Search tips
Search criteria

Results 1-25 (26)

Clipboard (0)

Select a Filter Below

Year of Publication
more »
1.  Active Site and Remote Contributions to Catalysis in Methylthioadenosine Nucleosidases 
Biochemistry  2015;54(15):2520-2529.
5′-Methylthioadenosine/S-adenosyl-L-homocysteine nucleosidases (MTANs) catalyze the hydrolysis of 5′-methylthioadenosine to adenine and 5-methylthioribose. The amino acid sequences of the MTANs from Vibrio cholerae (VcMTAN) and Escherichia coli (EcMTAN) are 60% identical and 75% similar. Protein structure folds and kinetic properties are similar. However, binding of transition-state analogues is dominated by favorable entropy in VcMTAN and by enthalpy in EcMTAN. Catalytic sites of VcMTAN and EcMTAN in contact with reactants differ by two residues; Ala113 and Val153 in VcMTAN are Pro113 and Ile152, respectively, in EcMTAN. We mutated the VcMTAN catalytic site residues to match those of EcMTAN in anticipation of altering its properties toward EcMTAN. Inhibition of VcMTAN by transition-state analogues required filling both active sites of the homodimer. However, in the Val153Ile mutant or double mutants, transition-state analogue binding at one site caused complete inhibition. Therefore, a single amino acid, Val153, alters the catalytic site cooperativity in VcMTAN. The transition-state analogue affinity and thermodynamics in mutant VcMTAN became even more unlike those of EcMTAN, the opposite of expectations from catalytic site similarity; thus, catalytic site contacts in VcMTAN are unable to recapitulate the properties of EcMTAN. X-ray crystal structures of EcMTAN, VcMTAN, and a multiple-site mutant of VcMTAN most closely resembling EcMTAN in catalytic site contacts show no major protein conformational differences. The overall protein architectures of these closely related proteins are implicated in contributing to the catalytic site differences.
PMCID: PMC4485437  PMID: 25806409
3.  HMG-CoA Reductase Inhibitors Inhibit Endothelial Exocytosis and Decrease Myocardial Infarct Size 
Circulation research  2005;96(11):1185-1192.
HMG-CoA reductase inhibitors protect the vasculature from inflammation and atherosclerosis by cholesterol dependent and cholesterol independent mechanisms. We hypothesized that HMG-CoA reductase inhibitors decrease exocytosis of Weibel-Palade bodies, endothelial cell granules whose contents promote thrombosis and vascular inflammation. We pre-treated human aortic endothelial cells with simvastatin for 24 h, then stimulated the cells with thrombin, and measured the amount of vWF released into the media. We then measured the effect of simvastatin upon myocardial infarction in mice. Simvastatin decreased thrombin-stimulated Weibel-Palade body exocytosis by 89%. Simvastatin inhibited exocytosis in part by increasing synthesis of nitric oxide (NO), which S-nitrosylated N-ethylmaleimide sensitive factor (NSF), a critical regulator of exocytosis. Simvastatin treatment attenuated myocardial infarct size by 58% in wild-type but not eNOS knockout mice. Furthermore, simvastatin decreased endothelial exocytosis and neutrophil infiltration into ischemic-reperfused myocardium, which was mediated in part by P-selectin contained in Weibel-Palade bodies. However, simvastatin did not affect exocytosis and inflammation in myocardial infarcts of eNOS knockout mice. Inhibition of endothelial exocytosis is a novel mechanism by which HMG-CoA reductase inhibitors may reduce vascular inflammation, inhibit thrombosis, and protect the ischemic myocardium. These findings may explain part of the pleiotropic effects of statin therapy for patients with cardiovascular disease.
