Identification of small-molecule inhibitors of the steroidogenic acute regulatory protein (STARD1) by structure-based design

A homology model of the steroidogenic acute regulatory protein (STAR)-related lipid transfer (START) domain of STARD1 was built, and the cholesterol binding site was identified. Structure-based design studies were performed to identify small molecule inhibitors of the START domain. The lead compounds were selected based on cAMP-induced, but not 22R-hydroxycholesterol-supported, inhibition of steroid synthesis by 50% at 10 μM. The results obtained by molecular docking & dynamics show a good correlation between bioactivity, docking scores and calculated binding energies of ligand-protein complexes. The best active compounds will be optimized further and used to develop potential drugs to control excessive steroid formation.     

Effect of operational and design parameters on removal efficiency of pilot-scale FWS constructed wetlands and comparison with HSF systems

In order to investigate the effect of temperature, hydraulic residence time (HRT), vegetation type, substrate material and wetland shape on the performance of free-water surface (FWS) constructed wetlands treating wastewater, 5 pilot-scale units were constructed and operated continuously from December 2004 until March 2007 in parallel experiments. Four of the units (A, B, C, D) were rectangular in plan view with dimensions 3.40 m in length and 0.85 m in width, and contained substrate material at a thickness of 0.45 m. The fifth unit (E) had a trapezoidal plan view shape, with a width at the inlet of 1.15 m and at the outlet of 0.55 m, while the length and the thickness of the substrate were the same as in the other four. All units operated at a water depth of 0.10 m. Units B–E contained clay substrate and unit A contained sand. The four units with clay were planted as follows: two with cattails (B and E), one with common reeds (C), and one with giant reeds (D). Unit A, containing sand, was planted with cattails. Planting and substrate material combinations were appropriate for comparison of the effect of vegetation and material type on the function of the system. Synthetic wastewater was introduced in the units. During the operation period four HRTs (i.e., 6 days, 8 days, 14 days and 20 days) were used, while wastewater temperatures varied from about 0.0 °C to 29.1 °C. The removal performance of the five constructed wetland units was good, since it reached on the average 77.5%, 67.9%, 60.4%, 53.9%, 56.0% and 51.7% for BOD, COD, TKN, ammonia (NH₄-N), ortho-phosphate (PO₄-P) and total phosphorus (TP), respectively. BOD and phosphorus removal efficiencies showed dependence on temperature in most units. The 14-day HRT was found adequate for acceptable removal of organic matter, nitrogen and phosphorus for most temperatures. A 20-day HRT is recommended for acceptable removal of BOD and PO₄-P in the cold season. The unit with the trapezoidal plan view shape showed the best performance, with mean removals of 80.1%, 73.5%, 70.4%, 68.6%, 64.7% and 63.5% for BOD, COD, TKN, NH₄-N, PO₄-P and TP, respectively. The cattail was found statistically more efficient than the other two plants in COD and PO₄-P removal. The unit that contained the clay substrate was found statistically more efficient in phosphorus removal than the unit containing sand. HSF CW units were found more efficient than FWS units in removal of most pollutant.     

Cysteine-scanning Analysis of Helices TM8, TM9a,and TM9b and Intervening Loops in the YgfO Xanthine Permease: A CARBOXYL GROUP IS ESSENTIAL AT ASP-276

