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John Wagner

Publications and source records attributed to John Wagner.

17 recordsLinked to original sources
PubMed2006

The architecture of the multisubunit TRAPP I complex suggests a model for vesicle tethering.

Transport protein particle (TRAPP) I is a multisubunit vesicle tethering factor composed of seven subunits involved in ER-to-Golgi trafficking. The functional mechanism of the complex and how the subunits interact to form a functional unit are unknown. Here, we have used a multidisciplinary approach that includes X-ray crystallography, electron microscopy, biochemistry, and yeast genetics to elucidate the architecture of TRAPP I. The complex is organized through lateral juxtaposition of the subunits into a flat and elongated particle. We have also localized the site of guanine nucleotide exchange activity to a highly conserved surface encompassing several subunits. We propose that TRAPP I attaches to Golgi membranes with its large flat surface containing many highly conserved residues and forms a platform for protein-protein interactions. This study provides the most comprehensive view of a multisubunit vesicle tethering complex to date, based on which a model for the function of this complex, involving Rab1-GTP and long, coiled-coil tethers, is presented.

Amino Acids↗
PubMed2006

Structural snapshots of Escherichia coli histidinol phosphate phosphatase along the reaction pathway.

HisB from Escherichia coli is a bifunctional enzyme catalyzing the sixth and eighth steps of l-histidine biosynthesis. The N-terminal domain (HisB-N) possesses histidinol phosphate phosphatase activity, and its crystal structure shows a single domain with fold similarity to the haloacid dehalogenase (HAD) enzyme family. HisB-N forms dimers in the crystal and in solution. The structure shows the presence of a structural Zn(2+) ion stabilizing the conformation of an extended loop. Two metal binding sites were also identified in the active site. Their presence was further confirmed by isothermal titration calorimetry. HisB-N is active in the presence of Mg(2+), Mn(2+), Co(2+), or Zn(2+), but Ca(2+) has an inhibitory effect. We have determined structures of several intermediate states corresponding to snapshots along the reaction pathway, including that of the phosphoaspartate intermediate. A catalytic mechanism, different from that described for other HAD enzymes, is proposed requiring the presence of the second metal ion not found in the active sites of previously characterized HAD enzymes, to complete the second half-reaction. The proposed mechanism is reminiscent of two-Mg(2+) ion catalysis utilized by DNA and RNA polymerases and many nucleases. The structure also provides an explanation for the inhibitory effect of Ca(2+).

Amino Acid Sequence↗
PubMed2006

Evolution of brain size and juvenile periods in primates.

This paper assesses selective pressures that shaped primate life histories, with particular attention to the evolution of longer juvenile periods and increased brain sizes. We evaluate the effects of social complexity (as indexed by group size) and foraging complexity (as indexed by percent fruit and seeds in the diet) on the length of the juvenile period, brain size, and brain ratios (neocortex and executive brain ratios) while controlling for positive covariance among body size, life span, and home range. Results support strong components of diet, life span, and population density acting on juvenile periods and of home range acting on relative brain sizes. Social-complexity arguments for the evolution of primate intelligence are compelling given strong positive correlations between brain ratios and group size while controlling for potential confounding variables. We conclude that both social and ecological components acting at variable intensities in different primate clades are important for understanding variation in primate life histories.

Age Factors↗
PubMed2006

Absorption, metabolism, and excretion of [14C]MK-0767 (2-methoxy-5-(2,4-dioxo-5-thiazolidinyl)-N-[[4-(trifluoromethyl)phenyl] methyl]benzamide) in humans.

