Mapping inhibitor binding modes on an active cysteine protease via nuclear magnetic resonance spectroscopy.

Cruzain is a member of the papain/cathepsin L family of cysteine proteases, and the major cysteine protease of the protozoan Trypanosoma cruzi, the causative agent of Chagas disease. We report an autoinduction methodology that provides soluble cruzain in high yields (>30 mg/L in minimal medium). These increased yields provide sufficient quantities of active enzyme for use in nuclear magnetic resonance (NMR)-based ligand mapping. Using circular dichroism and NMR spectroscopy, we also examined the solution-state structural dynamics of the enzyme in complex with a covalently bound vinyl sulfone inhibitor (K777). We report the backbone amide and side chain carbon chemical shift assignments of cruzain in complex with K777. These resonance assignments were used to identify and map residues located in the substrate binding pocket, including the catalytic Cys25 and His162. Selective [(15)N]Cys, [(15)N]His, and [(13)C]Met labeling was performed to quickly assess cruzain-ligand interactions for a set of eight low-molecular weight compounds exhibiting micromolar binding or inhibition. Chemical shift perturbation mapping verified that six of the eight compounds bind to cruzain at the active site. Three different binding modes were delineated for the compounds, namely, covalent, noncovalent, and noninteracting. These results provide examples of how NMR spectroscopy can be used to screen compounds for fast evaluation of enzyme-inhibitor interactions to facilitate lead compound identification and subsequent structural studies.

A reverse binding motif that contributes to specific protease inhibition by antibodies.

The type II transmembrane serine protease family consists of 18 closely related serine proteases that are implicated in multiple functions. To identify selective, inhibitory antibodies against one particular type II transmembrane serine protease, matriptase [MT-SP1 (membrane-type serine protease 1)], a phage display library was created with a natural repertoire of Fabs [fragment antigen binding (Fab)] from human naïve B cells. Fab A11 was identified with a 720 pM inhibition constant and high specificity for matriptase over other trypsin-fold serine proteases. A Trichoderma reesei system expressed A11 with a yield of ∼200 mg/L. The crystal structure of A11 in complex with matriptase has been determined and compared to the crystal structure of another antibody inhibitor (S4) in complex with matriptase. Previously discovered from a synthetic single-chain variable fragment library, S4 is also a highly selective and potent matriptase inhibitor. The crystal structures of the A11/matriptase and S4/matriptase complexes were solved to 2.1 Å and 1.5 Å, respectively. Although these antibodies, discovered from separate libraries, interact differently with the protease surface loops for their specificity, the structures reveal a similar novel mechanism of protease inhibition. Through the insertion of the H3 variable loop in a reverse orientation at the substrate-binding pocket, these antibodies bury a large surface area for potent inhibition and avoid proteolytic inactivation. This discovery highlights the critical role that the antibody scaffold plays in positioning loops to bind and inhibit protease function in a highly selective manner. Additionally, Fab A11 is a fully human antibody that specifically inhibits matriptase over other closely related proteases, suggesting that this approach could be useful for clinical applications.

Inhibitors of SARS-CoV entry--identification using an internally-controlled dual envelope pseudovirion assay.

Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) emerged as the causal agent of an endemic atypical pneumonia, infecting thousands of people worldwide. Although a number of promising potential vaccines and therapeutic agents for SARS-CoV have been described, no effective antiviral drug against SARS-CoV is currently available. The intricate, sequential nature of the viral entry process provides multiple valid targets for drug development. Here, we describe a rapid and safe cell-based high-throughput screening system, dual envelope pseudovirion (DEP) assay, for specifically screening inhibitors of viral entry. The assay system employs a novel dual envelope strategy, using lentiviral pseudovirions as targets whose entry is driven by the SARS-CoV Spike glycoprotein. A second, unrelated viral envelope is used as an internal control to reduce the number of false positives. As an example of the power of this assay a class of inhibitors is reported with the potential to inhibit SARS-CoV at two steps of the replication cycle, viral entry and particle assembly. This assay system can be easily adapted to screen entry inhibitors against other viruses with the careful selection of matching partner virus envelopes.