PMCID: PMC4002762  PMID: 15905463
Endothelium; Nitric Oxide; Myocardial Infarction; Hypercholesterolemia
4.  Ambient fine particulate air pollution triggers ST-elevation myocardial infarction, but not non-ST elevation myocardial infarction: a case-crossover study 
We and others have shown that increases in particulate air pollutant (PM) concentrations in the previous hours and days have been associated with increased risks of myocardial infarction, but little is known about the relationships between air pollution and specific subsets of myocardial infarction, such as ST-elevation myocardial infarction (STEMI) and non ST-elevation myocardial infarction (NSTEMI).
Using data from acute coronary syndrome patients with STEMI (n = 338) and NSTEMI (n = 339) and case-crossover methods, we estimated the risk of STEMI and NSTEMI associated with increased ambient fine particle (<2.5 um) concentrations, ultrafine particle (10-100 nm) number concentrations, and accumulation mode particle (100-500 nm) number concentrations in the previous few hours and days.
We found a significant 18% increase in the risk of STEMI associated with each 7.1 μg/m3 increase in PM2.5 concentration in the previous hour prior to acute coronary syndrome onset, with smaller, non-significantly increased risks associated with increased fine particle concentrations in the previous 3, 12, and 24 hours. We found no pattern with NSTEMI. Estimates of the risk of STEMI associated with interquartile range increases in ultrafine particle and accumulation mode particle number concentrations in the previous 1 to 96 hours were all greater than 1.0, but not statistically significant. Patients with pre-existing hypertension had a significantly greater risk of STEMI associated with increased fine particle concentration in the previous hour than patients without hypertension.
Increased fine particle concentrations in the hour prior to acute coronary syndrome onset were associated with an increased risk of STEMI, but not NSTEMI. Patients with pre-existing hypertension and other cardiovascular disease appeared particularly susceptible. Further investigation into mechanisms by which PM can preferentially trigger STEMI over NSTEMI within this rapid time scale is needed.
PMCID: PMC3891992  PMID: 24382024
Myocardial infarction; Acute coronary syndrome; Epidemiology; Air pollution
5.  Comparison of a High-Throughput High-Content Intracellular Leishmania donovani Assay with an Axenic Amastigote Assay 
Visceral leishmaniasis is a neglected tropical disease with significant health impact. The current treatments are poor, and there is an urgent need to develop new drugs. Primary screening assays used for drug discovery campaigns have typically used free-living forms of the Leishmania parasite to allow for high-throughput screening. Such screens do not necessarily reflect the physiological situation, as the disease-causing stage of the parasite resides inside human host cells. Assessing the drug sensitivity of intracellular parasites on scale has recently become feasible with the advent of high-content screening methods. We describe here a 384-well microscopy-based intramacrophage Leishmania donovani assay and compare it to an axenic amastigote system. A panel of eight reference compounds was tested in both systems, as well as a human counterscreen cell line, and our findings show that for most clinically used compounds both axenic and intramacrophage assays report very similar results. A set of 15,659 diverse compounds was also screened using both systems. This resulted in the identification of seven new antileishmanial compounds and revealed a high false-positive rate for the axenic assay. We conclude that the intramacrophage assay is more suited as a primary hit-discovery platform than the current form of axenic assay, and we discuss how modifications to the axenic assay may render it more suitable for hit-discovery.
PMCID: PMC3697379  PMID: 23571538
6.  Historical data and modern methods reveal insights in measles epidemiology: a retrospective closed cohort study 
BMJ Open  2013;3(1):e002033.
Measles was endemic in England during the early 1800s; however, it did not arrive in Australia until 1850 whereas other infectious diseases were known to have arrived much earlier—many with the First Fleet in 1788—leading to the question of why there was a difference.
Ships surgeons’ logbooks from historical archives, 1829–1882, were retrospectively reviewed for measles outbreak data. Infectious disease modelling techniques were applied to determine whether ships would reach Australia with infectious measles cases.
Historical ship surgeon logbooks of measles outbreaks occurring on journeys from Britain to Australia were examined to provide new insights into measles epidemiology.
Primary and secondary outcome measures
Serial intervals and basic reproduction numbers (R0), immunity, outbreak generations, age-distribution, within-family transmission and outbreak lengths for measles within these closed cohorts.
