Structural characterization of pyrrolic cross-links in collagen using a biotinylated Ehrlich's reagent

The structures of pyrrolic forms of cross-links in collagen have been confirmed by reacting collagen peptides with a biotinylated Ehrlich's reagent. This reagent was synthesized by converting the cyano group of N-methyl-N-cyanoethyl-4-aminobenzaldehyde to a carboxylic acid, followed by conjugation with biotin pentyl-amine. Derivatization of peptides from bone collagen both stabilized the pyrroles and facilitated selective isolation of the pyrrole-containing peptides using a monomeric avidin column. Reactivity of the biotinylated reagent with collagen peptides was similar to that of the standard Ehrlich reagent, but heat denaturation of the tissue before enzyme digestion resulted in the loss of about 50% of the pyrrole cross-links. Identification of a series of peptides by mass spectrometry confirmed the presence of derivatized pyrrole structures combined with between 1 and 16 amino acid residues. Almost all of the pyrrole-containing peptides appeared to be derived from N-terminal telopeptide sequences, and the nonhydroxylated (lysine-derived) form predominated over pyrrole cross-links derived from helical hydroxylysine.     

Inhibitors of NF-kappaB derived from thalidomide

A series of compounds originally derived from thalidomide were synthesized and evaluated. The most potent compounds in this series, 5HPP-33 and compound 20, inhibited NF-kappaB activation in HeLa cells. Preliminary study indicated that the mechanism of inhibition of NF-kappaB activation is through inhibition of its translocation from the cytoplasm to the nucleus.     

NF-kappaB signaling and human disease

Despite substantial progress in understanding the NF-kappaB signaling pathway, the connections between this pathway and human disease are only now being elucidated. Genes that function within or upstream of the NF-kappaB pathway have been found to cause four distinct disorders and two allelic conditions. Investigation of these genes and disorders has brought significant insight into the role of NF-kappaB in various aspects of physiological development.     

Depth of proteome issues: a yeast isotope-coded affinity tag reagent study

As a test case for optimizing how to perform proteomics experiments, we chose a yeast model system in which the UPF1 gene, a protein involved in nonsense-mediated mRNA decay, was knocked out by homologous recombination. The results from five complete isotope-coded affinity tag (ICAT) experiments were combined, two using matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS/MS) and three using electrospray MS/MS. We sought to assess the reproducibility of peptide identification and to develop an informatics structure that characterizes the identification process as well as possible, especially with regard to tenuous identifications. The cleavable form of the ICAT reagent system was used for quantification. Most proteins did not change significantly in expression as a consequence of the upf1 knockout. As expected, the Upf1 protein itself was down-regulated, and there were reproducible increases in expression of proteins involved in arginine biosynthesis. Initially, it seemed that about 10% of the proteins had changed in expression level, but after more thorough examination of the data it turned out that most of these apparent changes could be explained by artifacts of quantification caused by overlapping heavy/light pairs. About 700 proteins altogether were identified with high confidence and quantified. Many peptides with chemical modifications were identified, as well as peptides with noncanonical tryptic termini. Nearly all of these modified peptides corresponded to the most abundant yeast proteins, and some would otherwise have been attributed to "single hit" proteins at low confidence. To improve our confidence in the identifications, in MALDI experiments, the parent masses for the peptides were calibrated against nearby components. In addition, five novel parameters reflecting different aspects of identification were collected for each spectrum in addition to the Mascot score that was originally used. The interrelationship between these scoring parameters and confidence in protein identification is discussed.     

IKK epsilon signaling: not just NF-kappaB

IkappaB kinases (IKKs) are key components of NF-kappaB signaling pathways in innate immunity and inflammation. Surprisingly, three recent reports implicate IKKs in Drosophila in seemingly unrelated functions, including non-apoptotic caspase activation and cytoskeleton organization.     

Chemical synthesis of a biotinylated derivative of the simian immunodeficiency virus protease. Purification by avidin affinity chromatography and autocatalytic activation.