Idiopathic itch, rash, and urticaria/angioedema merit serum vitamin D evaluation: a descriptive case series.

BACKGROUND: Vitamin D insufficiency is epidemic. Rarely are cutaneous consequences attributed to low vitamin D. METHODS: A retrospective case series of 63 patients describes an association of pruritus, rash, and urticaria/angioedema with low 25-hydroxyvitamin D (25[OH]D <32 ng/mL). The 90% (57/63) of patients with low vitamin D were treated with 8 to 12 weeks of vitamin D 50,000 IU weekly followed by daily supplementation. Concurrent diagnoses were treated routinely. Complete resolution of cutaneous symptoms defined response. RESULTS: Patients were 3 to 80 years of age. The 90% (57/63) with low vitamin D (25[OH]D < 32 ng/mL) had a mean age of 47 (11 to 80) years old, 70% were atopic, and 77% were female. Median duration of idiopathic cutaneous symptoms was 18 months. Mean 25[OH]D was 18.0 ng/mL. With vitamin D treatment 70% (40/57) had complete resolution of symptoms. Mean 25[OH]D for vitamin D responsive patients (16.8 ng/mL) was significantly lower than for vitamin D non-responsive treated patients (20.9 ng/mL, P = 0.02 by unpaired t-Test). Resolution of cutaneous symptoms with vitamin D supplementation occurred in a mean of 4.2 weeks. Symptom recurrence was seen in subsequent months only if vitamin D insufficiency recurred. CONCLUSION: This retrospective case-series, with a 70% (40/57) vitamin D treatment success, suggests that vitamin D status should be assessed in patients with idiopathic cutaneous symptoms. If vitamin D is low, symptom resolution is often possible with oral supplementation of vitamin D. Controlled clinical studies are required to confirm these associations.

A mammalian siderophore synthesized by an enzyme with a bacterial homolog involved in enterobactin production.

Intracellular iron homeostasis is critical for survival and proliferation. Lipocalin 24p3 is an iron-trafficking protein that binds iron through association with a bacterial siderophore, such as enterobactin, or a postulated mammalian siderophore. Here, we show that the iron-binding moiety of the 24p3-associated mammalian siderophore is 2,5-dihydroxybenzoic acid (2,5-DHBA), which is similar to 2,3-DHBA, the iron-binding component of enterobactin. We find that the murine enzyme responsible for 2,5-DHBA synthesis, BDH2, is the homolog of bacterial EntA, which catalyzes 2,3-DHBA production during enterobactin biosynthesis. RNA interference-mediated knockdown of BDH2 results in siderophore depletion. Mammalian cells lacking the siderophore accumulate abnormally high amounts of cytoplasmic iron, resulting in elevated levels of reactive oxygen species, whereas the mitochondria are iron deficient. Siderophore-depleted mammalian cells and zebrafish embryos fail to synthesize heme, an iron-dependent mitochondrial process. Our results reveal features of intracellular iron homeostasis that are conserved from bacteria through humans.

Antagonistic anti-urokinase plasminogen activator receptor (uPAR) antibodies significantly inhibit uPAR-mediated cellular signaling and migration.

Interactions between urokinase plasminogen activator receptor (uPAR) and its various ligands regulate tumor growth, invasion, and metastasis. Antibodies that bind specific uPAR epitopes may disrupt these interactions, thereby inhibiting these processes. Using a highly diverse and naïve human fragment of the antigen binding (Fab) phage display library, we identified 12 unique human Fabs that bind uPAR. Two of these antibodies compete against urokinase plasminogen activator (uPA) for uPAR binding, whereas a third competes with beta1 integrins for uPAR binding. These competitive antibodies inhibit uPAR-dependent cell signaling and invasion in the non-small cell lung cancer cell line, H1299. Additionally, the integrin-blocking antibody abrogates uPAR/beta1 integrin-mediated H1299 cell adhesion to fibronectin and vitronectin. This antibody and one of the uPAR/uPA antagonist antibodies shows a significant combined effect in inhibiting cell invasion through Matrigel/Collagen I or Collagen I matrices. Our results indicate that these antagonistic antibodies have potential for the detection and treatment of uPAR-expressing tumors.

