This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ http://www.journal.chemistrycentral.com/ The latest articles from Chemistry Central Journal (ISSN 1752-153X) published by BioMed Central Background: Gram-negative bacteria use periplasmic-binding proteins (bPBP) to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two domains that are separated by a conserved hinge. The hinge allows the protein to cycle between open (apo) and closed (ligated) conformations. Conformational changes within the proteins depend on a complex interplay of mechanical and thermodynamic response, which is manifested as an increase in thermal stability and decrease of flexibility upon ligand binding. Results: We use a distance constraint model (DCM) to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR) are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings) also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network. Conclusions: Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect intrinsic flexibility. Moreover, varying numbers of H-bonds and their strengths control the likelihood for energetic fluctuations as H-bonds break and reform, thus directly affecting thermodynamic properties. Consequently, these results demonstrate how unexpected large differences, especially within cooperativity correlation, emerge from subtle differences within the underlying H-bond network. This inference is consistent with well-known results that show allosteric response within a family generally varies significantly. Identifying the hydrogen bond network as a critical determining factor for these large variances may lead to new methods that can predict such effects. http://www.journal.chemistrycentral.com/content/2/1/17 Dennis R. Livesay, Dang H. Huynh, Sargis Dallakyan and Donald J. Jacobs Chemistry Central Journal 2008, 2:17 2008-08-12 doi:10.1186/1752-153X-2-17 Chemistry Central Journal 1752-153X 2 17 2008-08-12 IntroductionIn proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function.DiscussionOptimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function. Conclusion: To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today. http://www.journal.chemistrycentral.com/content/2/1/16 Peter R Jungblut, Hermann G Holzhütter, Rolf Apweiler and Hartmut Schlüter Chemistry Central Journal 2008, 2:16 2008-07-18 doi:10.1186/1752-153X-2-16 Chemistry Central Journal 1752-153X 2 16 2008-07-18 Background: Although the necessity of divalent magnesium and manganese for full activity of sugar nucleotidyltransferases and glycosyltransferases is well known, the role of these metal cations in binding the substrates (uridine 5'-triphosphate, glucose-1-phosphate, N-acetylglucosamine-1-phosphate, and uridine 5'-diphosphate glucose), products (uridine 5'-diphosphate glucose, uridine 5'-diphosphate N-acetylglucosamine, pyrophosphate, and uridine 5'-diphosphate), and/or enzyme is not clearly understood. Results: Using isothermal titration calorimetry we have studied the binding relationship between the divalent metals, magnesium and manganese, and uridine 5'-phosphates to determine the role these metals play in carbohydrate biosynthesis. It was determined from the isothermal titration calorimetry (ITC) data that Mg+2 and Mn+2 are most tightly bound to PPi, Kb = 41,000 ± 2000 M-1 and 28,000 ± 50,000 M-1 respectively, and UTP, Kb = 14,300 ± 700 M-1 and 13,000 ± 2,000 M-1 respectively. Conclusion: Our results indicate that the formal charge state of the phosphate containing substrates determine the binding strength. Divalent metal cations magnesium and manganese showed similar trends in binding to the sugar substrates. Enthalpy of binding values were all determined to be endothermic except for the PPi case. In addition, entropy of binding values were all found to be positive. From this data, we discuss the role of magnesium and manganese in both sugar nucleotidyltransferase and glycosyltransferase reactions, the differences in metal-bound substrates expected under normal physiological metal concentrations and those of hypomagnesaemia, and the implications for drug design. http://www.journal.chemistrycentral.com/content/2/1/15 Corbin J Zea, Gulden Camci-Unal and Nicola L Pohl Chemistry Central Journal 2008, 2:15 2008-07-15 doi:10.1186/1752-153X-2-15 Chemistry Central Journal 1752-153X 2 15 2008-07-15 Background: A routine method for the quantification of beryllium in biological fluids is essential for the development of a chelation therapy for Chronic Beryllium Disease (CBD). We describe a procedure for the direct determination of beryllium in undigested micro quantities of human blood and serum using graphite furnace atomic absorption spectrometry. Blood and serum samples are prepared respectively by a simple 8-fold and 5-fold dilution with a Nash Reagent. Three experimental setups are compared: using no modifier, using magnesium nitrate and using palladium/citric acid as chemical modifiers. Results: In serum, both modifiers did not