The protease from simian immunodeficiency virus (SIV) was chemically synthesized by automated solid-phase technology as an NH2-terminally extended derivative, capped with biotin. Biotin-linker-(SIV protease (1-99)): the linker segment, Gly-Gly-Asp-Arg-Gly-Phe-Ala-Ala, corresponds to the amino acid sequence preceding that of the protease in the SIV gag/pol precursor polyprotein. Accordingly, the Ala-Pro bond joining the octapeptide linker to the protease constitutes a site naturally cleaved by the protease during viral maturation. This strategy for synthesis was designed to facilitate purification of the biotinylated protein derivative from a complex mixture of reaction products by avidin/agarose-affinity chromatography and to provide the means for autocatalytic removal of the biotin-linker segment. As anticipated, folding of the full-length construct leads to activation of the enzyme and excision of the desired 99-residue SIV protease (overall yield, approximately). The specificity of the synthetic SIV protease toward a number of well characterized protein substrates was the same as observed for the nearly identical enzyme from human immunodeficiency virus type 2 (HIV-2 protease) and distinct from that of the more disparate HIV-1 protease. The same functional ordering with respect to the human retroviral proteases was reflected in Ki values observed with a number of protease inhibitors. Thus, the folded synthetic SIV protease shows patterns of specificity and susceptibility to inhibition that are in accord with what would be expected based upon its degree of structural similarity to proteases from HIV-1 and HIV-2.     

Cyclopentadienyltricarbonylrheniumbenzazepines: synthesis and binding affinity

Analogues of the benzazepine dopamine D1 receptor antagonist SCH-23390 incorporating the cyclo-pentadienyltricarbonyl-rhenium (CPTR) moiety were synthesized and evaluated pharmacologically. The CPTR derivatives retained affinity (0.3-2.9 nM) and D1 selectivity of the parent compound, supporting their use as neuropharmacological surrogates for 99mTc-labeled SPECT radiopharmaceuticals.     

Rational design,synthesis, and verification of affinity ligands to a protein surface cleft

The structure-based design, synthesis, and screening of a glucuronic acid scaffold library of affinity ligands directed toward the catalytic cleft on porcine pancreas alpha-amylase are presented. The design was based on the simulated docking to the enzyme active site of 53 aryl glycosides from the Available Chemicals Directory (ACD) selected by in silico screening. Twenty-three compounds were selected for synthesis and screened in solution for binding toward alpha-amylase using nuclear magnetic resonance techniques. The designed molecules include a handle outside of the binding site to allow their attachment to various surfaces with minimal loss of binding activity. After initial screening in solution, one affinity ligand was selected, immobilized to Sepharose (Amersham Biosciences), and evaluated as a chromatographic probe. A column packed with ligand-coupled Sepharose specifically retained the enzyme, which could be eluted by a known inhibitor.     

S-Adenosyl-L-homocysteine dialdehyde: An affinity labeling reagent for histamine-N-methyltransferase

S-Adenosyl-L-homocysteine (SAH) was converted to 2′-O-[(R)-formyl(adenin-9-yl)methyl]-3′-S-homocysteinyl-3′-deoxy-(R)-glyceraldehyde (SAH dialdehyde) by periodic acid oxidation. SAH dialdehyde was then reduced with sodium borohydride to the corresponding diol, 2′,3′-acyclic SAH. SAH dialdehyde, but not 2′,3′-acyclic SAH, was found to inhibit histamine-N-methyltransferase (HMT). Neither analog showed significant inhibitory activity toward other methyltransferases. The inhibition of HMT by SAH dialdehyde was irreversible with the inactivation following first-order kinetics. A kinetic analysis suggests the formation of a dissociable enzyme-inhibitor complex prior to inactivation. The enzyme could be protected from inactivation by inclusion of S-adenosyl-L-methionine in the preincubation mixture.     

