Affinity Labeling Experiments Research Articles

The Interaction of Schistosoma Japonicum Glutathione Transferase with Cibacron Blue 3GA and its Fragments.

The 26kDa glutathione transferase (GST, EC 2.5.1.18) from Schistosoma japonicum (SjGST) is recognized as the major detoxification enzyme of S. japonicum, a pathogenic helminth causing schistosomiasis. In the present study, the interaction of the chlorotriazine dye Cibacron blue 3GA (CB3GA) and its structural analogues with SjGST was investigated. The work aimed to shed light on the non-substrate ligand-binding properties of the enzyme. Kinetic inhibition analysis, affinity labelling experiments and molecular modelling studies were employed. The results showed that CB3GA is a potent inhibitor (IC50 0.057 ± 0.003 μM) towards SjGST. The enzyme was specifically and irreversibly inactivated by the dichlorotriazine-analogue of CB3GA (IC50 0.190 ± 0.024 μM), following a biphasic pseudo-first-order saturation kinetics with approximately 1 mol of inhibitor per mol of the dimeric enzyme being incorporated. All other monochlorotriazine analogues behave as reversible inhibitors with lower inhibition potency (IC50 5.2-82.3 μM). Kinetic inhibition studies, together with molecular modelling and molecular dynamics simulations, established that the CB3GA binding site overlaps both the G- and H-sites. Both hydrophobic/ polar interactions, as well as steric effects, have decisive roles in determining the inhibitory strength of CB3GA and its analogues. The results of the present study might be useful in future drug design and development efforts towards SjGST.

Principles of agonist recognition in Cys-loop receptors.

Cys-loop receptors are ligand-gated ion channels that are activated by a structurally diverse array of neurotransmitters, including acetylcholine, serotonin, glycine, and GABA. After the term “chemoreceptor” emerged over 100 years ago, there was some wait until affinity labeling, molecular cloning, functional studies, and X-ray crystallography experiments identified the extracellular interface of adjacent subunits as the principal site of agonist binding. The question of how subtle differences at and around agonist-binding sites of different Cys-loop receptors can accommodate transmitters as chemically diverse as glycine and serotonin has been subject to intense research over the last three decades. This review outlines the functional diversity and current structural understanding of agonist-binding sites, including those of invertebrate Cys-loop receptors. Together, this provides a framework to understand the atomic determinants involved in how these valuable therapeutic targets recognize and bind their ligands.

A Covalently Dimerized Recombinant Human Bone Morphogenetic Protein-15 Variant Identifies Bone Morphogenetic Protein Receptor Type 1B as a Key Cell Surface Receptor on Ovarian Granulosa Cells

Genetic studies have identified bone morphogenetic protein-15 (BMP15) as an essential regulator of female fertility in humans and in sheep. Oocyte-derived BMP15 is a noncovalently linked dimeric growth factor mediating its effects to ovarian somatic cells in a paracrine manner. Although receptor ectodomains capable of binding BMP15 have previously been reported, no cell surface receptor complex involved in BMP15 signaling has previously been characterized. Here we have expressed and purified recombinant human BMP15 noncovalent and covalent dimer variants. The biological effects of these BMP15 variants were assessed in cultured human granulosa-luteal cells or COV434 granulosa cell tumor cells using BMP-responsive transcriptional reporter assays and an inhibin B ELISA. Biochemical characterization of ligand-receptor interactions was performed with affinity-labeling experiments using [(125)I]iodinated BMP15 variants. Both ligand variants were shown to form homodimers and to stimulate Smad1/5/8 signaling and inhibin B production in human granulosa cells in a similar manner. [(125)I]Iodination of both ligands was achieved, but only the covalent dimer variant retained receptor binding capacity. The [(125)I]BMP15(S356C) variant bound preferentially to endogenous BMP receptor 1B (BMPR1B) and BMPR2 receptors on COV434 cells. Binding experiments in COS cells with overexpression of these receptors confirmed that the [(125)I]BMP15(S356C) variant binds to BMPR1B and BMPR2 forming the BMP15 signaling complex. The results provide the first direct evidence in any species on the identification of specific cell surface receptors for a member of the GDF9/BMP15 subfamily of oocyte growth factors. The fact that BMP15 uses preferentially BMPR1B as its type I receptor suggests an important role for the BMPR1B receptor in human female fertility. The result is well in line with the demonstration of ovarian failure in a recently reported human subject with a homozygous BMPR1B loss-of-function mutant.

