Synthesis and characterization of allosteric probes of substrate channeling in the tryptophan synthase bienzyme complex

Allosteric interactions regulate substrate channeling in Salmonella typhimurium tryptophan synthase. The channeling of indole between the alpha- and beta-sites via the interconnecting 25 A tunnel is regulated by allosteric signaling arising from binding of ligand to the alpha-site, and covalent reaction of l-Ser at the beta-site. This signaling switches the alpha- and beta-subunits between open conformations of low activity and closed conformations of high activity. Our objective is to synthesize and characterize new classes of alpha-site ligands (ASLs) that mimic the binding of substrates, 3-indole-d-glycerol 3'-phosphate (IGP) or d-glyceraldehyde 3-phosphate (G3P), for use in the investigation of alpha-site-beta-site interactions. The new synthesized IGP analogues contain an aryl group linked to an O-phosphoethanolamine moiety through amide, sulfonamide, or thiourea groups. The G3P analogue, thiophosphoglycolohydroxamate, contains a hydroxamic acid group linked to a thiophosphate moiety. Crystal structures of the internal aldimine complexed with G3P and with three of the new ASLs are presented. These structural and solution studies of the ASL complexes with the internal aldimine form of the enzyme establish the following. (1) ASL binding occurs with high specificity and relatively high affinities at the alpha-site. (2) Binding of the new ASLs slows the entry of indole analogues into the beta-site by blocking the tunnel opening at the alpha-site. (3) ASL binding stabilizes the closed conformations of the beta-subunit for the alpha-aminoacrylate and quinonoid forms of the enzyme. (4) The new ASLs exhibit allosteric properties that parallel the behaviors of IGP and G3P.     

Allosteric regulation of tryptophan synthase channeling: the internal aldimine probed by trans-3-indole-3'-acrylate binding

Substrate channeling in the tryptophan synthase bienzyme complex from Salmonella typhimurium is regulated by allosteric interactions triggered by binding of ligand to the alpha-site and covalent reaction at the beta-site. These interactions switch the enzyme between low-activity forms with open conformations and high-activity forms with closed conformations. Previously, allosteric interactions have been demonstrated between the alpha-site and the external aldimine, alpha-aminoacrylate, and quinonoid forms of the beta-site. Here we employ the chromophoric l-Trp analogue, trans-3-indole-3'-acrylate (IA), and noncleavable alpha-site ligands (ASLs) to probe the allosteric properties of the internal aldimine, E(Ain). The ASLs studied are alpha-d,l-glycerol phosphate (GP) and d-glyceraldehyde 3-phosphate (G3P), and examples of two new classes of high-affinity alpha-site ligands, N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F6) and N-(4'-trifluoromethoxybenzenesulfonyl)-2-aminoethyl phosphate (F9), that were previously shown to bind to the alpha-site by optical spectroscopy and X-ray crystal structures [Ngo, H., Harris, R., Kimmich, N., Casino, P., Niks, D., Blumenstein, L., Barends, T. R., Kulik, V., Weyand, M., Schlichting, I., and Dunn, M. F. (2007) Synthesis and characterization of allosteric probes of substrate channeling in the tryptophan synthase bienzyme complex, Biochemistry 46, 7713-7727]. The binding of IA to the beta-site is stimulated by the binding of GP, G3P, F6, or F9 to the alpha-site. The binding of ASLs was found to increase the affinity of the beta-site of E(Ain) for IA by 4-5-fold, demonstrating for the first time that the beta-subunit of the E(Ain) species undergoes a switching between low- and high-affinity states in response to the binding of ASLs.     

Tritium radiolabelling of PB28, a potent sigma-2 receptor ligand: pharmacokinetic and pharmacodynamic characterization

A potent sigma-2 receptor ligand, known as PB28, was tritium radiolabelled and biologically evaluated. The results showed that [(3)H]PB28 and the corresponding unlabelled PB28 had superimposed pharmacodynamic properties. This radioligand appears as a potential candidate for receptor binding and in living cells assays.     

Novel sterically hindered cannabinoid CB1 receptor ligands

In the present study, 11 novel N-(3,3-diphenyl)propyl-2,2-diphenylacetamide derivatives (4a-d and 9a-g) and six triphenylacetamides (10a-c and 11a-c) were synthesized and tested as ligands of cannabinoid CB(1) and CB(2) receptors. All compounds exhibited affinity for CB(1) and CB(2) receptors. Four compounds (4b, 9a, 9b, and 11a) showed selectivity for CB(1) versus CB(2) receptors, although only the N-(3,3-diphenyl)propyl-2,2-diphenylacetamide (4b) can be considered a potent CB(1) ligand (K(i)=58 nM). It was 140-fold selective over CB(2) receptors (K(i)=7800 nM) and behaved as an inverse agonist by stimulating forskolin-induced cAMP formation in mouse N18TG2 neuroblastoma cells. This compound is the first of a novel class of tetraphenyl CB(1) ligands that, in view of its easy synthesis and high affinity for CB(1) receptors and despite its sterical hindrance, will be useful for the design of new blockers of this therapeutically exploitable receptor type.     