Five measles outbreaks were identified (163 cases). The mean serial interval (101 cases) was 12.3 days (95% CI 12.1 to 12.5). Measles R0 (95 cases) ranged from 7.7–10.9. Immunity to measles was lowest among children ≤10 years old (range 37–42%), whereas 94–97% of adults appeared immune. Outbreaks ranged from 4–6 generations and, before 1850, were 41 and 38 days in duration. Two outbreaks after 1850 lasted longer than 70 days and one lasted 32 days.
Measles syndrome reporting in a ship surgeon's logs provided remarkable detail on prevaccination measles epidemiology in the closed environment of ship voyages. This study found lower measles R0 and a shorter mean clinical serial interval than is generally reported. Archival ship surgeon log books indicate it was unlikely that measles was introduced into Australia before 1850, owing to high levels of pre-existing immunity in ship passengers, low numbers of travelling children and the journey's length from England to Australia.
PMCID: PMC3549217  PMID: 23315518
Epidemiology; Infectious Diseases
8.  Control of directional change after mechanical stimulation in Drosophila 
Molecular Brain  2012;5:39.
Proper adjustment of moving direction after external mechanical stimulation is essential for animals to avoid danger (e.g. predators), and thus is vital for survival. This process involves sensory inputs, central processing and motor outputs. Recent studies have made considerable progress in identifying mechanosensitive neurons and mechanosensation receptor proteins. Our understandings of molecular and cellular mechanisms that link mechanosensation with the changes in moving direction, however, remain limited.
In this study, we investigate the control of movement adjustment in Drosophila. In response to gentle touch at the anterior segments, Drosophila larvae reorient and select a new direction for forward movement. The extent of change in moving direction is correlated with the intensity of tactile stimuli. Sensation of gentle touch requires chordotonal organs and class IV da neurons. Genetic analysis indicates an important role for the evolutionarily conserved immunoglobulin (Ig) superfamily protein Turtle (Tutl) to regulate touch-initiated directional change. Tutl is required specifically in post-mitotic neurons at larval stage after the completion of embryonic development. Circuit breaking analysis identified a small subset of Tutl-positive neurons that are involved in the adjustment of moving direction.
We identify Tutl and a small subset of CNS neurons in modulating directional change in response to gentle touch. This study presents an excellent starting point for further dissection of molecular and cellular mechanisms controlling directional adjustment after mechanical stimulation.
PMCID: PMC3514245  PMID: 23107101
10.  The crystal structure of Leishmania major N5,N10-methylenetetrahydrofolate dehydrogenase/cyclohydrolase and assessment of a potential drug target☆ 
Molecular and Biochemical Parasitology  2012;181(2-6):178-185.
Graphical abstract
The crystal structure of Leishmania major N5,N10-methylenetetrahydrofolate dehydrogenase/N5,N10-methenyltetrahydrofolate cyclohydrolase is used to assess the potential of this bifunctional enzyme as a drug target.
► We report the structure of Leishmania major methylenetetrahydrofolate dehydrogenase/cyclohydrolase. ► Sequence–structure comparisons are carried out with homologues from kinetoplastids and the human host. ► The potential of this bifunctional enzyme as a drug target is assessed. ► The similarities between parasite and human enzymes suggest a difficult target for drug discovery.
Three enzyme activities in the protozoan Leishmania major, namely N5,N10-methylenetetrahydrofolate dehydrogenase/N5,N10-methenyltetrahydrofolate cyclohydrolase (DHCH) and N10-formyltetrahydrofolate ligase (FTL) produce the essential intermediate N10-formyltetrahydrofolate. Although trypanosomatids possess at least one functional DHCH, the same is not true for FTL, which is absent in Trypanosoma brucei. Here, we present the 2.7 Å resolution crystal structure of the bifunctional apo-DHCH from L. major, which is a potential drug target. Sequence alignments show that the cytosolic enzymes found in trypanosomatids share a high level of identity of approximately 60%. Additionally, residues that interact and participate in catalysis in the human homologue are conserved amongst trypanosomatid sequences and this may complicate attempts to derive potent, parasite specific DHCH inhibitors.