Bacterial and fungal members of the ubiquitous nucleobase-ascorbate transporter (NAT/NCS2) family use the NAT signature motif, a conserved 11-amino acid sequence between amphipathic helices TM9a and TM9b, to define function and selectivity of the purine binding site. To examine the role of flanking helices TM9a, TM9b, and TM8, we employed Cys-scanning analysis of the xanthine-specific homolog YgfO from Escherichia coli. Using a functional mutant devoid of Cys residues (C-less), each amino acid residue in sequences ²⁵⁹FLVVGTIYLLSVLEAVGDITATAMVSRRPIQGEEYQSRLKGGVLADGLVSVIASAV³¹⁴ and ³⁴²TIAVMLVILGLFP³⁵⁴ including these TMs (underlined) was replaced individually with Cys, except the irreplaceable Glu-272 and Asp-304, which had been studied previously. Of 67 single Cys mutants, 55 accumulate xanthine to 35–140% of the steady state observed with C-less, five (I265C, D276C, I277C, G299C, L350C) accumulate to low levels (10–20%) and seven (T278C, A279C, T280C, A281C, G305C, G351C, P354C) show negligible expression in the membrane. Extensive mutagenesis reveals that a carboxyl group is needed at Asp-276 for high activity and that D276E differs from wild type as it recognizes 8-methylxanthine (K_i 79 μm) but fails to recognize 2-thioxanthine, 3-methylxanthine or 6-thioxanthine; bulky replacements of Ala-279 or Thr-280 and replacements of Gly-305, Gly-351, or Pro-354 impair activity or expression. Single Cys mutants V261C, A273C, G275C, and S284C are sensitive to inactivation by N-ethylmaleimide and sensitivity of G275C (IC₅₀ 15 μm) is enhanced in the presence of substrate. The data suggest that residues crucial for the transport mechanism cluster in two conserved motifs, at the cytoplasmic end of TM8 (EXXGDXXAT) and in TM9a (GXXXDG).     

Multiscale Hy3S: Hybrid stochastic simulation for supercomputers

Background

DNA copy number alterations are one of the main characteristics of the cancer cell karyotype and can contribute to the complex phenotype of these cells. These alterations can lead to gains in cellular oncogenes as well as losses in tumor suppressor genes and can span small intervals as well as involve entire chromosomes. The ability to accurately detect these changes is central to understanding how they impact the biology of the cell.

Results

We describe a novel algorithm called CARAT (Copy Number Analysis with Regression And Tree) that uses probe intensity information to infer copy number in an allele-specific manner from high density DNA oligonuceotide arrays designed to genotype over 100, 000 SNPs. Total and allele-specific copy number estimations using CARAT are independently evaluated for a subset of SNPs using quantitative PCR and allelic TaqMan reactions with several human breast cancer cell lines. The sensitivity and specificity of the algorithm are characterized using DNA samples containing differing numbers of X chromosomes as well as a test set of normal individuals. Results from the algorithm show a high degree of agreement with results from independent verification methods.

Conclusion

Overall, CARAT automatically detects regions with copy number variations and assigns a significance score to each alteration as well as generating allele-specific output. When coupled with SNP genotype calls from the same array, CARAT provides additional detail into the structure of genome wide alterations that can contribute to allelic imbalance.     

Dipeptides containing the alpha-aminoisobutyric residue (Aib) as ligands: preparation,spectroscopic studies and crystal structures of copper(II) complexes with H-Aib-X-OH (X=Gly,L-Leu,L-Phe)

Synthetic procedures are described that allow access to new copper(II) complexes with dipeptides containing the alpha-aminoisobutyric residue (Aib) as ligands. The solid complexes [Cu(H(-1)L(A))](n).nH(2)O (1) (L(A)H=H-Aib-Gly-OH), [Cu(H(-1)L(B))(MeOH)](n).nMeOH (2) (L(B)H=H-Aib-L-Leu-OH) and [Cu(H(-1)L(C))](n) (3) (L(C)H=H-Aib-L-Phe-OH) have been isolated and characterized by single-crystal X-ray crystallography, solid-state IR spectra and UV-Vis spectroscopy in solution (H(-1)L(2-) is the dianionic form of the corresponding dipeptide). Complexes 1 and 3 are three-dimensional coordination polymers with similar structures. The doubly deprotonated dipeptide behaves as a N(amino), N(peptide), O(carboxylate), O'(carboxylate), O(peptide) mu(3) ligand and binds to one Cu(II) atom at its amino and peptide nitrogens and at one carboxylate oxygen, to a second metal at the other carboxylate oxygen, while a third Cu(II) atom is attached to the peptide oxygen. The geometry around copper(II) is distorted square pyramidal with the peptide oxygen at the apex of the pyramid. The structure of 2 consists of zigzag polymeric chains, where the doubly deprotonated dipeptide behaves as a N(amino), N(peptide), O(carboxylate), O'(carboxylate) mu(2) ligand. The geometry at copper(II) is square pyramidal with the methanol oxygen at the apex. The IR data are discussed in terms of the nature of bonding and known structures. The UV-Vis spectra show that the solid-state structures of 1, 2 and 3 do not persist in H(2)O.     

