A new chemical tool for exploring the role of the PDE4D isozyme in leukocyte function

Nicotinamide (2) is a potent and selective inhibitor of the PDE4D isozyme and as a chemical tool selectively blocks eosinophil mediator release and chemotaxis thus linking the role of PDE4D to eosinophil function.     

MPEx: A tool for exploring membrane proteins

Hydropathy plot methods form a cornerstone of membrane protein research, especially in the early stages of biochemical and structural characterization. Membrane Protein Explorer (MPEx), described in this article, is a refined and versatile hydropathy‐plot software tool for analyzing membrane protein sequences. MPEx is highly interactive and facilitates the characterization and identification of favorable protein transmembrane regions using experiment‐based physical and biological hydrophobicity scales. Besides allowing the consequences of sequence mutations to be examined, it provides tools for aiding the design of membrane‐active peptides. MPEx is freely available as a Java Web Start application from our web site at http://blanco.biomol.uci.edu/mpex .     

Abscinazole-E1, a novel chemical tool for exploring the role of ABA 8'-hydroxylase CYP707A

We developed abscinazole-E1 (Abz-E1), a specific inhibitor of abscisic acid (ABA) 8′-hydroxylase (CYP707A). This inhibitor was designed and synthesized as an enlarged analogue of uniconazole (UNI), a well-known plant growth retardant, which inhibits a gibberellin biosynthetic enzyme (ent-kaurene oxidase, CYP701A) as well as CYP707A. Our results showed that Abz-E1 functions as a potent inhibitor of CYP707A and a poor inhibitor of CYP701A both in vitro and in vivo. Abz-E1 application to plants resulted in improved desiccation tolerance and an increase in endogenous ABA.     

A new chemical tool for characterization and partial depolymerization of red algal galactans

Complete acid hydrolysis of red algal galactans in the presence of borane - 4-methylmorpholine complex has been shown to prevent the acid degradation of 3,6-anhydrogalactose derivatives by their reduction to the corresponding 3,6-anhydro-galactitols, whereas all the other monosaccharides are liberated essentially in the non-reduced form; the reductive hydrolysis products may be determined quantitatively using gas-liquid chromatography (GLC). The method is recommended for preliminary characterization of the polysaccharide composition of red algal biomass. Partial acid hydrolysis of galactans in the presence of the same reducing agent gives rise to reduced oligosaccharides having terminal 3,6-anhydrogalactitol residues. Based on this reaction, the attribution of unknown galactans to the agar or carrageenan groups is possible by partial reductive hydrolysis of small samples of algal biomass with subsequent identification of agarobiitol or carrabiitol acetates by GLC. Sulfate groups are substantially retained under partial reductive hydrolysis conditions; the isolation by liquid chromatography and elucidation of structures of reduced sulfated oligosaccharides may be of great value for the structural analysis of complex red algal galactans.     

Comparative proteomics as a new tool for exploring human mitochondrial tRNA disorders.

More than 70 different point mutations in human mitochondrial tRNA genes are correlated with severe disorders, including fatal cardiopathies, encephalopathies, myopathies, and others. So far, investigation of the molecular impact(s) of mutations has focused on the affected tRNA itself by seeking structural and/or functional perturbations capable of interfering with synthesis of the 13 mitochondrion-encoded subunits of respiratory chain complexes. Here, a proteomic approach was used to investigate whether such mutations would affect the pattern of mitochondrial proteins at a broader level. Analysis of several hundred mitochondrial proteins from sibling cybrid cell lines by two-dimensional electrophoresis, an approach that takes into account all regulatory steps of mitochondrial and nuclear gene expression, indeed reveals a number of up- and downregulated proteins when healthy and single-point-mutation-carrying mitochondria representative of either MELAS or MERRF syndrome were compared. Assignment by mass spectrometry of the two proteins which exhibit obvious large quantitative decreases in the levels of both pathologic mitochondria identified nuclear-encoded subunits of cytochrome c oxidase, a respiratory chain complex. This clearly shows a linkage between the effects of mutations in mitochondrial tRNA genes and the steady-state level of nuclear-encoded proteins in mitochondria. It opens new routes toward a large-scale exploration of potential proteic partners involved in the genotype-phenotype correlation of mitochondrial disorders.     

Zebrafish: A tool for chemical screens

The zebrafish has proven to be an invaluable vertebrate animal model for developmental biology. Recent technological advances have added an arsenal of tools to expand its use into the realm of drug discovery. This includes methodology to generate transgenic reporter lines that allow for the direct visualization of fluorescent markers in live embryos. With the addition of automated imaging and analysis of embryos treated with small molecules, these innovations have expanded its utility into high throughput chemical screens. This review will highlight some of these advances that have propelled zebrafish as a tool for drug discovery. Birth Defects Research (Part C) 90:185–192, 2010. © 2010 Wiley‐Liss, Inc.     

Approaching the molecular and physiological function of macroH2A variants

The transition of a cell from one state to another involves large changes in the organization of its chromatin. Indeed, it has become increasingly clear that modifications of the chromatin are the molecular basis of an epigenetic memory that defines cellular identity. Histone variants are likely candidates to contribute to epigenetic regulations. Genome-wide profiling of the unusual macroH2A histone variants and the identification of interacting proteins provided important clues to their molecular and physiological function.     