MK-0767 (KRP-297; 2-methoxy-5-(2,4-dioxo-5-thiazolidinyl)-N-[[4-(trifluoromethyl)phenyl] methyl]benzamide) is a thiazolidinedione (TZD)-containing dual agonist of the peroxisome proliferator-activated receptors alpha and gamma that has been studied as a potential treatment for patients with type 2 diabetes. The metabolism and excretion of [14C]MK-0767 were evaluated in six human volunteers after a 5-mg (200 microCi) oral dose. Excretion of 14C radioactivity was found to be nearly equal into the urine (approximately 50%) and feces (approximately 40%). Elimination of [14C]MK-0767 was primarily by metabolism, with minimal excretion of parent compound into the urine (<0.5% of dose) and feces (approximately 14% of the dose). [14C]MK-0767 was the major circulating compound-related entity (>96% of radioactivity) through 48 h postdose. It was also found that approximately 91% of the total radioactivity area under the curve was due to intact MK-0767. Several minor metabolites were detected in plasma (<1% of radioactivity, each), formed by cleavage of the TZD ring and subsequent S-methylation and oxidation. All the metabolites excreted into urine were formed by TZD cleavage, whereas the major metabolite in feces was the O-demethylated derivative of MK-0767.

Absorption↗
PubMed2006

The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains.

Polyphosphate (polyP) is a linear polymer consisting of tens to hundreds of phosphate molecules joined together by high-energy anhydride bonds. These polymers are found in virtually all prokaryotic and eukaryotic cells and perform many functions; prominent among them are the responses to many stresses. Polyphosphate is synthesized by polyP kinase (PPK), using the terminal phosphate of ATP as the substrate, and degraded to inorganic phosphate by both endo- and exopolyphosphatases. Here we report the crystal structure and analysis of the polyphosphate phosphatase PPX from Escherichia coli O157:H7 refined at 2.2 Angstroms resolution. PPX is made of four domains. Domains I and II display structural similarity with one another and share the ribonuclease-H-like fold. Domain III bears structural similarity to the N-terminal, HD domain of SpoT. Domain IV, the smallest domain, has structural counterparts in cold-shock associated RNA-binding proteins but is of unknown function in PPX. The putative PPX active site is located at the interface between domains I and II. In the crystal structure of PPX these two domains are close together and represent the "closed" state. Comparison with the crystal structure of PPX/GPPA from Aquifex aeolicus reveals close structural similarity between domains I and II of the two enzymes, with the PPX/GPPA representing an "open" state. A striking feature of the dimer is a deep S-shaped canyon extending along the dimer interface and lined with positively charged residues. The active site region opens to this canyon. We postulate that this is a likely site of polyP binding.

Acid Anhydride Hydrolases↗
PubMed2005

The crystal structure of CREG, a secreted glycoprotein involved in cellular growth and differentiation.

The cellular repressor of E1A-stimulated genes (CREG) is a secreted glycoprotein that inhibits proliferation and enhances differentiation of human embryonal carcinoma cells. CREG binds to the cation-independent mannose 6-phosphate (M6P)/insulin-like growth factor II (IGF2) receptor (IGF2R) (M6P/IGF2R), and this receptor has been shown to be required for CREG-induced growth suppression. To better understand CREG function in cellular growth and differentiation, we solved the 3D crystal structure of this protein to 1.9-A resolution. CREG forms a tight homodimeric complex, and CREG monomers display a beta-barrel fold. The three potential glycosylation sites on CREG map to a confined patch opposite the dimer interface. Thus, dimerization of glycosylated CREG likely presents a bivalent ligand for the M6P/IGF2R. Closely related structural homologs of CREG are FMN-binding split-barrel fold proteins that bind flavin mononucleotide. Our structure shows that the putative flavin mononucleotide-binding pocket in CREG is sterically blocked by a loop and several key bulky residues. A mutant of CREG lacking a part of this loop maintained overall structure and dimerization, as well as M6P/IGF2R binding, but lost the growth suppression activity of WT CREG. Thus, analysis of a structure-based mutant of CREG revealed that binding to M6P/IGF2R, while necessary, is not sufficient for CREG-induced growth suppression. These findings indicate that CREG utilizes a known fold for a previously undescribed function [corrected]

Amino Acid Sequence↗
PubMed2005

A plausible model for the digital response of p53 to DNA damage.