Improvement of right heart structure and function by BAY 41-8543 in pulmonary artery banded mice

Background Receptors for the natriuretic peptides (NPs) ANP, BNP and CNP are highly expressed in lung, suggesting that this organ is an important physiological target for NP signalling. By stimulating vasoand bronchodilation and inhibiting cell proliferation and fibrotic processes, NPs may have therapeutic potential in various lung diseases. Mechanisms responsible for the relatively short half-life (few min) of NPs and the control of their local concentrations include (i) receptor-mediated internalization by the so called clearance receptor (NPR-C) and (ii) degradation by a membrane metalloprotease, called neutral endopeptidase (NEP) or neprilysin [1]. The velocity of peptide degradation/inactivation differs between ANP, BNP and CNP. Interestingly, cleavage of NPs by insulindegrading enzyme (IDE) [2] may have a particular role in NP signalling by generating peptide fragments that are hyperactive in receptor stimulation [3]. The physiological significance of NEP was supported by several studies in rodents showing that NEP inhibition leads to increased NP concentrations and activity. Moreover, we found that NEP inhibition is necessary and sufficient for detection of GC-A and GC-B by affinity labelling experiments with radioactive ANP or CNP in mouse and rat lung membrane preparations. Analogous assays, however, failed to label these receptors in human lung membranes, suggesting potent NP-degrading activity of NEP inhibitor-insensitive proteases. Methods and results ANP degradation by lung membranes in either the absence or presence of NEP inhibitors was analyzed by thin-layer-chromatography and mass spectrometry [2]. We found that NEP inhibition strongly reduces ANP degradation by rat and mouse but not human membranes. ANP-degrading activity in human lung membranes under conditions of NEP inhibition was very potent and even detectable with 1 ng of membrane protein. Like ANP, CNP was rapidly hydrolyzed. In both peptides, initial cleavage occurred at the same position within the conserved peptide ring structure being essential for biological activity. A second cleavage each was localized to the amino-terminus (behind Arg-4 or Lys-4, respectively). The cleavage sites are unrelated to those by NEP and IDE and indicate trypsin-like enzyme activity. Unlike ANP and CNP, BNP is a poor substrate and shows a completely different and complex cleavage pattern after prolonged incubation. The NEP inhibitor-insensitive protease was also detectable, albeit at much lower levels, in membranes from human aorta and mesenteric arteries, but not at all in placenta. Studies with various protease inhibitors revealed that leupeptin exposure potently inhibits NP degradation by this activity.

A novel natriuretic peptide

Background Receptors for the natriuretic peptides (NPs) ANP, BNP and CNP are highly expressed in lung, suggesting that this organ is an important physiological target for NP signalling. By stimulating vasoand bronchodilation and inhibiting cell proliferation and fibrotic processes, NPs may have therapeutic potential in various lung diseases. Mechanisms responsible for the relatively short half-life (few min) of NPs and the control of their local concentrations include (i) receptor-mediated internalization by the so called clearance receptor (NPR-C) and (ii) degradation by a membrane metalloprotease, called neutral endopeptidase (NEP) or neprilysin (1). The velocity of peptide degradation/inactivation differs between ANP, BNP and CNP. Interestingly, cleavage of NPs by insulindegrading enzyme (IDE) (2) may have a particular role in NP signalling by generating peptide fragments that are hyperactive in receptor stimulation (3). The physiological significance of NEP was supported by several studies in rodents showing that NEP inhibition leads to increased NP concentrations and activity. Moreover, we found that NEP inhibition is necessary and sufficient for detection of GC-A and GC-B by affinity labelling experiments with radioactive ANP or CNP in mouse and rat lung membrane preparations. Analogous assays, however, failed to label these receptors in human lung membranes, suggesting potent NP-degrading activity of NEP inhibitor-insensitive proteases.