Mycobacterium tuberculosis MycP1 protease plays a dual role in regulation of ESX-1 secretion and virulence.

Mycobacterium tuberculosis uses the ESX-1 secretion system to deliver virulence proteins during infection of host cells. Here we report a mechanism of posttranscriptional control of ESX-1 mediated by MycP1, a M. tuberculosis serine protease. We show that MycP1 is required for ESX-1 secretion but that, unexpectedly, genetic inactivation of MycP1 protease activity increases secretion of ESX-1 substrates. We demonstrate that EspB, an ESX-1 substrate required for secretion, is a target of MycP1 in vitro and in vivo. During macrophage infection, an inactive MycP1 protease mutant causes hyperactivation of ESX-1-stimulated innate signaling pathways. MycP1 is required for growth in mice during acute infection, while loss of its protease activity leads to attenuated virulence during chronic infection. As the key ESX-1 substrates ESAT-6 and CFP-10 are highly immunogenic, fine-tuning of their secretion by MycP1 may balance virulence and immune detection and be essential for successful maintenance of long-term M. tuberculosis infection.

Seasonal inhalant insect allergy: Harmonia axyridis ladybug.

PURPOSE OF REVIEW: The exotic Asian lady beetle, Harmonia axyridis, has become a prominent cause of seasonal inhalant allergy (allergic rhinitis, asthma, and urticaria) in the last two decades in North America and Europe after being introduced into the environment as an agricultural pest-control predator. RECENT FINDINGS: Seeking winter hibernation sites, ladybug swarms will invade human habitats in the fall. Large fall swarms and smaller spring dispersions produce corresponding peaks in ladybug allergy. Ladybug allergy prevalence in endemic areas has been reported as high as 10%. For some individuals ladybug allergy is their first expression of allergic disease. Exposures at home, work, school, and in other settings may be sensitizing. Ladybug hemolymph is the primary source of allergens. Har a 1 and Har a 2 major ladybug allergens have been characterized. 'Reflex bleeding' from tibiofemoral joints (for communication and during alarm) disperses these allergens. SUMMARY: Ladybug skin testing should be routine in endemic areas. Avoidance continues to be the first step in treatment. Allergen vaccine therapy may be effective, but a commercial extract of H. axyridis is needed.

Characterization of a multimeric, eukaryotic prolyl aminopeptidase: an inducible and highly specific intracellular peptidase from the non-pathogenic fungus Talaromyces emersonii.

Fungi are capable of degrading proteins in their environment by secreting peptidases. However, the link between extracellular digestion and intracellular proteolysis has scarcely been investigated. Mycelial lysates of the filamentous fungus Talaromyces emersonii were screened for intracellular peptidase production. Five distinct proteolytic activities with specificity for the p-nitroanilide (pNA) peptides Suc-AAPF-pNA, Suc-AAA-pNA, K-pNA, F-pNA and P-pNA were identified. The native enzyme responsible for the removal of N-terminal proline residues was purified to homogeneity by ammonium sulfate fractionation followed by five successive chromatographic steps. The enzyme, termed Talaromyces emersonii prolyl aminopeptidase (TePAP), displayed a 50-fold specificity for cleaving N-terminal Pro-X (k(cat)/K(m)=2.1 x 10(6) M(-1) s(-1)) compared with Ala-X or Val-X bonds. This intracellular aminopeptidase was optimally active at pH 7.4 and 50 degrees C. Peptide sequencing facilitated the design of degenerate oligonucleotides from homologous sequences encoding putative fungal proline aminopeptidases, enabling subsequent cloning of the gene. TePAP was shown to be relatively uninhibited by classical serine peptidase inhibitors and to be sensitive to selected cysteine- and histidine-modifying reagents, yet gene sequence analysis identified the protein as a serine peptidase with an alpha/beta hydrolase fold. Northern analysis indicated that Tepap mRNA levels were regulated by the composition of the growth medium. Highest Tepap transcript levels were observed when the fungus was grown in medium containing glucose and the protein hydrolysate casitone. Interestingly, both the induction profile and substrate preference of this enzyme suggest potential co-operativity between extracellular and intracellular proteolysis in this organism. Gel filtration chromatography suggested that the enzyme exists as a 270 kDa homo-hexamer, whereas most bacterial prolyl aminopeptidases (PAPs) are monomers. Phylogenetic analysis of known PAPs revealed two diverse subfamilies that are distinguishable on the basis of primary and secondary structure and appear to correlate with the subunit composition of the native enzymes. Sequence comparisons revealed that PAPs with key conserved topological features are widespread in bacterial and fungal kingdoms, and this study identified many putative PAP candidates within sequenced genomes. This work represents, to our knowledge, the first detailed biochemical and molecular analysis of an inducible PAP from a eukaryote and the first intracellular peptidase isolated from the thermophilic fungus T. emersonii.