Rice peptide deformylase PDF1B is crucial for development of chloroplasts

Because protein synthesis begins with N-formylmethionine in plant endosymbiotic organelles, removal of the formyl group by peptide deformylase (PDF) is essential to allowing the excision of the first methionine. Rice contains three copies (OsPDF1A, OsPDF1B and OsPDF1B2) of the PDF genes. Unlike OsPDF1A and OsPDF1B, OsPDF1B2 is apparently non-functional, with several deleterious substitutions and deletions. OsPDF1A is more strongly expressed in the roots, while OsPDF1B is expressed at higher levels in mature leaves. Transient expression of PDF-green fluorescent protein (GFP) fusion proteins in the protoplasts demonstrates that, unlike OsPDF1A, OsPDF1B is localized in both the chloroplasts and the mitochondria. We used T-DNA insertional alleles to elucidate functional roles associated with OsPDF1B. Homozygous plants of pdf1b/pdf1b exhibited the phenotypes of chlorina and growth retardation. Histochemical analysis showed that the length of their mesophyll cells was increased 4- to 5-fold, resulting in a reduction in the total number of cells. Transmission electron microscopy analyses revealed that chloroplasts were severely damaged and mitochondria appeared to be mildly altered in the pdf1b mutants. Expression of genes encoded in the chloroplasts and mitochondria was altered in the mutants. Based on these results, we conclude that OsPDF1B is essential for the development of chloroplast and perhaps mitochondria.     

Constitutive heterochromatin: a surprising variety of expressed sequences

The organization of chromosomes into euchromatin and heterochromatin is amongst the most important and enigmatic aspects of genome evolution. Constitutive heterochromatin is a basic yet still poorly understood component of eukaryotic chromosomes, and its molecular characterization by means of standard genomic approaches is intrinsically difficult. Although recent evidence indicates that the presence of transcribed genes in constitutive heterochromatin is a conserved trait that accompanies the evolution of eukaryotic genomes, the term heterochromatin is still considered by many as synonymous of gene silencing. In this paper, we comprehensively review data that provide a clearer picture of transcribed sequences within constitutive heterochromatin, with a special emphasis on Drosophila and humans.     

Further studies on the pharmacological features of the nociceptin/orphanin FQ receptor ligand ZP120

ZP120 is a nociceptin/orphanin FQ (N/OFQ) peptide receptor (NOP) ligand. In previous studies, the effects of ZP120 were found to be sensitive to J-113397 in mouse tissues while resistant to UFP-101 in rat tissues. The aim of this study was to further investigate the ZP120 pharmacological profile using mouse and rat preparations, J-113397 and UFP-101, as well as NOP receptor knockout (NOP(-/-)) mice. Electrically stimulated mouse and rat vas deferens were used to characterize the pharmacology of ZP120 in vitro. For in vivo studies the tail-withdrawal assay was performed in wild type (NOP(+/+)) and NOP knockout (NOP(-/-)) mice. In the mouse and rat vas deferens ZP120 mimicked the effects of N/OFQ showing higher potency but lower maximal effects. In both preparations, J-113397 antagonized N/OFQ and ZP120 effects showing similar pK(B) values ( approximately 7.8). UFP-101 antagonized the actions of N/OFQ (pK(B) values approximately 7.3) but did not modify the effects of ZP120. The inhibitory effects of N/OFQ and ZP120 were no longer evident in vas deferens tissues taken from NOP(-/-) mice. In NOP(+/+) mice subjected to the tail-withdrawal assay, ZP120 (1 nmol) mimicked the pronociceptive action of N/OFQ (10 nmol), producing longer lasting effects. The effects of both peptides were absent in NOP(-/-) animals. The NOP receptor ligand ZP120 is a high potency NOP selective partial agonist able to evoke long-lasting effects; its diverse antagonist sensitivity in comparison with N/OFQ may derive from different modality of binding to the NOP receptor.     

No effects of UMTS exposure on the function of rat outer hair cells

UMTS communication devices are becoming common in everyday use. This could raise public concern about their possible detrimental effects on human health. The aim of this study, in the framework of the EMF nEAR Project, was to evaluate possible influence of UMTS electromagnetic fields (EMF) exposure on cochlear outer hair cells' (OHCs) functionality in laboratory animals. Forty‐eight male Sprague–Dawley rats were locally exposed (right ear) or sham‐exposed to a controlled UMTS EMF, frequency of 1946 MHz, at SAR level of 10 W/kg, 2 h a day, 5 days a week, for 4 weeks. A group of 12 rats treated with kanamycin (KM) was also included as positive control. Rats were tested by recording Distortion Product Otaoacoustic Emissions (DPOAEs), a non‐invasive test capable of assessing the status of the OHCs in the inner ear. DPOAEs were performed before, during (one or three times a week) and after (1‐week) exposure to the EMF. The analysis of the data shows that no statistically significant differences were found between the audiological signals recorded from the different experimental groups. The ototoxic effect of KM has been confirmed. Bioelectromagnetics 30:385–392, 2009. © 2009 Wiley‐Liss, Inc.     