improve the method sensitivity, the optimal pyrolysis and atomization temperatures are 1000°C and 2900°C, respectively. In blood, 6 μg of magnesium nitrate was found to improve the method sensitivity. The optimal pyrolysis and atomization temperatures were 800°C and 2800°C respectively. Conclusion: In serum, the method detection limit was 2 ng l-1, the characteristic mass was 0.22 (± 0.07) pg and the accuracy ranged from 95 to 100%. In blood, the detection limit was 7 ng l-1, the characteristic mass was 0.20 (± 0.02) pg and the accuracy ranged from 99 to 101%. http://www.journal.chemistrycentral.com/content/2/1/14 Chadi H Stephan, Michel Fournier, Pauline Brousseau and Sébastien Sauvé Chemistry Central Journal 2008, 2:14 2008-07-02 doi:10.1186/1752-153X-2-14 Chemistry Central Journal 1752-153X 2 14 2008-07-02 Background: Considerable research has been directed towards the roles of metal ions in nutrition with metal ion toxicity attracting particular attention. The aim of this study is to measure the levels of metal ions found in selected beverages (red wine, stout and apple juice) and to determine their potential detrimental effects via calculation of the Target Hazard Quotients (THQ) for 250 mL daily consumption. Results: The levels (mean ± SEM) and diversity of metals determined by ICP-MS were highest for red wine samples (30 metals totalling 5620.54 ± 123.86 ppb) followed by apple juice (15 metals totalling 1339.87 ± 10.84 ppb) and stout (14 metals totalling 464.85 ± 46.74 ppb). The combined THQ values were determined based upon levels of V, Cr, Mn, Ni, Cu, Zn and Pb which gave red wine samples the highest value (5100.96 ± 118.93 ppb) followed by apple juice (666.44 ± 7.67 ppb) and stout (328.41 ± 42.36 ppb). The THQ values were as follows: apple juice (male 3.11, female 3.87), stout (male 1.84, female 2.19), red wine (male 126.52, female 157.22) and ultra-filtered red wine (male 110.48, female 137.29). Conclusion: This study reports relatively high levels of metal ions in red wine, which give a very high THQ value suggesting potential hazardous exposure over a lifetime for those who consume at least 250 mL daily. In addition to the known hazardous metals (e.g. Pb), many metals (e.g. Rb) have not had their biological effects systematically investigated and hence the impact of sustained ingestion is not known. http://www.journal.chemistrycentral.com/content/2/1/13 Theresa Hague, Andrea Petroczi, Paul LR Andrews, James Barker and Declan P Naughton Chemistry Central Journal 2008, 2:13 2008-06-25 doi:10.1186/1752-153X-2-13 Chemistry Central Journal 1752-153X 2 13 2008-06-25 Background: The Hedgehog signaling pathway is essential for embryogenesis and for tissue homeostasis in the adult. However, it may induce malignancies in a number of tissues when constitutively activated, and it may also have a role in other forms of normal and maladaptive growth. Cyclopamine, a naturally occurring steroidal alkaloid, specifically inhibits the Hedgehog pathway by binding directly to Smoothened, an important Hedgehog response element. To use cyclopamine as a tool to explore and/or inhibit the Hedgehog pathway in vivo, a substantial quantity is required, and as a practical matter cyclopamine has been effectively unavailable for usage in animals larger than mice. Results: In this paper, we report a rapid and efficient isolation and purification of large quantities of cyclopamine from the roots and rhizomes of Veratrum californicum Dur. (the Corn Lily or Western false hellebore). We also provide unambiguous assignments of the carbon and proton resonances by using the multinuclear spectra and the spin coupling networks. Conclusion: This method could meet a very real need within diverse scientific communities by allowing cyclopamine to become more readily available. http://www.journal.chemistrycentral.com/content/2/1/12 John E Oatis, Pam Brunsfeld, James W Rushing, Peter D Moeller, Daniel W Bearden, Thomas N Gallien and George Cooper Chemistry Central Journal 2008, 2:12 2008-06-24 doi:10.1186/1752-153X-2-12 Chemistry Central Journal 1752-153X 2 12 2008-06-24 Background: Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR.ImplementationPubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem.Results and DiscussionThe program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used. http://www.journal.chemistrycentral.com/content/2/1/11 Junguk Hur and David J Wild Chemistry Central Journal 2008, 2:11 2008-05-15 doi:10.1186/1752-153X-2-11 Chemistry Central Journal 1752-153X 2 11 2008-05-15 Background: Occupational exposure to beryllium may cause Chronic Beryllium Disease (CBD), a lung disorder initiated by an electrostatic interaction with the MHC class II human leukocyte antigen (HLA). Molecular studies have found a significant correlation between the electrostatic potential at the HLA-DP surface and disease susceptibility. CBD can therefore be treated by chelation therapy. In this work, we studied the effect of two