mg/kg) as determined by supercritical fluid extraction (SC-CO2)-CE-UV were comparable to those obtained by MeCN extraction, although the latter technique was found to be more efficient at higher concentrations (>300 mg/kg). Modifiers such as MeCN and water enhanced the SC-CO2 extractability of HMX from plant tissues.

Photodegradation of RDX in aqueous solution: a mechanistic probe for biodegradation with Rhodococcus sp.

Recently we demonstrated that Rhodococcus sp. strain DN22 degraded hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) (1) aerobically via initial denitration followed by ring cleavage. Using UL 14C-[RDX] and ring labeled 15N-[RDX] approximately 30% of the energetic chemical mineralized (one C atom) and 64% converted to a dead end product that was tentatively identified as 4-nitro-2,4-diaza-butanal (OHCHNCH2NHNO2). To have further insight into the role of initial denitration on RDX decomposition, we photolyzed the energetic chemical at 350 nm and pH 5.5 and monitored the reaction using a combination of analytical techniques. GC/ MS-PCI showed a product with a [M+H] at 176 Da matching a molecular formula of C3H5N5O4 that was tentatively identified as the initially denitrated RDX product pentahydro-3,5-dinitro-1,3,5-triazacyclohex-1-ene (II). LC/MS (ES-) showed that the removal of RDX was accompanied by the formation of two other key products, each showing the same [M-H] at 192 Da matching a molecular formula of C3H7N5O5. The two products were tentatively identified as the carbinol (III) of the enamine (II) and its ring cleavage product O2NNHCH2NNO2CH2NHCHO (IV). Interestingly, the removal of III and IV was accompanied by the formation and accumulation of OHCHNCH2NHNO2 that we detected with strain DN22. At the end of the experiment, which lasted 16 h, we detected the following products HCHO, HCOOH, NH2CHO, N2O, NO2-, and NO3-. Most were also detected during RDX incubation with strain DN22. Finally, we were unable to detect any of RDX nitroso products during both photolysis and incubation with the aerobic bacteria, emphasizing that initial denitration in both cases was responsible for ring cleavage and subsequent decomposition in water.

Experimental and computational mapping of the binding surface of a crystalline protein.

Multiple Solvent Crystal Structures (MSCS) is a crystallographic technique to identify energetically favorable positions and orientations of small organic molecules on the surface of proteins. We determined the high-resolution crystal structures of thermolysin (TLN), generated from crystals soaked in 50--70% acetone, 50--80% acetonitrile and 50 mM phenol. The structures of the protein in the aqueous-organic mixtures are essentially the same as the native enzyme and a number of solvent interaction sites were identified. The distribution of probe molecules shows clusters in the main specificity pocket of the active site and a buried subsite. Within the active site, we compared the experimentally determined solvent positions with predictions from two computational functional group mapping techniques, GRID and Multiple Copy Simultaneous Search (MCSS). The experimentally determined small molecule positions are consistent with the structures of known protein--ligand complexes of TLN.

Detection of the cyclic nitramine explosives hexahydro-1,3,5-trinitro- 1,3,5-triazine (RDX) and octahydro- 1,3,5,7-tetranitro- 1,3,5,7-tetrazine (HMX) and their degradation products in soil environments.

The cyclic nitramine explosives hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazine (HMX) were examined in field and microcosm soil samples to determine their patterns of degradation and environmental fates. A number of analytical techniques, including solid-phase microextraction with on-fiber derivatization, gas chromatography-mass spectrometry, gas chromatography with electron-capture detection, liquid chromatography-mass spectrometry, and micellar electrokinetic chromatography were required for the analyses. Two different classes of intermediates were detected, both of which lead ultimately to the formation of nitrous oxide (N2O) and carbon dioxide (CO2). The first class was identified as the nitroso derivatives formed by the sequential reduction of -NO2 functional groups. The second class of intermediates, which was favored at higher humidities and in the presence of anaerobic sludge amendments, consisted of ring cleavage products including bis-(hydroxymethyl)-nitramine and methylenedinitramine. Rye-grass (Lolium perenne) present in field samples was found to extract and accumulate HMX from soil without further degradation. In all cases (excepting the plant samples), the indigenous microbes or amended domestic anaerobic sludge consortia degraded the cyclic nitramine explosives eventually to produce N2O and CO2.