Maitotoxin-Photoactive Probe Binds to Membrane Proteins in Blood Cells

- The photoactive and biotinylating ligand was prepared from MTX and maleimide-conjugated Hatanaka reagent with use of Diels-Alder reaction. Blood cells were subjected to affinity labelling experiments using the ligand thus obtained. The labelled band on SDS-PAGE was replaced not by MTX but by brevetoxin B (PbTx2), which suggested the presence of binding proteins in blood cells. Screening of polyether compounds for MTX inhibitory activity using Ca 2+ flux assays in C6 cells disclosed that a synthetic fragment of the hydrophilic portion of MTX inhibited the MTX activity.

Regulation of Escherichia coli Polynucleotide Phosphorylase by ATP

Polynucleotide phosphorylase (PNPase), an enzyme conserved in bacteria and eukaryotic organelles, processively catalyzes the phosphorolysis of RNA, releasing nucleotide diphosphates, and the reverse polymerization reaction. In Escherichia coli, both reactions are implicated in RNA decay, as addition of either poly(A) or heteropolymeric tails targets RNA to degradation. PNPase may also be associated with the RNA degradosome, a heteromultimeric protein machine that can degrade highly structured RNA. Here, we report that ATP binds to PNPase and allosterically inhibits both its phosphorolytic and polymerization activities. Our data suggest that PNPase-dependent RNA tailing and degradation occur mainly at low ATP concentrations, whereas other enzymes may play a more significant role at high energy charge. These findings connect RNA turnover with the energy charge of the cell and highlight unforeseen metabolic roles of PNPase.

The 1.3 Å crystal structure of a novel endo‐β‐1,3‐glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96

The 1.3 A crystal structure of a novel endo-b-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96 Guntur Fibriansah, Sumiko Masuda, Naoya Koizumi, Satoshi Nakamura, and Takashi Kumasaka* 1 Department of Life Science, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan 2 Department of Bioengineering, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan

Recognition of Oxidized Thymine Base on the Single-Stranded DNA by Replication Protein A

Replication protein A (RAP) is a eukaryotic single-stranded DNA binding protein involved in DNA replication, repair, and recombination. Recent studies indicate that RPA preferentially binds the damaged sites rather than the undamaged sites. Therefore, RPA is thought to be a member of repair factories or a sensor of lesion on DNA. To obtain further information of behavior of RPA against the oxidized lesion, we studied the binding affinity of RPA for the single-stranded DNA containing 5-formyluracil, a major lesion of thymine base yielded by the oxidation, using several synthetic oligonucleotides. The affinity of RPA for oligonucleotides was determined by gel shift assay. Results suggest that the surrounding sequence of 5-formyluracil may affect the affinity for RPA, and that the 5-formyluracil on the purine stretch but not the pyrimidine stretch increases the affinity for RPA. Results of affinity labeling experiment of RPA with the oligonucleotides containing 5-formyluracil indicate that RPA1 subunit may directly recognize and bind to the 5-formyluracil on the single-stranded DNA.

Metamorphosis of Hydractinia echinata (Cnidaria) is caspase-dependent

Apoptotic cell death plays an important role in many developmental pathways in multicellular animals. Here, we show that metamorphosis in the basal invertebrate Hydractinia echinata (Cnidaria) depends on the activity of caspases, the central enzymes in apoptosis. Caspases are activated during metamorphosis and this activity can be measured with caspase-3 specific fluorogenic substrates. In affinity labelling experiments 23/25 kDa bands were obtained, which represented active caspase. Specific inhibition of caspase activity with caspase-3 inhibitors abolished metamorphosis completely, reversibly and in a dose-dependent manner. This suggests that caspase activity is indispensable for metamorphosis in Hydractinia echinata.