Recent observations show that the single-cell response of p53 to ionizing radiation (IR) is "digital" in that it is the number of oscillations rather than the amplitude of p53 that shows dependence on the radiation dose. We present a model of this phenomenon. In our model, double-strand break (DSB) sites induced by IR interact with a limiting pool of DNA repair proteins, forming DSB-protein complexes at DNA damage foci. The persisting complexes are sensed by ataxia telangiectasia mutated (ATM), a protein kinase that activates p53 once it is phosphorylated by DNA damage. The ATM-sensing module switches on or off the downstream p53 oscillator, consisting of a feedback loop formed by p53 and its negative regulator, Mdm2. In agreement with experiments, our simulations show that by assuming stochasticity in the initial number of DSBs and the DNA repair process, p53 and Mdm2 exhibit a coordinated oscillatory dynamics upon IR stimulation in single cells, with a stochastic number of oscillations whose mean increases with IR dose. The damped oscillations previously observed in cell populations can be explained as the aggregate behavior of single cells.

Ataxia Telangiectasia Mutated Proteins↗
PubMed2005

Umbilical cord blood transplantation in adults: results of the prospective Cord Blood Transplantation (COBLT).

The Cord Blood Transplantation study group conducted a prospective study of unrelated cord blood transplantation (CBT) to better define the role of this stem cell source for subjects requiring unrelated allogeneic transplantation. We report on 1 stratum of the study designated for adult subjects. The primary end point of the study was survival at 180 days. Secondary end points included engraftment, graft-versus-host disease, relapse, and long-term survival. Eligibility criteria for malignant and nonmalignant diseases were specified. Subjects with active central nervous system disease, Karnofsky performance status <70%, grade 3 or 4 or primary myelofibrosis, or suitable related donors were excluded. Enrollment required a single cord blood unit containing >10(7) nucleated cells per kilogram of recipient weight and matched at > or =4 HLA-A and -B (low or intermediate resolution) and -DRB1 (high resolution) types. Thirty-four subjects were entered, with a median age of 34.5 years (range, 18.2-55 years). Most subjects (n = 23) had a 4 of 6 match, 10 subjects had a 5 of 6 match, and 1 subject had a 6 of 6 match. Diagnoses at transplantation included acute myelogenous leukemia (n = 19), acute lymphoblastic leukemia (n = 9), chronic myelogenous leukemia (n = 3), myelodysplastic syndrome (n = 1), paroxysmal nocturnal hemoglobinuria (PNH) (n = 1), and non-Hodgkin lymphoma (n = 1); 94% were classified as poor risk according to National Marrow Donor Program criteria. Subjects received total body irradiation/cyclophosphamide (n = 27) or busulfan/melphalan (n = 7) conditioning regimens. Four subjects died before CBT and are described here but are not included in the main analysis. The cumulative incidence rates and median times to neutrophil (500/microL) and platelet (>20,000/microL) engraftment were 0.66 by day 42 (median, 31 days) and 0.35 by day 180 (median, 117 days). The cumulative incidence rate for grade II-IV GVHD was 0.34 by day 100. For the primary end point, survival at 180 days, Kaplan-Meier survival estimates were 0.30 (95% confidence interval, 0.14-0.46) by day 180 after transplantation. To date there are 2 survivors, and both are >36 months from enrollment. A retrospective analysis was performed by using high-resolution HLA-A and -B typing, which revealed that approximately one third of subjects had 1 or more additional HLA mismatches compared with results of low- or intermediate-resolution HLA typing. The findings of high treatment-related mortality and slow engraftment kinetics indicate that CBT should continue to be performed in specialized centers with a research focus on cord blood cells.

Adolescent↗
PubMed2005

Issues in the quality of umbilical cord blood stem cells for transplantation.