Chemical composition and biological activity of Nepeta parnassica oils and isolated nepetalactones

Essential oils of Nepeta parnassica, collected at different developmental stages, were analyzed by means of GC/MS. From the fifty-five identified constituents in samples A and B, representing 94.8% and 98.7% of the oils respectively, 4a(alpha),7alpha,7alpha(beta)-nepetalactone (22.0%), 1,8-cineole (21.1%), alpha-pinene (9.5%) and 4a(alpha),7,beta,7alpha(beta)-nepetalactone (7.9%) were the major components of sample A (vegetative stage), whereas in sample B (flowering stage) the main contributors were 1,8-cineole (34.6%), 4a(alpha),7alpha,7a(alpha)-nepetalactone (17.3%), alpha-pinene (11.4%) and 4a(alpha),7alpha,7alpha(beta)-nepetalactone (8.9%). The oils were tested on human health important insects such as the Pogonomyrmex sp. ants and the Culex pipiens molestus mosquitoes with promising results on insect repellency/toxicity.     

Cytotoxic lupane-type triterpenoids from Acacia mellifera

One new and eight previously described lupane-type metabolites were isolated for the first time from Acacia mellifera (Leguminosae). Based on spectral analyses, the structure of the new compound was elucidated as 28-hydroxy-3-oxo-lup-20-(29)-en-30-al (1), while the known compounds were identified as 3-oxo-lup-20-(29)-en-30-al (2), 3-hydroxy-lup-20-(29)-en-30-al (3), 28-hydroxy-lup-20-(29)-en-3-one (4), lupenone (5), lupeol (6), betulin (7), betulinic acid (8), and betulonic acid (9). Metabolites 2, 3, and 4 are reported for the first time in the Leguminosae family. The cytotoxicity of the isolated metabolites was evaluated on the NSCLC-N6 cell line, derived from a human non-small-cell bronchopulmonary carcinoma. Compounds 1 and 3 exhibited significant levels of activity.     

Solution conformation of the antibody-bound tyrosine phosphorylation site of the nicotinic acetylcholine receptor beta-subunit in its phosphorylated and nonphosphorylated states

Phosphorylation of the acetylcholine receptor (AChR) seems to be responsible for triggering several effects including its desensitization and aggregation at the postsynaptic membrane and probably initiates a signal transduction pathway at the postsynaptic membrane. To study the structural and functional role of the tyrosine phosphorylation site of the AChR beta-subunit and contribute to the in-depth understanding of the structural basis of the ion channel function, we synthesized four peptides containing the phosphorylated and nonphosphorylated sequences (380-391) of the human and Torpedo AChR beta-subunits and studied their interaction with a monoclonal antibody (mAb 148) that is known to bind to this region and that is capable of blocking ion channel function. All four peptides were efficient inhibitors of mAb 148 binding to AChR, although the nonphosphorylated human peptide was considerably less effective than the three others. We then investigated the conformation acquired by all four peptides in their antibody-bound state, which possibly illustrates the local conformation of the corresponding sites on the intact AChR molecule. The phosphorylated human and Torpedo peptides adopted a distorted 3(10) helix conformation. The nonphosphorylated Torpedo peptide, which is also an efficient inhibitor, was also folded. In contrast, the nonphosphorylated human peptide (a less efficient inhibitor) presented an extended structure. It is concluded that the phosphorylation of the AChR at its beta-subunit Tyr site leads to a significant change in its conformation, which may affect several functions of the AChR.