Characterization of metabolites during biodegradation of hexahydro-1, 3,5-trinitro-1,3,5-triazine (RDX) with municipal anaerobic sludge.

The biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in liquid cultures with municipal anaerobic sludge showed that at least two degradation routes were involved in the disappearance of the cyclic nitramine. In one route, RDX was reduced to give the familiar nitroso derivatives hexahydro-1-nitroso-3,5-dinitro-1,3, 5-triazine (MNX) and hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine (DNX). In the second route, two novel metabolites, methylenedinitramine [(O(2)NNH)(2)CH(2)] and bis(hydroxymethyl)nitramine [(HOCH(2))(2)NNO(2)], formed and were presumed to be ring cleavage products produced by enzymatic hydrolysis of the inner C---N bonds of RDX. None of the above metabolites accumulated in the system, and they disappeared to produce nitrous oxide (N(2)O) as a nitrogen-containing end product and formaldehyde (HCHO), methanol (MeOH), and formic acid (HCOOH) that in turn disappeared to produce CH(4) and CO(2) as carbon-containing end products.

Attentional bias for emotional faces in generalized anxiety disorder.

OBJECTIVES: Recent cognitive theories propose that attentional biases cause or maintain anxiety disorders. This study had several aims: (i) to investigate such biases in generalized anxiety disorder (GAD) using naturalistic, ecologically valid stimuli, namely, emotional facial expressions; (ii) to test the emotionality hypothesis by examining biases for happy as well as threat faces; and (iii) to assess the time course of the attentional bias. DESIGN: The dependent variable was an index of attentional bias derived from manual RTs to probe stimuli. There were four independent variables: one between-subjects variable of group (2: GAD, control), and three within-subjects variables: Type of emotional face (2: threat, happy), Stimulus duration (2: 500 ms, 1250 ms) and Half of task (2: first, second). METHOD: Attentional bias was assessed with a dot probe task. The stimuli comprised photographs of threatening, happy and neutral faces, presented using two exposure durations: 500 ms and 1250 ms. RESULTS: Anxious patients showed greater vigilance for threatening faces relative to neutral faces, compared with normal controls. This effect did not significantly vary as a function of stimulus duration. Anxious patients also showed enhanced vigilance for happy faces, but this was only significant in the second half of the task. CONCLUSIONS: The study confirmed not only that GAD patients show a bias in selective attention to threat, relative to controls, but also that this bias operates for naturalistic, non-verbal stimuli. As the attentional biases for threat and happy faces appeared to develop over a different time frame, different underlying mechanisms may be responsible.

Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol.

Multiple-solvent crystal structure determination (MSCS) allows the position and orientation of bound solvent fragments to be identified by determining the structure of protein crystals soaked in organic solvents. We have extended this technique by the determination of high-resolution crystal structures of thermolysin (TLN), generated from crystals soaked in 2% to 100% isopropanol. The procedure causes only minor changes to the conformation of the protein, and an increasing number of isopropanol interaction sites could be identified as the solvent concentration is increased. Isopropanol occupies all four of the main subsites in the active site, although this was only observed at very high concentrations of isopropanol for three of the four subsites. Analysis of the isopropanol positions shows little correlation with interaction energy computed using a molecular mechanics force field, but the experimentally determined positions of isopropanol are consistent with the structures of known protein-ligand complexes of TLN.

Sulfobutylether-beta-cyclodextrin-mediated capillary electrophoresis for separation of chlorinated and substituted phenols.

Cyclodextrin-mediated capillary electrophoresis has been developed for separation and analysis of chlorinated as well as substituted phenolic compounds. The procedure used a negatively charged sulfobutylether-beta-cyclodextrin (SB-betaCD) to effect differential partitioning of the phenols between the buffer and CD phases. In 50 mM phosphate buffer containing as low as 1 mM SB-betaCD, 25 phenolic compounds including 11 Environmental Protection Agency (EPA) priority phenols were separated with theoretical plate numbers well above 100,000, for 50 cm of effective length in most cases. An equilibrium complexation model was used for investigating the effect of pH as well as different cyclodextrin concentrations on the electrophoretic mobility. The cyclodextrin-mediated capillary electrophoresis system was also applicable for separating and quantifying the level of pentachlorophenol in contaminated soil samples.