Inhibition of a secreted glutamic peptidase prevents growth of the fungus Talaromyces emersonii.

The thermophilic filamentous fungus Talaromyces emersonii secretes a variety of hydrolytic enzymes that are of interest for processing of biomass into fuel. Many carbohydrases have been isolated and characterized from this fungus, but no studies had been performed on peptidases. In this study, two acid-acting endopeptidases were isolated and characterized from the culture filtrate of T. emersonii. One of these enzymes was identified as a member of the recently classified glutamic peptidase family and was subsequently named T. emersonii glutamic peptidase 1 (TGP1). The second enzyme was identified as an aspartyl peptidase (PEP1). TGP1 was cloned and sequenced and shown to exhibit 64 and 47% protein identity to peptidases from Aspergillus niger and Scytalidium lignocolum, respectively. Substrate profiling of 16 peptides determined that TGP1 has broad specificity with a preference for large residues in the P1 site, particularly Met, Gln, Phe, Lys, Glu, and small amino acids at P1' such as Ala, Gly, Ser, or Thr. This enzyme efficiently cleaves an internally quenched fluorescent substrate containing the zymogen activation sequence (k(cat)/K(m)=2 x 10(5) m(-1) s(-1)). Maximum hydrolysis occurs at pH 3.4 and 50 degrees C. The reaction is strongly inhibited by a transition state peptide analog, TA1 (K(i)=1.5 nM), as well as a portion of the propeptide sequence, PT1 (K(i)=32 nM). Ex vivo studies show that hyphal extension of T. emersonii in complex media is unaffected by the aspartyl peptidase inhibitor pepstatin but is inhibited by TA1 and PT1. This study provides insight into the functional role of the glutamic peptidase TGP1 for growth of T. emersonii.

Harmonia axyridis ladybug invasion and allergy.

Beginning in 1916 Harmonia axyridis, an orange/red lady beetle with variable black spotting, was imported into the United States from Asia. This agricultural pest-control predator established independent feral populations in North America by 1988. Subsequently, Harmonia axyridis has become a pest to homeowners and various horticultural enterprises. Seeking winter hibernation sites, ladybug swarms invade human homes/habitats primarily in the fall. With increased Harmonia axyridis exposures, human ladybug allergy was first reported in 1998. Ladybug-specific IgE hypersensitivity has been reported in all ages (1-78 years old) and both sexes. Clinical ladybug allergy manifests variously as rhinoconjunctivitis, asthma, urticaria, and angioedema. A majority, but not all, allergic individuals are primarily exposed at home. Large fall swarms and smaller spring dispersions produce corresponding peaks in ladybug allergy. Ladybug hemolymph is a primary source of allergen. Har a 1 and Har a 2 major ladybug allergens have been characterized. Ladybug allergy prevalence in one endemic area was reported as 10%. Self-report of ladybug pests at home did not predict ladybug allergy, suggesting other exposures are important also. Some individuals have no history of atopy before manifestation of ladybug allergy. Ladybug, cat, cockroach, and house-dust mites are the most likely allergens to present as isolated single positive skin tests in an allergist's office. Ladybug should be a standard skin test allergen for all allergy patients tested in endemic areas. Avoidance of ladybug exposure is paramount to treatment.