BACKGROUND: Because the frequency of umbilical cord blood (UCB) stem cell transplantation has increased, the quality of UCB available in banks is an important part of the success of UCB stem cell transplants. STUDY DESIGN AND METHODS: A quality assurance monitoring system was used to evaluate 268 UCB units provided to us for transplant by UCB banks in the United States and Europe. RESULTS: Quality issues were found in 151 (56%) of 268 units, and there were a total of 246 specific issues in 151 units. The issues involved quality control (54%), medical history (40%), and labels and documentation (6%). Risks to patients from these issues were likely in 10 percent, potential in 35 percent, and unlikely in 55 percent. CONCLUSION: Because standards have evolved over time, cord blood banks contain units that have different levels of quality. Some units have been placed in the usable inventory with incomplete test results and/or documentation or that may not meet the bank's own current criteria. Information about any quality or operating procedure deviation should be provided in sufficient detail and at the initiation of the search process so that transplant physicians can consider these quality issues against the unique value of a particular UCB unit.

Blood Banks↗
PubMed2005

Biochemical and crystallographic studies reveal a specific interaction between TRAPP subunits Trs33p and Bet3p.

Transport protein particle (TRAPP) comprises a family of two highly related multiprotein complexes, with seven common subunits, that serve to target different classes of transport vesicles to their appropriate compartments. Defining the architecture of the complexes will advance our understanding of the functional differences between these highly related molecular machines. Genetic analyses in yeast suggested a specific interaction between the TRAPP subunits Bet3p and Trs33p. A mammalian bet3-trs33 complex was crystallized, and the structure was solved to 2.2 angstroms resolution. Intriguingly, the overall fold of the bet3 and trs33 monomers was similar, although the proteins had little overall sequence identity. In vitro experiments using yeast TRAPP subunits indicated that Bet3p binding to Trs33p facilitates the interaction between Bet3p and another TRAPP subunit, Bet5p. Mutational analysis suggests that yeast Trs33p facilitates other Bet3p protein-protein interactions. Furthermore, we show that Trs33p can increase the Golgi-localized pool of a mutated Bet3 protein normally found in the cytosol. We propose that one of the roles of Trs33p is to facilitate the incorporation of the Bet3p subunit into assembling TRAPP complexes.

Amino Acid Sequence↗
PubMed2004

The structure of the MAPK scaffold, MP1, bound to its partner, p14. A complex with a critical role in endosomal map kinase signaling.

Scaffold proteins of the mitogen-activated protein kinase (MAPK) pathway have been proposed to form an active signaling module and enhance the specificity of the transduced signal. Here, we report a 2-A resolution structure of the MAPK scaffold protein MP1 in a complex with its partner protein, p14, that localizes the complex to late endosomes. The structures of these two proteins are remarkably similar, with a five-stranded beta-sheet flanked on either side by a total of three helices. The proteins form a heterodimer in solution and interact mainly through the edge beta-strand in each protein to generate a 10-stranded beta-sheet core. Both proteins also share structural similarity with the amino-terminal regulatory domains of the membrane trafficking proteins, sec22b and Ykt6p, as well as with sedlin (a component of a Golgi-associated membrane-trafficking complex) and the sigma2 and amino-terminal portion of the mu2 subunits of the clathrin adaptor complex AP2. Because neither MP1 nor p14 have been implicated in membrane traffic, we propose that the similar protein folds allow these relatively small proteins to be involved in multiple and simultaneous protein-protein interactions. Mapping of highly conserved, surface-exposed residues on MP1 and p14 provided insight into the potential sites of binding of the signaling kinases MEK1 and ERK1 to this complex, as well as the areas potentially involved in other protein-protein interactions.

Adaptor Proteins, Signal Transducing↗
PubMed2004

A wave of IP3 production accompanies the fertilization Ca2+ wave in the egg of the frog, Xenopus laevis: theoretical and experimental support.