PMCID: PMC3368264  PMID: 22108435
Antifolate; Cyclohydrolase; Dehydrogenase; Drug target; Leishmania; Trypanosoma
11.  Drosophila and mammalian models uncover a role for the myoblast fusion gene TANC1 in rhabdomyosarcoma  
Rhabdomyosarcoma (RMS) is a malignancy of muscle myoblasts, which fail to exit the cell cycle, resist terminal differentiation, and are blocked from fusing into syncytial skeletal muscle. In some patients, RMS is caused by a translocation that generates the fusion oncoprotein PAX-FOXO1, but the underlying RMS pathogenetic mechanisms that impede differentiation and promote neoplastic transformation remain unclear. Using a Drosophila model of PAX-FOXO1–mediated transformation, we show here that mutation in the myoblast fusion gene rolling pebbles (rols) dominantly suppresses PAX-FOXO1 lethality. Further analysis indicated that PAX-FOXO1 expression caused upregulation of rols, which suggests that Rols acts downstream of PAX-FOXO1. In mammalian myoblasts, gene silencing of Tanc1, an ortholog of rols, revealed that it is essential for myoblast fusion, but is dispensable for terminal differentiation. Misexpression of PAX-FOXO1 in myoblasts upregulated Tanc1 and blocked differentiation, whereas subsequent reduction of Tanc1 expression to native levels by RNAi restored both fusion and differentiation. Furthermore, decreasing human TANC1 gene expression caused RMS cancer cells to lose their neoplastic state, undergo fusion, and form differentiated syncytial muscle. Taken together, these findings identify misregulated myoblast fusion caused by ectopic TANC1 expression as a RMS neoplasia mechanism and suggest fusion molecules as candidates for targeted RMS therapy.
PMCID: PMC3248305  PMID: 22182840
12.  5-Chloro-6-hy­droxy-7,8-dimethyl­chroman-2-one 
In the title mol­ecule, C11H11ClO3, the fused pyran ring adopts a half-chair conformation. In the crystal, inter­molecular O—H⋯O hydrogen bonds link mol­ecules into chains along [100]. These chains are inter­connected by weak inter­molecular C—H⋯O contacts which generate R 2 2(8) ring motifs, forming sheets parallel to (001). Tetra­gonal symmetry generates an equivalent motif along b. Furthermore, the sheets are linked along the c axis by offset π–π stacking inter­actions involving the benzene rings of adjacent mol­ecules [with centroid–centroid distances of 3.839 (2) Å], together with an additional weak C—H⋯O hydrogen bond, resulting in an overall three-dimensional network.
PMCID: PMC3213581  PMID: 22091158
13.  Molecular mechanisms of tiling and self-avoidance in neural development 
Molecular Brain  2010;3:28.
Recent studies have begun to unravel the molecular basis of tiling and self-avoidance, two important cellular mechanisms that shape neuronal circuitry during development in both invertebrates and vertebrates. Dscams and Turtle (Tutl), two Ig superfamily proteins, have been shown to mediate contact-dependent homotypic interactions in tiling and self-avoidance. By contrast, the Activin pathway regulates axonal tiling in a contact-independent manner. These cell surface signals may directly or indirectly regulate the activity of the Tricornered kinase pathway and/or other intracellular signaling pathways to prevent the overlap between same-type neuronal arbors in the sensory or synaptic input field.
PMCID: PMC2959082  PMID: 20937126
14.  Structure of Staphylococcus aureus adenylo­succinate lyase (PurB) and assessment of its potential as a target for structure-based inhibitor discovery 
The 2.5 Å resolution structure of S. aureus adenylosuccinate lyase is reported and compared with those of orthologues to assess its potential as a template for early stage drug discovery. AMP and a putative assignment of oxalate, the latter an artefact possibly arising from an impurity in the PEG used for crystallization, occupy the active site.