complexing agents, nitrilotriproprionic acid (NTP) and 4,5-dihydroxy-1,3-benzene disulphonate (Tiron), on the fractionation of beryllium in human serum analysed by graphite furnace atomic absorption spectrometry (GFAAS). Results: We found the average serum beryllium concentration of fourteen non-exposed individuals to be 0.53 (± 0.14) μg l-1, with 21 (± 3)% of the beryllium mass bound to the low molecular weight fraction (LMW), and 79 (± 3)% bound to the high molecular weight fraction (HMW). The addition of Tiron increased the beryllium mass in the HMW fraction, while NTP was not seen to have any influence on the fractionation of beryllium between the two fractions. NTP was, however, shown to complex 94.5% of the Be mass in the LMW fraction. The beryllium GFAAS detection limit, calculated as three times the standard deviation of 10 replicates of the lowest standard (0.05 μg L-1), was 6.0 (± 0.2) ng L-1. Conclusion: The concentration of beryllium or its fractionation in human serum was not affected by sex or smoking habit. On average, three quarters of the beryllium in serum were found in the HMW fraction. Of the two ligands tested, only Tiron was effective in mobilising beryllium under physiological conditions, thus increasing the Be content in the HMW fraction. http://www.journal.chemistrycentral.com/content/2/1/10 Chadi H Stephan, Michel Fournier, Pauline Brousseau and Sébastien Sauvé Chemistry Central Journal 2008, 2:10 2008-05-14 doi:10.1186/1752-153X-2-10 Chemistry Central Journal 1752-153X 2 10 2008-05-14 Background: This work reports the determination of the levels of phthalate esters (dimethyl phthalate (DMP), diethyl phthalate (DEP), dibutyl phthalate (DBP), diethyl hexyl phthalate (DEHP)) and metals (lead, cadmium, manganese, zinc, iron, calcium) in composite soil samples. The soil samples were collected randomly within the Muledane open dump, Thohoyandou, Limpopo province, South Africa. Control samples were collected about 200 m away from the open dump. The phthalate esters were separated and determined by capillary gas chromatography with a flame ionization detector, whilst the metals were determined by atomic absorption spectrophotometry. Results: Open dump values for the phthalate esters and metals to be generally higher in comparison to control samples for DMP, DEP, DBP and DEHP – the mean values calculated were 0.31 ± 0.12, 0.21 ± 0.05, 0.30 ± 0.07, and 0.03 ± 0.01 mg/kg, respectively, for the open dump soil samples. Nonetheless, the mean open dump values for lead, cadmium, manganese, zinc, iron and calcium were 0.07 ± 0.04, 0.003 ± 0.001, 5.02 ± 1.92, 0.31 ± 0.02, 11.62 ± 9.48 and 0.12 ± 0.13 mg/kg, respectively. The results were compared statistically. Conclusion: Our results revealed that the discarding of wastes into the open dump is a potential source of soil contamination in the immediate vicinity and beyond, via dispersal. Increased levels of phthalate esters and metals in the soil pose a risk to public health, plants and animals. Sustained monitoring of these contaminants is recommended, in addition to upgrading the facility to a landfill. http://www.journal.chemistrycentral.com/content/2/1/9 Adeleke Adeniyi, Matthew Dayomi, Pitso Siebe and Olumuyiwa Okedeyi Chemistry Central Journal 2008, 2:9 2008-05-12 doi:10.1186/1752-153X-2-9 Chemistry Central Journal 1752-153X 2 9 2008-05-12 Background: In soils contaminated by hydrophobic organic compounds, the concentrations are less indicative of potential exposure and distribution than are the associated chemical activities, fugacities and freely dissolved concentrations. The latter can be measured by diffusive sampling into thin layers of polymer, as in, for example, solid phase micro-extraction. Such measurements require equilibrium partitioning of analytes into the polymer while ensuring that the sample is not depleted. We introduce the validation of these requirements based on parallel sampling into polymer layers of different thicknesses. Results: Equilibrium sampling devices were made by coating glass vials internally with 3–12 μm thick layers of polydimethylsiloxane (PDMS). These were filled with slurries of a polluted soil and gently agitated for 5 days. The concentrations of 7 polycyclic aromatic hydrocarbons (PAHs) in the PDMS were measured. Validation confirmed fulfilment of the equilibrium sampling requirements and high measurement precision. Finally, chemical activities of the PAHs in the soil were determined from their concentrations and activity coefficients in the PDMS. Conclusion: PAHs' thermodynamic activities in a soil test material were determined via a method of uptake into PDMS. This can be used to assess chemical exposure and predict diffusion and partitioning processes. http://www.journal.chemistrycentral.com/content/2/1/8 Fredrik Reichenberg, Foppe Smedes, Jan-Åke Jönsson and Philipp Mayer Chemistry Central Journal 2008, 2:8 2008-05-06 doi:10.1186/1752-153X-2-8 Chemistry Central Journal 1752-153X 2 8 2008-05-06