Substrate modulation of enzyme activity in the herpesvirus protease family.

The herpesvirus proteases are an example in which allosteric regulation of an enzyme activity is achieved through the formation of quaternary structure. Here, we report a 1.7 A resolution structure of Kaposi's sarcoma-associated herpesvirus protease in complex with a hexapeptide transition state analogue that stabilizes the dimeric state of the enzyme. Extended substrate binding sites are induced upon peptide binding. In particular, 104 A2 of surface are buried in the newly formed S4 pocket when tyrosine binds at this site. The peptide inhibitor also induces a rearrangement of residues that stabilizes the oxyanion hole and the dimer interface. Concomitant with the structural changes, an increase in catalytic efficiency of the enzyme results upon extended substrate binding. A nearly 20-fold increase in kcat/KM results upon extending the peptide substrate from a tetrapeptide to a hexapeptide exclusively due to a KM effect. This suggests that the mechanism by which herpesvirus proteases achieve their high specificity is by using extended substrates to modulate both the structure and activity of the enzyme.

Harmonia axyridis ladybug hypersensitivity in clinical allergy practice.

The imported Harmonia axyridis ladybug infests homes in northern West Virginia from fall through spring, causing allergic disease. Retrospective single-practice chart reviews were performed: (1) all skin prick tests (1400 included ladybug) in a community allergy practice over 4 years and (2) clinical analysis of 400 randomly chosen patients. The usual adult aeroallergen skin test panel included ladybug and 57 other allergens. Statistics used were contingency table analyses and the kappa-statistic for concordance. Home infestation with ladybugs was most common in rural areas but did not predict ladybug sensitization (kappa = -0.02). Ladybug sensitization and allergy occurred at all ages. Ladybug sensitization occurred with 21% frequency compared with cat at 24% frequency, cockroach at 27% frequency, and dust mites at 40% frequency. Only ladybug showed a significant (p < 0.0001) skin test sensitization decreasing from rural (30%), mixed (21%), to urban (16%) home demographics. Isolated single-positive skin tests constituted 10% of dust mites, 6% of cockroach, 6% of ladybug, and 4% of cat-positive skin tests. Skin test concordance was strongest between the pairs: ladybug-cockroach (kappa = 0.36), cockroach-dust mite (kappa = 0.29), and dust mite-cat (kappa = 0.25). Ladybug is a major allergen in endemic areas, causing rhinoconjunctivitis (8% prevalence), asthma (2% prevalence), and urticaria (1% prevalence). Ladybug skin test sensitization is more common in rural areas and is comparable in frequency and age distribution with cat and cockroach. Cockroach and ladybug have a high degree of skin test concordance. A quality commercial ladybug allergen extract and increased ladybug allergen research are needed.

Cross-reactivity among edible nuts: double immunodiffusion, crossed immunoelectrophoresis, and human specific igE serologic surveys.

BACKGROUND: As many as one third of all food allergen anaphylactic events are related to tree nut ingestion. Although concurrent allergen sensitivity to tree nuts is common, cross-reactivity among nut antigens is less well defined. OBJECTIVE: To survey serologic cross-reactivities among 7 tree nuts (walnut, pecan, hazelnut, cashew, Brazil nut, pistachio, and almond) and peanut. METHODS: Human specific IgE enzyme-linked immunosorbent assay inhibition was used to identify nut allergen cross-reactivities. Single-nut rabbit antisera were used in double immunodiffusion, crossed-line immunoelectrophoresis, and crossed immunoelectrophoresis with intermediate gel studies of nut antigen cross-reactivity. RESULTS: Nut specific IgE enzyme-linked immunosorbent assay inhibition demonstrated no cross-reactivities between peanut and tree nuts. Among tree nuts, 2 groups with allergen cross-reactivity were defined: (1) walnut, pecan, and hazelnut and (2) hazelnut, cashew, Brazil nut, pistachio, and almond. Double immunodiffusion, crossed-line immunoelectrophoresis, and crossed immunoelectrophoresis with intermediate gel results supported the same groupings of cross-reactive tree nuts and identified several less prominent nut-nut antigen cross-reactivities between groups and with peanut. CONCLUSION: With few exceptions (notably limited peanut cross-reactivity with pistachio and walnut), peanut antigens did not serologically cross-react with tree nuts. Walnut, pecan, and hazelnut form a group of strongly cross-reactive tree nuts. Hazelnut, cashew, Brazil nut, pistachio, and almond form a group of moderately cross-reactive tree nuts. Cross-reactivities between these groups are less pronounced (notably limited cross-reactivity of walnut and pecan with Brazil nut). The strongest cross-reactivities among tree nuts follow botanical family associations: (1) walnut and pecan in the family Juglandaceae and (2) cashew and pistachio in the family Anacardiaceae.