The medium-resolution structure of adenylosuccinate lyase (PurB) from the bacterial pathogen Staphylococcus aureus in complex with AMP is presented. Oxalate, which is likely to be an artifact of crystallization, has been modelled in the active site and occupies a position close to that where succinate is observed in orthologous structures. PurB catalyzes reactions that support the provision of purines and the control of AMP/fumarate levels. As such, the enzyme is predicted to be essential for the survival of S. aureus and to be a potential therapeutic target. Comparisons of this pathogen PurB with the enzyme from Escherichia coli are presented to allow discussion concerning the enzyme mechanism. Comparisons with human PurB suggest that the close similarity of the active sites would make it difficult to identify species-specific inhibitors for this enyme. However, there are differences in the way that the subunits are assembled into dimers. The distinct subunit–subunit interfaces may provide a potential area to target by exploiting the observation that creation of the enzyme active site is dependent on oligomerization.
PMCID: PMC2917274  PMID: 20693687
adenylosuccinate lyase; AMP; oxalate; purine biosynthesis; purine cycle
15.  unc-3-dependent repression of specific motor neuron fates in Caenorhabditis elegans 
Developmental biology  2008;323(2):207-215.
unc-3 encodes the C. elegans ortholog of the Olf-1/Early B cell factor family of transcription factors, which in vertebrates regulate development and differentiation of B lymphocytes, adipocytes, and cells of the nervous system. unc-3 mutants are uncoordinated in locomotion. Here we show that unc-3 represses a VC-like motor neuron program in the VA and VB motor neurons, which in wild-type animals control backwards and forwards locomotion, respectively. We identify a physical interaction between UNC-3 and the C2H2 zinc finger transcription factor PAG-3, the mammalian homologs of which are coexpressed in olfactory epithelium and hematopoietic cells. Our data explain the locomotory defects of unc-3 mutants and suggest that interactions between unc-3 and pag-3 orthologs in other species may be functionally important.
PMCID: PMC2590940  PMID: 18817768
motor neuron fate; unc-3; pag-3; olf-1; Ebf-1; Gfi-1
16.  Community Management of Endemic Scabies in Remote Aboriginal Communities of Northern Australia: Low Treatment Uptake and High Ongoing Acquisition 
Scabies and skin infections are endemic in many Australian Aboriginal communities. There is limited evidence for effective models of scabies treatment in high prevalence settings. We aimed to assess the level of treatment uptake amongst clinically diagnosed scabies cases and amongst their household contacts. In addition, we aimed to determine the likelihood of scabies acquisition within these households over the 4 weeks following treatment provision.
Methods and Findings
We conducted an observational study of households in two scabies-endemic Aboriginal communities in northern Australia in which a community-based skin health program was operating. Permethrin treatment was provided for all householders upon identification of scabies within a household during home visit. Households were visited the following day to assess treatment uptake and at 2 and 4 weeks to assess scabies acquisition among susceptible individuals. All 40 households in which a child with scabies was identified agreed to participate in the study. Very low levels of treatment uptake were reported among household contacts of these children (193/440, 44%). Household contacts who themselves had scabies were more likely to use the treatment than those contacts who did not have scabies (OR 2.4, 95%CI 1.1, 5.4), whilst males (OR 0.6, 95%CI 0.42, 0.95) and individuals from high-scabies-burden households (OR 0.2, 95%CI 0.08, 0.77) were less likely to use the treatment. Among 185 susceptible individuals, there were 17 confirmed or probable new diagnoses of scabies recorded in the subsequent 4 weeks (9.2%). The odds of remaining scabies-free was almost 6 times greater among individuals belonging to a household where all people reported treatment uptake (OR 5.9, 95%CI 1.3, 27.2, p = 0.02).
There is an urgent need for a more practical and feasible treatment for community management of endemic scabies. The effectiveness and sustainability of the current scabies program was compromised by poor treatment uptake by household contacts of infested children and high ongoing disease transmission.