SitePainter: a tool for exploring biogeographical patterns

As microbial ecologists take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools that reveal the intrinsic spatial patterns and structures of these populations is crucial. Here we present SitePainter, an interactive graphical tool that allows investigators to create or upload pictures of their study site, load diversity analyses data and display both diversity and taxonomy results in a spatial context. Features of SitePainter include: visualizing α -diversity, using taxonomic summaries; visualizing β -diversity, using results from multidimensional scaling methods; and animating relationships among microbial taxa or pathways overtime. SitePainter thus increases the visual power and ability to explore spatially explicit studies. AVAILABILITY: https://sourceforge.net/projects/sitepainter SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: antoniog@colorado.edu, Rob.Knight@colorado.edu.     

XplorMed: a tool for exploring MEDLINE abstracts

The most frequent access to the MEDLINE database of scientific abstracts is by keyword search. However, this is often not sufficient because although the user might find all the useful abstracts, these are buried in hundreds that are irrelevant. The exploratory tool XplorMed has been developed to analyse the result of any MEDLINE query. It suggests main groups of related topics and documents, sparing the user the need of reading all abstracts.     

Structure Motivator: A tool for exploring small three-dimensional elements in proteins

Backround

Aspartyl aminopeptidase (DNPEP), with specificity towards an acidic amino acid at the N-terminus, is the only mammalian member among the poorly understood M18 peptidases. DNPEP has implicated roles in protein and peptide metabolism, as well as the renin-angiotensin system in blood pressure regulation. Despite previous enzyme and substrate characterization, structural details of DNPEP regarding ligand recognition and catalytic mechanism remain to be delineated.

Results

The crystal structure of human DNPEP complexed with zinc and a substrate analogue aspartate-??-hydroxamate reveals a dodecameric machinery built by domain-swapped dimers, in agreement with electron microscopy data. A structural comparison with bacterial homologues identifies unifying catalytic features among the poorly understood M18 enzymes. The bound ligands in the active site also reveal the coordination mode of the binuclear zinc centre and a substrate specificity pocket for acidic amino acids.

Conclusions

The DNPEP structure provides a molecular framework to understand its catalysis that is mediated by active site loop swapping, a mechanism likely adopted in other M18 and M42 metallopeptidases that form dodecameric complexes as a self-compartmentalization strategy. Small differences in the substrate binding pocket such as shape and positive charges, the latter conferred by a basic lysine residue, further provide the key to distinguishing substrate preference. Together, the structural knowledge will aid in the development of enzyme-/family-specific aminopeptidase inhibitors.     

A new photolabile precursor of glycine with improved properties: A tool for chemical kinetic investigations of the glycine receptor

The synthesis and characterization of a new photolabile precursor of glycine (caged glycine) is described. The alpha-carboxyl group of glycine is covalently coupled to the alpha-carboxy-2-nitrobenzyl (alphaCNB) protecting group. Photolysis of the caged glycine with UV light produces free glycine. At 308 nm, the compound photolyzes with a quantum yield of 0.38. The absorption spectrum and the pH dependence of a transient absorption produced after laser-flash illumination are typical for aci-nitro intermediates of alphaCNB-protected compounds. The time constant for the major component of the aci-nitro intermediate decay ( approximately 84% of the total aci-nitro absorbance) was determined to be 7 micros at physiological pH. A minor component ( approximately 16%) decays with a rate constant of 170 micros. The compound does not activate or inhibit the alpha(1)-homomeric glycine receptor transiently expressed in HEK293 cells. After photolysis with a 10 ns pulse of 325 nm laser light, the glycine released from the caged compound activates glycine-mediated whole-cell currents in the same cells. The rise of these currents can be measured in a time-resolved fashion and occurs on a millisecond to sub-millisecond time scale. It can be described with a single-exponential function over >85% of the total current. The rate constant of the current rise is about 2 orders of magnitude slower than the rate constant of caged glycine photolysis. Thermal hydrolysis of the alphaCNB-caged glycine takes place with a half-life of 15.6 h at physiological pH. The new caged glycine is the first in a series of photoprotected glycine derivatives that has the required properties for use with chemical kinetic methods for investigation of glycine-activated cell surface receptors. Photolysis is rapid and efficient with respect to the receptor reactions to be studied; hydrolysis in aqueous solution is sufficiently slow, and the compound is biologically inert. It will, therefore, be a useful tool for investigation of the processes leading to channel opening of glycine receptor channels and the effects of mutations of the glycine receptor and of inhibitors on these processes.     

A chemical mapping technique for exploring the location of proteins along the ribosome-bound peptide chain

A series of peptidyl-tRNA analogs with varying peptide chain length, BrAc(Gly) _nPhe-tRNA^phe, n = 0 to 16 has been prepared. When bound to Escherichia coli 70 S ribosomes these all react covalently with certain ribosomal proteins. The overwhelming majority of the reaction is with 50 S ribosomal proteins L2, L16, L24, L26–L27 and L32–L33. The extent of reaction with each protein is a function of peptide chain length, making it possible to estimate the relative proximity of these proteins to the 3′-terminus of tRNA bound in the ribosomal P site. This fact, coupled with the findings of others about the length dependence of the binding and peptide donor activity of peptidyl-tRNAs suggests that there is actually a binding site for the growing peptide chain. If this is true, the results presented here permit the ordering of the proteins in this site: L2 is closest to the 3′-end of tRNA followed by L26–L27, L32–L33 and last L24. Evidence is also given that the direction of the growing peptide chain must point away from the A site.     

Concept of new tool to simulate human physiological reactions in microgravity

This paper describes a new tool for weightlessness simulation--the Acceleration-Immersion Imitator of Sensation of Microgravity (AIISM), which aims to incorporate the otolithic input, the unloading of proprioceptors, and the fluid shifts that occur in microgravity. The facility is a kind of centrifuge chamber filled with water. The workings of the facility are described as well as the way the chamber simulates microgravity conditions.