The fertilization Ca2+ wave in Xenopus laevis is a single, large wave of elevated free Ca2+ that is initiated at the point of sperm-egg fusion and traverses the entire width of the egg. This Ca2+ wave involves an increase in inositol-1,4,5-trisphosphate (IP3) resulting from the interaction of the sperm and egg, which then results in the activation of the endoplasmic reticulum Ca2+ release machinery. The extraordinarily large size of this cell (1.2 mm diameter) together with the small surface region of sperm-receptor activation makes special demands on the IP3-dependent Ca2+ mobilizing machinery. We propose a detailed model of the fertilization Ca2+ wave in Xenopus eggs that requires an accompanying wave of IP3 production. While the Ca2+ wave is initiated by a localized increase of IP3 near the site of sperm-egg fusion, the Ca2+ wave propagates via IP3 production correlated with the Ca2+ wave-possibly via Ca(2+)-mediated PLC activation. Such a Ca(2+)-mediated IP(3) production wave has not been required previously to explain the fertilization Ca2+ wave in eggs; we argue this is necessary to explain the observed IP3 dynamics in Xenopus eggs. To test our hypothesis, we have measured the IP3 levels from 20 nl "sips" of the egg cortex during wave propagation. We were unable to detect the low IP3 levels in unfertilized eggs, but after fertilization, [IP3] ranged from 175 to 430 nM at the sperm entry point and from 120 to 700 nM 90 degrees away once the Ca2+ wave passed that region about 2 min after fertilization. Prior to the Ca2+ wave reaching that region the IP3 levels were undetectable. Since significant IP3 could not diffuse to this region from the sperm entry point within 2 min, this observation is consistent with a regenerative wave of IP3 production.

Animals↗
PubMed2003

Prospective grading of graft-versus-host disease after unrelated donor marrow transplantation: a grading algorithm versus blinded expert panel review.

In conjunction with a randomized trial of T-cell depletion versus conventional graft-versus-host disease (GVHD) prophylaxis, we assessed GVHD grading by comparing the transplant center 100-day score, a clinically calculated algorithm, and a blinded expert panel review (PR). Weekly skin, gut, and liver clinical staging; clinically verified differential diagnosis; biopsy information; cyclosporine levels; and initiation of treatment were reviewed and graded according to the consensus GVHD grading method modified by a prospectively determined grading algorithm that specified liver and gut downstaging if a differential diagnosis in that organ was identified. Transplant center (TC) determination of maximum grade was compared with the algorithm-calculated grade and the final expert PR. Of 404 patients reviewed, the TC grade concurred with the calculated algorithm grade in 72% (the algorithm upgraded 18% and downgraded 10%), whereas the TC grade agreed with the PR in 77% (the PR upgraded 12% and downgraded 11%). The calculated algorithm grade was nearly fully (92%) concordant with the final PR grade (the PR upgraded 0.7% and downgraded 7%). Blinded, duplicate reviews for quality control (n = 108) agreed with the initial review in 89% of cases. Algorithm and/or PR review reduced the TC-reported incidence of grade II (28% to 23%) and increased grade III (11% to 20%), whereas grade 0 (41% to 42%), grade I (13% to 12%), and grade IV (7% to 6%) were invariant. Recalculation of the algorithm grading without differential diagnosis downstaging reduced agreement with the TC to a small extent. The original algorithm changed 51 (13%) of 404 from grade 0 to II into grade III or IV or vice versa; calculation without the downgrade modified 44 cases (11%). Maximum acute GVHD grade had a major effect on 2-year disease-free survival, but assignment by TC, calculated algorithm, or final PR grade had little effect on survival within grades or grade categories 0 through II versus III or IV. We conclude that detailed and expert PR yields GVHD scoring that is internally consistent and reproducible with 89% concordance. Weekly recording of GVHD stage along with a calculated grading algorithm acknowledging differential diagnoses results in a final and maximum grade nearly fully concordant with the expert blinded PR. Multicenter prospective GVHD scoring using all available weekly staging and differential diagnosis data can be reliably assessed with a clinically relevant algorithm. This approach can thereby reduce investigator bias, facilitate comparison between centers, and perhaps eliminate the need for an expert PR. This technique should be used in future prospective studies of GVHD prophylaxis.

Adolescent↗
PubMed2003

A comparison of related donor peripheral blood and bone marrow transplants: importance of late-onset chronic graft-versus-host disease and infections.