Author Summary
Like many impoverished areas around the world, Aboriginal communities in Australia experience an unacceptably high burden of scabies, skin infections, and secondary complications. Young children are most at risk. Our study investigated scabies in a remote setting with very high rates of skin disease, a high level of household overcrowding, and limited infrastructure for sanitation and preventive health measures. We assessed uptake of scabies treatment and scabies acquisition following provision of treatment by a community-based skin program. In a household where scabies was present, we found that treatment with topical permethrin cream of all close contacts can significantly reduce a susceptible individual's risk of infection. Our findings also demonstrate the challenges of achieving a high level of treatment participation, with limited permethrin use observed among household contacts. This suggests an urgent need for a more practical treatment option. International efforts to reduce childhood morbidity and mortality have demonstrated the efficacy of numerous child health interventions but have also highlighted the deficits in their delivery and implementation. Experiences like this, where the effectiveness of a coordinated local program delivering an efficacious intervention is hampered by poor treatment uptake and ongoing transmission, are an important and timely message for researchers, program managers, and policy-makers.
PMCID: PMC2680947  PMID: 19478832
17.  Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase complexed with 6-phosphogluconate 
The structure of 6-phosphogluconate dehydrogenase from a moderate thermophile, G. stearothermophilus, is presented and compared with those of orthologous enzymes.
Two crystal structures of recombinant Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase (Gs6PDH) in complex with the substrate 6-­phosphogluconate have been determined at medium resolution. Gs6PDH shares significant sequence identity and structural similarity with the enzymes from Lactococcus lactis, sheep liver and the protozoan parasite Trypanosoma brucei, for which a range of structures have previously been reported. Comparisons indicate that amino-acid sequence conservation is more pronounced in the two domains that contribute to the architecture of the active site, namely the N-terminal and C-terminal domains, compared with the central domain, which is primarily involved in the subunit–subunit associations required to form a stable dimer. The active-site residues are highly conserved, as are the interactions with the 6-phosphogluconate. There is interest in 6PDH as a potential drug target for the protozoan parasite T. brucei, the pathogen responsible for African sleeping sickness. The recombinant T. brucei enzyme has proven to be recalcitrant to enzyme–ligand studies and a surrogate protein might offer new opportunities to investigate and characterize 6PDH inhibitors. The high degree of structural similarity, efficient level of expression and straightforward crystallization conditions mean that Gs6PDH may prove to be an appropriate model system for structure-based inhibitor design targeting the enzyme from Trypanosoma species.
PMCID: PMC2675582  PMID: 19407374
pentose phosphate pathway; 6-phosphogluconate dehydrogenase; Geobacillus stearothermophilus
18.  Pseudohyponatremia in a Patient with HIV and Hepatitis C Coinfection 
Pseudohyponatremia refers to low serum sodium in the presence of normal plasma tonicity. Whereas pseudohyponatremia secondary to hyperlipidemia is a commonly recognized occurrence, falsely low sodium levels secondary to elevated protein are less frequently observed. We present in this paper the case of a man coinfected with HIV and hepatitis C who had pseudohyponatremia from hypergammaglobulinemia. As hypergammaglobulinemia is a frequent occurrence in both HIV and HCV, we suggest that pseudohyponatremia is an important and likely underdiagnosed phenomenon in this patient population. Clinicians need to be aware of the electrolyte exclusion effect and become familiar with the techniques used by their local laboratory in the measurement of serum electrolytes. Pseudohyponatremia should also be included in the differential diagnosis of an elevated osmolal gap, as the falsely lowered sodium level will lead to a falsely low calculated serum osmolality.
PMCID: PMC2359164  PMID: 17994269
pseudohyponatremia; HIV; hepatitis C; electrolyte exclusion effect
19.  TarO: a target optimisation system for structural biology 
Nucleic Acids Research  2008;36(Web Server issue):W190-W196.