Evidence that annexin II is not a putative membrane receptor for 1alpha,25(OH)2-vitamin D3.

The seco-steroid hormone 1alpha,25(OH)(2)-vitamin D(3) (1,25-D(3)) is known to generate biological responses via both genomic and non-genomic rapid signal transduction pathways. The calcium regulated annexin II/p11 heterotetramer (AII(2)/p11(2)] was proposed by Baran and co-authors to be the membrane receptor responsible for mediating non-genomic, rapid actions of 1,25-D(3), based on ligand affinity labeling, competition, and saturation analysis experiments. Given the cytosolic presence of both the monomeric and heterotetrameric form of AII and their functional regulation by intracellular calcium concentrations, which are known to be affected by 1,25-D(3) rapid, non-genomic activities, we investigated in vitro the affinity of [(3)H]1,25-D(3) for the AII monomer and AII(2)/p11(2) in the absence and presence of calcium using saturation analysis and gel-filtration chromatography. Using two different techniques for separating bound from free ligand (perchlorate and hydroxylapatite (HAP)) over a series of 30 experiments, no evidence for specific binding of [(3)H]1,25-D(3) was obtained with or without the presence of 700 nM exogenous calcium, using either the AII monomer or AII(2)/p11(2). However saturable binding of [(3)H]1,25-D(3) to the lipid raft/caveolae enriched rat intestinal fraction was consistently observed (K(d) = 3.0 nM; B(max) = 45 fmols/mg total protein). AII was detected in lipid raft/caveolae enriched fractions from rat and mouse intestine and ROS 17/2.8 and NB4 cells by Western blot, but incubation in the presence of exogenous calcium did not ablate 1,25-D(3) binding as reported by Baran et al. Our results suggest that AII does not bind 1,25-D(3) in a physiologically relevant manner; however, recent studies linking AII(2)/p11(2) phosphorylation to vesicle fusion and its calcium regulated localization may make AII a possible down-stream substrate for 1,25-D(3) induced rapid cellular effects.

The Voltage-dependent Anion Channel Is the Target for a New Class of Inhibitors of the Mitochondrial Permeability Transition Pore

The relevance of the mitochondrial permeability transition pore (PTP) in Ca2+ homeostasis and cell death has gained wide attention. Yet, despite detailed functional characterization, the structure of this channel remains elusive. Here we report on a new class of inhibitors of the PTP and on the identification of their molecular target. The most potent among the compounds prepared, Ro 68-3400, inhibited PTP with a potency comparable to that of cyclosporin A. Since Ro 68-3400 has a reactive moiety capable of covalent modification of proteins, [3H]Ro 68-3400 was used as an affinity label for the identification of its protein target. In intact mitochondria isolated from rodent brain and liver and in SH-SY5Y human neuroblastoma cells, [3H]Ro 68-3400 predominantly labeled a protein of approximately 32 kDa. This protein was identified as the isoform 1 of the voltage-dependent anion channel (VDAC). Both functional and affinity labeling experiments indicated that VDAC might correspond to the site for the PTP inhibitor ubiquinone0, whereas other known PTP modulators acted at distinct sites. While Ro 68-3400 represents a new useful tool for the study of the structure and function of VDAC and the PTP, the results obtained provide direct evidence that VDAC1 is a component of this mitochondrial pore.

Identification of a high-affinity binding protein for N-acetylchitooligosaccharide elicitor in theplasma membrane from rice leaf and root cells

Presence of a high-affinity binding protein for N-acetylchitooligosaccharide (fragments of chitin) elicitor in the plasma membrane from rice leaf and root cells was shown by affinity labeling experiments with an 125I-labeled N-acetylchitooligosaccharide derivative. Binding studies also showed that binding site in the leaf cells has a high affinity to highly elicitor-active, larger chitin fragments but much lower or no affinity to less elicitor-active or elicitor-inactive oligosaccharides. The amount of the binding protein in the leaf cells was slightly smaller than that in the suspension-cultured cells but much larger compared to that in the root cells. These results indicate the possible- involvement of the elicitor binding protein in the perception of the elicitor signal in intact rice plant.