Inhibitors of neuronal regeneration: mediators and signaling mechanisms

Neuritogenesis and its inhibition are opposite and balancing processes during development as well as pathological states of adult neuron. In particular, the inability of adult central nervous system (CNS) neurons to regenerate upon injury has been attributed to both a lack of neuritogenic ability and the presence of neuronal growth inhibitors in the CNS environment. I review here recent progress in our understanding of neuritogenic inhibitors, with particular emphasis on those with a role in the inhibition of neuronal regeneration in the CNS, their signaling cascades and signal mediators. Neurotrophines acting through the tropomyosin-related kinase (Trk) family and p75 receptors promote neuritogenesis, which appears to require sustained activation of the mitogen activated protein (MAP) kinase pathway, and/or the activation of phosphotidylinositol 3-kinase (PI3 kinase). During development, a plethora of guidance factors and their receptors navigate the growing axon. However, much remained to be learned about the signaling receptors and pathways that mediate the activity of inhibitors of CNS regeneration. There is growing evidence that neuronal guidance molecules, particularly semaphorins, may also have a role as inhibitors of CNS regeneration. Although direct links have not yet been established in many cases, signals from these agents may ultimately converge upon the modulators and effectors of the Rho-family GTPases. Rho-family GTPases and their effectors modulate the activities of actin modifying molecules such as cofilin and profilin, resulting in cytoskeletal changes associated with growth cone extension or retraction.     

Study on synthesis and bioactivity of biotinylated emodin

Applied Microbiology and Biotechnology - A novel compound biotinylated emodin was synthesized by a two-step acyl chloride method which connects the biotin to emodin with esterification reaction....     

Purification of caveolae by affinity two-phase partitioning using biotinylated antibodies and NeutrAvidin-dextran

A new concept for affinity two-phase partitioning was tested. The partitioning was based on the interaction of target membranes with a primary antibody which, in turn, interacted with a biotinylated secondary antibody and NeutrAvidin-dextran in a poly(ethylene glycol)/dextran two-phase system. Caveolae selectively redistributed from the top phase to the NeutrAvidin-dextran-containing bottom phase by employing anti-caveolin as the primary antibody. This immunoaffinity approach was more selective than the established sucrose gradient centrifugation method and resulted in highly purified caveolae from Triton X-100-treated liver and lung plasma membranes. The same approach, employing other selective primary antibodies, should facilitate the purification also of other membrane fractions.     

A Link Between Histone Deacetylase Inhibitors and NF-kappaB Signaling

Commentary to:

An Intact NF-κB Pathway is Required for Histone Deacetylase Inhibitor-Induced G₁ Arrest and Maturation in Human Myeloid Leukemia (U937)

Yun Dai, Mohamed Rahmani, Steven Grant     

The design, synthesis and evaluation of affinity ligands for prion proteins

Bifunctional affinity ligands based on a triazine scaffold were rationally designed to target prion protein and shown to bind recombinant prion protein with high affinity and selectivity. The ligands were capable of discriminating between prion protein glycoforms and monomeric and dimeric forms of the prion protein. The ligands also discriminate between conformational differences in the prion protein, resulting from point mutations in the prion protein gene. These results suggest that derived compounds could be used selectively to detect the disease-associated form of the prion protein, and as such, could provide diagnostic or therapeutic tools for prion diseases.     

RelA control of IkappaBalpha phosphorylation: a positive feedback loop for high affinity NF-kappaB complexes

NF-kappaB-IkappaB complex formation regulates the level and specificity of NF-kappaB activity. Quantitative analyses showed that RelA-NF-kappaB-induced IkappaBalpha binding is regulated through inhibitor retention and phosphorylation. RelA caused an increase in IkappaBalpha phosphorylation and in degradation, which was enhanced monotonically with inhibitor concentration. In vivo analysis demonstrated the RelA-induced IkappaBalpha/RelA interactions to be specific, saturable, and phosphorylation-dependent. In addition, it showed that phosphorylation regulates both the level and affinity of the complexes and demonstrated an increased average affinity to coincide with reduction in the level of complexes during cytokine-induced pathway activation. The data show that RelA regulation of NF-kappaB-IkappaBalpha complex formation is IkappaBalpha phosphorylation-dependent and that IkappaBalpha/NF-kappaB binding is dynamic and determined by concentration of the subunits. In addition, they suggest that regulation of both complex levels and affinities through phosphorylation, with effects on the system steady state, participate in selective activation of the NF-kappaB pathway.     

NF-kappaB signaling: flipping the switch with polyubiquitin chains

Protein modification by ubiquitin has emerged as an important cellular regulatory mechanism. Recent studies illustrate the surprising ways in which polyubiquitin chains are manipulated in the regulation of NF-kappaB signaling.