Gene expression pattern in hepatic stem/progenitor cells during rat fetal development using complementary DNA microarrays.

To identify new and differentially expressed genes in rat fetal liver epithelial stem/progenitor cells during their proliferation, lineage commitment, and differentiation, we used a high throughput method-mouse complementary DNA (cDNA) microarrays-for analysis of gene expression. The gene expression pattern of rat hepatic cells was studied during their differentiation in vivo: from embryonic day (ED) 13 until adulthood. The differentially regulated genes were grouped into two clusters: a cluster of up-regulated genes comprised of 281 clones and a cluster of down-regulated genes comprised of 230 members. The expression of the latter increased abruptly between ED 16 and ED 17. Many of the overexpressed genes from the first cluster fall into distinct, differentially expressed functional groups: genes related to development, morphogenesis, and differentiation; calcium- and phospholipid-binding proteins and signal transducers; and cell adhesion, migration, and matrix proteins. Several other functional groups of genes that are initially down-regulated, then increase during development, also emerged: genes related to inflammation, blood coagulation, detoxification, serum proteins, amino acids, lipids, and carbohydrate metabolism. Twenty-eight genes overexpressed in fetal liver that were not detected in adult liver are suggested as potential markers for identification of liver progenitor cells. In conclusion, our data show that the gene expression program of fetal hepatoblasts differs profoundly from that of adult hepatocytes and that it is regulated in a specific manner with a major switch at ED 16 to 17, marking a dramatic change in the gene expression program during the transition of fetal liver progenitor cells from an undifferentiated to a differentiated state. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html).

The oligomeric structure of human granzyme A is a determinant of its extended substrate specificity.

The cell death-inducing serine protease granzyme A (GzmA) has a unique disulfide-linked quaternary structure. The structure of human GzmA bound to a tripeptide CMK inhibitor, determined at a resolution of 2.4 A, reveals that the oligomeric state contributes to substrate selection by limiting access to the active site for potential macromolecular substrates and inhibitors. Unlike other serine proteases, tetrapeptide substrate preferences do not correlate well with natural substrate cleavage sequences. This suggests that the context of the cleavage sequence within a macromolecular substrate imposes another level of selection not observed with the peptide substrates. Modeling of inhibitors bound to the GzmA active site shows that the dimer also contributes to substrate specificity in a unique manner by extending the active-site cleft. The crystal structure, along with substrate library profiling and mutagenesis, has allowed us to identify and rationally manipulate key components involved in GzmA substrate specificity.

The neutrophil lipocalin NGAL is a bacteriostatic agent that interferes with siderophore-mediated iron acquisition.

First identified as a neutrophil granule component, neutrophil gelatinase-associated lipocalin (NGAL; also called human neutrophil lipocalin, 24p3, uterocalin, or neu-related lipocalin) is a member of the lipocalin family of binding proteins. Putative NGAL ligands, including neutrophil chemotactic agents such as N-formylated tripeptides, have all been refuted by recent biochemical and structural results. NGAL has subsequently been implicated in diverse cellular processes, but without a characterized ligand, the molecular basis of these functions remained mysterious. Here we report that NGAL tightly binds bacterial catecholate-type ferric siderophores through a cyclically permuted, hybrid electrostatic/cation-pi interaction and is a potent bacteriostatic agent in iron-limiting conditions. We therefore propose that NGAL participates in the antibacterial iron depletion strategy of the innate immune system.