The stereospecificity of hydrogen transfer to NAD(P)+ catalyzed by lactol dehydrogenases.

The stereochemistry of hydrogen transfer to NAD(P)+ has been determined for five lactol dehydrogenases. It was found that D-glucose dehydrogenases from Bacillus megaterium and Cryptococcus uniguttulatus and L-rhamnose dehydrogenase from Aureobasidium pullulans are pro-S (B) specific, while D-glucose dehydrogenase from Thermoplasma acidophilum and D-xylose dehydrogenase from procine liver are pro-R (A) specific. The latter two enzymes are the first examples of A-specific dehydrogenases oxidizing aldoses at the anomeric carbon. These findings are discussed in terms of functional and historical models that seek to make predictive generalizations regarding dehydrogenase stereospecificity.

Three-dimensional structure of diferric bovine lactoferrin at 2.8 A resolution.

The three-dimensional structure of diferric bovine lactoferrin (bLf) has been determined by X-ray crystallography in order to investigate the factors that influence iron binding and release by transferrins. The structure was solved by molecular replacement, using the coordinates of diferric human lactoferrin (hLf) as a search model, and was refined with data to 2.8 A resolution by simulated annealing (X-PLOR) and restrained least squares (TNT). The final model comprises 5310 protein atoms (residues 5 to 689), 124 carbohydrate atoms (from ten monosaccharide units, in three glycan chains), 2 Fe3+, 2 CO32- and 50 water molecules. This model gives an R-factor of 0.232 for 21440 reflections in the resolution range 30.0 to 2.8 A. The folding of the bLf molecule is essentially the same as that of hLf, but bLf differs in the extent of closure of the two domains of each lobe, and in the relative orientations of the two lobes. Differences in domain closure are attributed to amino acid changes in the interface, and differences in lobe orientations to slightly altered packing of two hydrophobic patches between the lobes. Changed interdomain interactions may explain the lesser iron affinity of bLf, compared with hLf, and two lysine residues behind the N-lobe iron site of bLf offer new insights into the "dilysine trigger" mechanism proposed for iron release by transferrins. The bLf structure is also notable for several well-defined oligosaccharide units which demonstrate the structural factors that stabilise carbohydrate structure. One glycan chain, attached to Asn545, appears to contribute to interdomain interactions and may modulate iron release from the C-lobe.

Dual functionalities of 4-aminodiphenylamine in enzymatic assay and mediated biosensor construction.

4-Aminodiphenylamine (N-phenyl-1,4-phenylenediamine, CAS 101-54-2) and its water-soluble HCl salt (CAS 2198-59-6) were demonstrated to be efficient mediators for glucose oxidase, lactate oxidase, xanthine oxidase, and lysine oxidase. Using cyclic voltammetry, single oxidative peak potentials were observed for scans ranging from 0 to 0.5 V vs Ag/AgCl. The half-wave potential for both preparations was 0.11 V vs Ag/AgCl at pH 7 and decreased 59 mV per unit pH increase. Peak current data were analyzed to estimate diffusivities of 0.8 x 10(-5) cm2/s for soluble 4-ADPA HCl, and 2.36 x 10(-5) cm2/s for 4-ADPA solubilized in 2.5 mM 2-hydroxypropyl-beta-cyclodextrin. The overall second-order kinetic constants (k) for the reaction of reduced glucose oxidase with oxidized 4-ADPA HCl and 4-ADPA in cyclodextrin were estimated to be 1.8 x 10(5) and 1.7 x 10(-5) M-1 s-1, respectively, using cyclic voltammetry measurements at varied scan rates and enzyme concentrations. Both preparations proved to be suitable electron acceptors for horseradish peroxidase, as indicated by changes in absorbance spectra upon oxidation or reduction. The electrochemical and spectral behavior of the preparations were applied in conjunction with glucose oxidase to devise mediated amperometric and hydrogen peroxide-coupled spectrophotometric assays for glucose. The results of both assays compared favorably with the hexokinase reference method.