TarO ( offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC ‘Structural Proteomics of Rational Targets’ initiative
PMCID: PMC2447720  PMID: 18385152
20.  Initiating a crystallographic analysis of recombinant (S)-2-hydroxypropylphosphonic acid epoxidase from Streptomyces wedmorensis  
The gene encoding the unusual metal-ion-dependent epoxidase involved in fosfomycin biosynthesis, S. wedmorensis (S)-2-hydroxypropylphosphonic acid epoxidase, has been cloned and the protein expressed, purified and crystallized. Two crystal forms have been obtained, one of which diffracts to high resolution.
The oxirane (1R,2S)-1,2-epoxypropylphosphonic acid (fosfomycin) is a natural product antibiotic produced in Streptomyces wedmorensis by the metal-ion-dependent (S)-2-hydroxypropylphosphonic acid epoxidase. This epoxidase is highly unusual since it has no requirement for a haem prosthetic group. The gene encoding the enzyme, fom4, has been cloned and a highly efficient recombinant source of the enzyme established. Two different crystal forms, tetragonal and hexagonal, have been obtained. The hexagonal form displays symmetry consistent with space group P61/522 and unit-cell parameters a = 86.44, c = 221.56 Å, γ = 120°. The Matthews coefficient, V M, of 2.7 Å3 Da−1 corresponds to two subunits, each of approximate weight 21.4 kDa, in the asymmetric unit with 55% solvent content. These crystals diffract to high resolution and experimental phases are being sought to determine the structure.
PMCID: PMC1952317  PMID: 16511089
antibiotics; epoxidases; metalloenzymes; Streptomyces
21.  Screening of Compounds Toxicity against Human Monocytic cell line-THP-1 by Flow Cytometry 
The worldwide rapid increase in bacterial resistance to numerous antibiotics requires on-going development of new drugs to enter the market. As the development of new antibiotics is lengthy and costly, early monitoring of compound's toxicity is essential in the development of novel agents. Our interest is in a rapid, simple, high throughput screening method to assess cytotoxicity induced by potential agents. Some intracellular pathogens, such as Mycobacterium tuberculosis primary site of infection is human alveolar macrophages. Thus, evaluation of candidate drugs for macrophage toxicity is crucial. Protocols for high throughput drug toxicity screening of macrophages using flow cytometry are lacking in the literature. For this application we modified a preexisting technique, propidium iodide (PI) exclusion staining and utilized it for rapid toxicity tests. Samples were prepared in 96 well plates and analyzed by flow cytometry, which allowed for rapid, inexpensive and precise assessment of compound's toxicity associated with cell death.
PMCID: PMC521344  PMID: 15472722
Flow cytometry; Propidium; Lethal Dose 50
22.  Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins 
BMC Bioinformatics  2004;5:79.
Post-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins.
Phospho.ELM is a new resource containing experimentally verified phosphorylation sites manually curated from the literature and is developed as part of the ELM (Eukaryotic Linear Motif) resource. Phospho.ELM constitutes the largest searchable collection of phosphorylation sites available to the research community. The Phospho.ELM entries store information about substrate proteins with the exact positions of residues known to be phosphorylated by cellular kinases. Additional annotation includes literature references, subcellular compartment, tissue distribution, and information about the signaling pathways involved as well as links to the molecular interaction database MINT. Phospho.ELM version 2.0 contains 1703 phosphorylation site instances for 556 phosphorylated proteins.
Phospho.ELM will be a valuable tool both for molecular biologists working on protein phosphorylation sites and for bioinformaticians developing computational predictions on the specificity of phosphorylation reactions.
PMCID: PMC449700  PMID: 15212693
post-transcriptional modification; protein kinase; bioinformatics
23.  T helper cell polarisation as a measure of the maturation of the immune response. 
Mediators of Inflammation  2003;12(5):285-292.