Dead-End Hollow-Fiber Ultrafiltration for Recovery of Diverse Microbes from Water

Dead-end ultrafiltration (DEUF) is an alternative approach to tangential-flow hollow-fiber ultrafiltration that can be readily employed under field conditions to recover microbes from water. The hydraulics of DEUF and microbe recovery for a new DEUF method were investigated using 100-liter tap water samples. Pressure, flow rate, and temperature were investigated using four hollow-fiber ultrafilter types. Based on hydraulic performance, the Asahi Kasei REXEED 25S ultrafilter was selected for microbe recovery experiments. Microbe recovery experiments were performed using MS2 bacteriophage, Enterococcus faecalis, Clostridium perfringens spores, and Cryptosporidium parvum oocysts. Microbes were recovered from ultrafilters by backflushing using a surfactant solution. Average flow rates were 2.1 liters/min for 100-liter water samples having turbidities of 0.28 to 4.3 nephelometric turbidity units (NTU), and no evidence of appreciable filter clogging was observed. The DEUF average recovery efficiencies for each study analyte in tap water were as follows: for E. faecalis, 93% ± 16%; for MS2, 57% ± 7.7%; for C. perfringens spores, 94% ± 22%; and for C. parvum, 87% ± 18%. Average microbe recoveries for tap water amended with surface water (average turbidity = 4.3 NTU) were as follows: for E. faecalis, 78% ± 12%; for MS2, 73% ± 13%; for C. perfringens, 57% ± 21%; and for C. parvum, 83% ± 21%. These data demonstrate that DEUF is an effective method for recovering diverse microbes from water and should be a useful tool for field-based environmental investigations.There are an estimated 4 million to 33 million cases of acute gastrointestinal illness each year in the United States due to drinking water (3, 11). From 2005 to 2006, 20 reports of waterborne disease and outbreaks (WBDOs) associated with drinking water were submitted to the national Waterborne Disease and Outbreak Surveillance System (19). In addition, a record number (78 reports) of WBDOs associated with recreational water were also submitted to the Waterborne Disease and Outbreak Surveillance System in 2005 and 2006 (20). Detecting the etiologic agents for WBDOs is challenging due to such factors as the time delay between case exposure and water sampling, microbial die-off, and water dilution or treatment prior to sampling. Because it is likely that pathogens will be present at low concentrations in water sampled for outbreak investigations, relatively large volumes of water (e.g., 40 to 100 liters) should be collected. In addition, sampling water for a diverse array of microbes is sometimes a goal when multiple etiologic agents are suspected for a WBDO (13) or during emergency responses when the contaminant has not been identified.Hollow-fiber ultrafiltration (UF) has been shown to be an effective technique for collecting large-volume water samples for recovery of diverse microbes, including viruses, vegetative bacteria, bacterial spores, and parasites (5, 6, 10, 12, 14). However, most hollow-fiber UF techniques utilize a tangential-flow approach that requires comprehensive operator training and which is generally not conducive to rapid-response implementation for field sampling. While the tangential-flow (i.e., recirculating flow) UF technique has been shown to be effective for microbe recovery, it is a more complicated sampling technique than traditional direct-filtration techniques, such as membrane filtration for coliforms (1), microfiltration for Cryptosporidium and Giardia (oo)cysts (18), and adsorption-elution microfiltration for viruses (4). For emergency response, outbreak investigations, or other field investigations performed by personnel with limited training in water sample collection, a dead-end UF (DEUF) technique would be useful for capturing and recovering multiple microbe classes.Relatively few studies have reported using hollow-fiber UF in a DEUF configuration. Kearns et al. (7) reported using an automated DEUF system to recover Bacillus atrophaeus spores from tap water, with reported recovery efficiencies of 23 to 40% in ∼100-liter samples with low-level seeding (330 to 1,000 CFU). These researchers performed filter backflushing using a phosphate buffer containing either Tween 20 or sodium polyphosphate. Kearns et al. also reported suspected ultrafilter fouling based on measured reductions in flow rates for ∼100-liter samples (7). The Kearns et al. observations indicate that the ultrafilter pore size and filter area are important hydraulic performance variables for the DEUF technique. Leskinen and Lim (9) reported using hollow-fiber DEUF for recovery of enterococci from 100-liter samples of beach water. These researchers used a urea-lysine solution to elute (instead of backflush) enterococci from ultrafilters. Leskinen and Lim reported a wide range of recovery efficiencies (4 to 708%; average = 251%) for their DEUF method but did not discuss whether water quality (other than a potential variability in microbe distribution in the 100-liter samples) could have contributed to ultrafilter fouling or variable method performance (9).The present study was designed to investigate DEUF using different commercially available hollow-fiber ultrafilters having a range of pore sizes and filter medium sizes. The parameters tested included the effect of the water sample flow rate and temperature on system pressure and the effect of turbidity on the permeate flow rate and microbial recovery efficiencies. A suite of four distinctly different microbes (MS2 bacteriophage, Enterococcus faecalis, Clostridium perfringens spores, and Cryptosporidium parvum oocysts) was studied to determine the performance of the DEUF method for simultaneous recovery of diverse microbes.