1.8 A crystal structure of the C-terminal domain of rabbit serum haemopexin.

BACKGROUND: Haemopexin is a serum glycoprotein that binds haem reversibly and delivers it to the liver where it is taken up by receptor-mediated endocytosis. Haemopexin has two homologous domains, each having a characteristic fourfold internal sequence repeat. Haemopexin-type domains are also found in other proteins, including the serum adhesion protein vitronectin and various collagenases, in which they mediate protein-protein interactions. RESULTS: We have determined the crystal structure of the C-terminal domain of haemopexin at 1.8 A resolution. The domain is folded into four beta-leaflet modules, arranged in succession around a central pseudo-fourfold axis. A funnel-shaped tunnel through the centre of this disc-shaped domain serves as an ion-binding site. CONCLUSIONS: A model for haem binding by haemopexin is proposed, utilizing an anion-binding site at the wider end of the central tunnel, together with an associated cleft. This parallels the active-site location in other beta-propeller structures. The capacity to bind both cations and anions, together with the disc shape of the domain, suggests that such domains may be used widely for macromolecular recognition.

Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography.

The principal protein excreted in male rat urine, urinary alpha 2-globulin and the homologous mouse protein, major urinary protein, have been well characterized, although their functions remain unclear. Male rat urine affects the behaviour and sexual response of female rats, leading to the proposal that rodent urinary proteins are responsible for binding pheromones and their subsequent release from drying urine. Urinary alpha 2-globulin is also involved in hyaline droplet nephropathy, an important toxicological syndrome in male rats resulting from exposure to a number of industrial chemicals and characterized by the accumulation of liganded urinary alpha 2-globulin in lysosomes in the kidney, followed by the induction of renal cancer. We now report the three-dimensional structures of mouse major urinary protein (at 2.4 A resolution) and rat urinary alpha 2-globulin (at 2.8 A resolution). The results corroborate the role of these proteins in pheromone transport and elaborate the structural basis of ligand binding.

Crystallization and initial X-ray analysis of the C2-subunit of crustacyanin.

Crystals of the C2-subunit of crustacyanin have been grown from solutions containing ammonium sulphate and 2-methyl-2,4-pentanediol as co-precipitants. The crystals belong to space group P2(1)2(1)2(1) (a = 42.0 A, b = 80.9 A, c = 110.8 A) with two subunits per asymmetric unit and diffract beyond 2.2 A resolution.

Trimethoprim binds in a bacterial mode to the wild-type and E30D mutant of mouse dihydrofolate reductase.

Previous crystallographic studies of the antibacterial trimethoprim in complexes with bacterial and avian dihydrofolate reductases have shown substantial differences in the mode of binding, providing plausible explanations for the origin of the remarkable species selectivity of this inhibitor (Matthews, D. A., Bolin, J. T., Burridge, J. M., Filman, D. J., Volz, K. W., Kaufman, B. T., Beddell, C. R., Champness, J. N., Stammers, D. K., and Kraut, J. (1985) J. Biol. Chem. 260, 381-391; Matthews, D. A., Bolin, J. T., Burridge, J. M., Filman, D. J., Volz, K. W., and Kraut, J. (1985) J. Biol. Chem. 260, 392-399). A major species difference between the active sites is that the only carboxylate present is always Glu in vertebrates and Asp in bacteria. Crystallographic studies of the wild-type and E30D mutant of the enzyme from mouse now reveal that in both cases trimethoprim is bound in an identical fashion to that observed with the bacterial enzyme, and there is no obvious single explanation for the origin of the 10(5)-fold selectivity of trimethoprim binding. In an earlier study of a mouse wild-type enzyme using more limited data it was proposed that trimethoprim bound in the avian mode (Stammers, D. K., Champness, J. N., Beddell, C. R., Dann, J. G., Eliopoulos, E. E., Geddes, A. J., Ogg, D., and North, A. C. T. (1987) FEBS Lett. 218, 178-184), but a re-examination indicates that the occupancy of the active site by trimethoprim is less than had been thought, and we are currently unable to make an unambiguous interpretation of the electron density maps and cannot confirm the avian mode of binding in those crystals.

The potential role of biosensors in the food and drink industries.

Despite their apparent potential as analytical tools in the food and drink industries, only a few biosensors are used routinely. This article describes the development of biosensors for these sectors and discusses the technical and economic problems of applying this technology to the monitoring of food and drink products.