Location of template on the human ribosome as revealed from data on cross-linking with reactive mRNA analogs.

In this review we summarize data on the location of template on the human ribosome that we obtained from cross-linking (affinity labeling) experiments using reactive mRNA analogs. Types of mRNA analogs, model complexes of these analogs with 80S ribosomes, and methods for analysis of the ribosomal components (proteins and rRNA nucleotides) cross-linked with the mRNA analogs are reviewed. From analysis of the cross-linking data, we suggest a scheme for the arrangement of mRNA on the human ribosome and compare the organization of the mRNA binding center on human and Escherichia coli ribosomes.

Nicotinic receptors at the amino acid level.

nAChRs are pentameric transmembrane proteins into the superfamily of ligand-gated ion channels that includes the 5HT3, glycine, GABAA, and GABAC receptors. Electron microscopy, affinity labeling, and mutagenesis experiments, together with secondary structure predictions and measurements, suggest an all-beta folding of the N-terminal extracellular domain, with the connecting loops contributing to the ACh binding pocket and to the subunit interfaces that mediate the allosteric transitions between conformational states. The ion channel consists of two distinct elements symmetrically organized along the fivefold axis of the molecule: a barrel of five M2 helices, and on the cytoplasmic side five loops contributing to the selectivity filter. The allosteric transitions of the protein underlying the physiological ACh-evoked activation and desensitization possibly involve rigid body motion of the extracellular domain of each subunit, linked to a global reorganization of the transmembrane domain responsible for channel gating.

Molecular and Biochemical Characterization of Lecithin Retinol Acyltransferase

The enzyme responsible for conversion of all-trans-retinol into retinyl esters, the lecithin retinol acyltransferase (LRAT) has been characterized at the molecular level. The cDNA coding for this protein was cloned and its amino acid sequence deduced. LRAT is composed of a polypeptide of 230 amino acid residues with a calculated mass of 25.3 kDa. Tissue distribution analysis by Northern blot showed expression of a 5.0-kilobase transcript in the human retinal pigment epithelium as well as in other tissues that are known for their high LRAT activity and vitamin A processing. Affinity labeling experiments using specific compounds with high affinity for LRAT and monospecific polyclonal antibodies raised in rabbits against two peptide sequences for LRAT confirmed the molecular mass of LRAT as a 25-kDa protein. High performance liquid chromatography analysis of the reaction product formed by HEK-293 cells transfected with LRAT cDNA confirmed the ability of the transfected cells to convert [3H]all-trans-retinol into authentic [3H]all-trans-retinyl palmitate as chemically determined.

Production, Purification and Activity of an Extracellular Depolymerase from Aspergillus fumigatus

A strain of Aspergillus fumigatus, which was observed to rapidly degrade poly-3-hydroxybutyrate (PHB) in a leaf compost, was found to secrete an extracellular hydrolase when grown on PHB as the sole carbon source. Isolation and characterization of the PHB hydrolase (depolymerase) from this fungus revealed that the enzyme had a molecular weight of 57 kDa, an isoelectric point of 7.2, and a PHB hydrolysis activity maxima which occurred at 70°C and pH 8.0. Affinity labeling experiments suggested that this fungal hydrolase is a type of serine esterase. The cyclic trimers of 3-hydroxybutyrate were found to reversibly inhibit the enzymes.

Morphogenetic effects of neuregulin (neu differentiation factor) in cultured epithelial cells.