Peripheral blood hematopoietic stem cell (PBSC) transplants have been shown to result in more rapid engraftment than standard bone marrow transplants (BMTs). Little comparative data exist regarding complications in patients receiving transplants using these stem cell sources. In our study, 97 adults with advanced hematologic malignancies who received allogeneic PBSC transplants were compared with 97 adults who received allogeneic BMTs using identical preparative regimens and support parameters. The incidence of systemic infections and other major complications occurring within the first year after transplantation were calculated in both groups. Proportional hazard analysis was used to examine risk factors for death and complications in both groups. Patients receiving PBSC transplants had more rapid neutrophil (17 days versus 24 days; P <.001) and platelet engraftment (28 days versus 47 days; P <.001) than BMT recipients. The survival rate at 2 years was 38% in PBSC transplant recipients and 28% in marrow recipients (P =.08). There was no difference in rates of grade II to IV acute graft-versus-host disease (GVHD) between groups (PBSC 46%, BMT 51%; P =.3). PBSC transplant recipients were more likely to develop chronic GVHD after 180 days (hazard ratio 2.2; P =.05). Accompanying this "late-onset chronic GVHD," a pattern of more frequent late systemic fungal and cytomegalovirus infections was observed in PBSC transplant recipients. In conclusion, although PBSC transplant recipients engraft more quickly than BMT recipients and have somewhat better 2-year survival rates, they develop more frequent late-onset chronic GVHD and may have more late fungal and cytomegalovirus infections than marrow recipients. Further studies must examine this late-onset chronic GVHD and better characterize immune reconstitution in PBSC transplant recipients to understand their effects on patient recovery.

Adolescent↗
PubMed2003

Characterization of etoricoxib, a novel, selective COX-2 inhibitor.

Etoricoxib is a potent selective COX-2 inhibitor in man. Ex vivo whole-blood assays assessed COX-2 inhibition after oral administration of etoricoxib in single (5-500 mg) and multiple (25-150 mg) once-daily doses to healthy human subjects. A separate study examined ex vivo gastric mucosal PGE2 synthesis after etoricoxib (120 mg qd), naproxen (500 mg bid), or placebo for 5 days. The effect of etoricoxib 120 mg qd on the COX-1-mediated antiplatelet effects of low-dose aspirin (ASA) was also assessed. The mean (time)-weighted average inhibition (WAI) of lipopolysaccharide (LPS)-stimulated PGE2 (COX-2 assay) vcrsus placebo was dose related after single (range: 3.1%-99.1%) and multiple doses (range: 52.5%-96.7%). PGE2 remained significantly inhibited 24 hours postdose at steady state. Inhibition of LPS-stimulated PGE2 showed a strong relationship with etoricoxib plasma concentrations; ex vivo, IC50 was almost identical to in vitro. Multiple dosing of etoricoxib (up to 150 mg qd) showed no important effects on serum TXB2, bleeding time, or platelet aggregation (COX-1-mediated effects). The nonselective nonsteroidal anti-inflammatory (NSAID) naproxen significantly inhibited (approximately 78%) ex vivo prostaglandin synthesis in gastric mucosa; etoricoxib had no effect. Etoricoxib did not interfere with the antiplatelet effects of low-dose ASA, as assessed by serum TXB2 and platelet aggregation. Etoricoxib was generally well tolerated, even at doses above the clinical dose range. Based on these results, etoricoxib is a potent selective inhibitor of COX-2 after single and multiple dosing regimens and does not inhibit prostaglandin synthesis in the gastric mucosa, even at doses above the clinical dose range of 60 to 120 mg.

Adult↗
PubMed2001

Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell.

The Virtual Cell is a modeling tool that allows biologists and theorists alike to specify and simulate cell-biophysical models on arbitrarily complex geometries. The framework combines an intuitive, front-end graphical user interface that runs in a web browser, sophisticated server-side numerical algorithms, a database for storage of models and simulation results, and flexible visualization capabilities. In this paper, we present an overview of the capabilities of the Virtual Cell, and, for the first time, the detailed mathematical formulation used as the basis for spatial computations. We also present summaries of two rather typical modeling projects, in order to illustrate the principal capabilities of the Virtual Cell. (c) 2001 American Institute of Physics.

Journal Article↗