BACKGROUND: T helper cell polarisation is important under chronic immune stimulatory conditions and drives the type of the evolving immune response. Mice treated with superantigens in vivo display strong effects on Th subset differentiation. The aim of the study was to detect the intrinsic capacity of T cells to polarise under various ex vivo conditions. METHODS: Purified CD4+ T cells obtained from super-antigen-treated mice were cultured under Th polarising conditions in vitro. By combining intracellular cytokine staining and subsequent flow cytometric analysis with quantitative cytokine measurements in culture supernatants by enzyme-linked immunosorbent assay (ELISA), the differential Th polarising capacity of the treatment can be detected in a qualitative and quantitative manner. RESULTS AND CONCLUSIONS: BALB/c mice were shown to be biased to develop strong Th2 polarised immune responses using Th0 stimulation of purified CD4+ T cells from phosphate-buffered saline-treated mice. Nevertheless, our analysis methodology convincingly showed that even in these mice, Toxic Shock Syndrome Toxin-1 treatment in vivo resulted in a significantly stronger Th1 polarising effect than control treatment. Our results indicate that populations of Th cells can be assessed individually for their differential Th1 or Th2 maturation capacity in vivo by analysing robust in vitro polarisation cultures combined with intracellular cytokine staining and ELISA.
PMCID: PMC1781629  PMID: 14760935
24.  ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins 
Nucleic Acids Research  2003;31(13):3625-3630.
Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line resources are available for revealing globular domains in sequences, there has hitherto been no comprehensive collection of small functional sites/motifs comparable to the globular domain resources, yet these are as important for the function of multidomain proteins. Short linear peptide motifs are used for cell compartment targeting, protein–protein interaction, regulation by phosphorylation, acetylation, glycosylation and a host of other post-translational modifications. ELM, the Eukaryotic Linear Motif server at, is a new bioinformatics resource for investigating candidate short non-globular functional motifs in eukaryotic proteins, aiming to fill the void in bioinformatics tools. Sequence comparisons with short motifs are difficult to evaluate because the usual significance assessments are inappropriate. Therefore the server is implemented with several logical filters to eliminate false positives. Current filters are for cell compartment, globular domain clash and taxonomic range. In favourable cases, the filters can reduce the number of retained matches by an order of magnitude or more.
PMCID: PMC168952  PMID: 12824381
25.  Essential Role for Verotoxin in Sustained Stress-Activated Protein Kinase and Nuclear Factor Kappa B Signaling, Stimulated by Escherichia coli O157:H7 in Vero Cells  
Infection and Immunity  2002;70(10):5370-5380.
The effects of Escherichia coli O157:H7 (strains E30480 and PM601) and the associated verotoxins (VTs), VT1 and VT2, on stress-activated protein kinase and nuclear factor kappa B (NF-κB) signaling were investigated with Vero cells, which are extremely sensitive to the cytotoxic effects of E. coli O157:H7 in vitro. Cell-free supernatants prepared from E30480 and PM601 cultures and purified VT1 and VT2 stimulated a strong and prolonged (>4-h) activation of both c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase. However, JNK activity stimulated in response to E30480 supernatants was substantially reduced following pretreatment with anti-VT1 and anti-VT2 antibodies, while a VT1 and VT2 gene knockout mutant of PM601 was unable to stimulate JNK activity. E30480 supernatants also caused a sustained activation of NF-κB DNA binding, degradation of inhibitory kappa B alpha (IκBα), and an increase in inhibitory kappa B kinase α activity, although PM601 supernatants and VT1 and VT2 had no effect. However, preincubation with VTs prolonged the transient activation of NF-κB and IκBα degradation stimulated by either tumor necrosis factor alpha or interleukin 1β, while preincubation with anti-VT antibodies prevented the prolonged loss of IκBα and partially reduced DNA binding in response to E30480 supernatants. These results strongly suggest that in Vero cells, VT plays an essential role in sustained JNK and NF-κB signaling in response to E. coli O157:H7 and that this action may underpin their cell-selective cytotoxic effects. These studies also suggest that another component released by strain E30480 contributes to the early activation of JNK and NF-κB.
PMCID: PMC128335  PMID: 12228261

Results 1-25 (26)