Neuregulin, or neu differentiation factor, induces cell proliferation or differentiation through interaction with members of the ErbB family of receptor tyrosine kinases. We report that neuregulin can also induce profound morphogenic responses in cultured epithelial cells of different origins. These effects include scattering of small epithelial islands and rearrangement of larger cell islands into ordered ring-shaped arrays with internal lumens. The ring-forming cells are interconnected by cadherin- and beta-catenin-containing adherens junctions. In confluent cultures, neuregulin treatment induces formation of circular lumenlike gaps in the monolayer. Both cell scattering and ring formation are accompanied by a marked increase in cell motility that is independent of hepatocyte growth factor/scatter factor and its receptor (c-Met). Affinity-labeling experiments implied that a combination of ErbB-2 with ErbB-3 mediates the morphogenic signal of neuregulin in gastric cells. Indeed, a similar morphogenic effect could be reconstituted in nonresponsive cells by coexpression of ErbB-2 and -3. We conclude that a heterodimer between the kinase-defective neuregulin receptor, ErbB-3, and the coreceptor, ErbB-2, mediates the morphogenetic action of neuregulin.

The 100-kDa Neurotensin Receptor Is gp95/Sortilin, A Non-G-Protein-coupled Receptor

In this work, the 100-kDa neurotensin (NT) receptor previously purified from human brain by affinity chromatography (Zsürger, N., Mazella, J., and Vincent, J. P. (1994) Brain Res. 639, 245-252) was cloned from a human brain cDNA library. This cDNA encodes a 833-amino acid protein 100% identical to the recently cloned gp95/sortilin and was then designated NT3 receptor-gp95/sortilin. The N terminus of the purified protein is identical to the sequence of the purified gp95/sortilin located immediately after the furin cleavage site. The binding of iodinated NT to 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonic acid-solubilized extracts of COS-7 cells transfected with the cloned cDNA was saturable and reversible with an affinity of 10-15 nM. The localization of the NT3 receptor-gp95/sortilin into intracellular vesicles was in agreement with previous results obtained with the purified receptor and with gp95/sortilin. Affinity labeling and binding experiments showed that the 110-kDa NT3 receptor can be partly transformed into a higher affinity (Kd = 0.3 nM) 100-kDa protein receptor by cotransfection with furin. This 100-kDa NT receptor corresponded to the mature form of the receptor. The NT3/gp95/sortilin protein is the first transmembrane neuropeptide receptor that does not belong to the superfamily of G-protein-coupled receptors.

Probing the Mechanism of Bacillus 1,3-1,4-β-d-Glucan 4-Glucanohydrolases by Chemical Rescue of Inactive Mutants at Catalytically Essential Residues

The role of the key catalytic residues Glu134 and Glu138 in the retaining 1,3-1,4-beta-glucanase from Bacillus licheniformis is probed by a chemical rescue methodology based on enzyme activation of inactive mutants by the action of added nucleophiles. While Glu134 was proposed as the catalytic nucleophile on the basis of affinity labeling experiments, no functional proof supported the assignment of Glu138 as the general acid-base catalyst. Alanine replacements are prepared by site-directed mutagenesis to produce the inactive E138A and E134A mutants. Addition of azide reactivates the mutants in a concentration-dependent manner using an activated 2, 4-dinitrophenyl glycoside substrate. The chemical rescue operates by a different mechanism depending on the mutant as deduced from 1H NMR monitoring and kinetic analysis of enzyme reactivation. E138A yields the beta-glycosyl azide product arising from nucleophilic attack of azide on the glycosyl-enzyme intermediate, thus proving that Glu138 is the general acid-base residue. Azide activates the deglycosylation step (increasing kcat), but it also has a large effect on a previous step (as seen by the large decrease in KM, the increase in kcat/KM, and the pH dependence of activation), probably increasing the rate of glycosylation through Bronsted acid catalysis by enzyme-bound HN3. By contrast, azide reactivates the E134A mutant through a single inverting displacement to give the alpha-glycosyl azide product, consistent with Glu134 being the catalytic nucleophile. Formate as an exogenous nucleophile has no effect on the E138A mutant, whereas it is a better activator of E134A than azide. Although the reaction yields the normal hydrolysis product, a transient compound was detected by 1H NMR, tentatively assigned to the alpha-glycosyl formate adduct. This is the first case where a nonmodified sugar gives a long-lived covalent intermediate that mimics the proposed glycosyl-enzyme intermediate of retaining glycosidases.