73 research outputs found
The Elusive Third Subunit IIa of the Bacterial B-Type Oxidases: The Enzyme from the Hyperthermophile Aquifex aeolicus
The reduction of molecular oxygen to water is catalyzed by complicated membrane-bound metallo-enzymes containing variable numbers of subunits, called cytochrome c oxidases or quinol oxidases. We previously described the cytochrome c oxidase II from the hyperthermophilic bacterium Aquifex aeolicus as a ba3-type two-subunit (subunits I and II) enzyme and showed that it is included in a supercomplex involved in the sulfide-oxygen respiration pathway. It belongs to the B-family of the heme-copper oxidases, enzymes that are far less studied than the ones from family A. Here, we describe the presence in this enzyme of an additional transmembrane helix âsubunit IIaâ, which is composed of 41 amino acid residues with a measured molecular mass of 5105 Da. Moreover, we show that subunit II, as expected, is in fact longer than the originally annotated protein (from the genome) and contains a transmembrane domain. Using Aquifex aeolicus genomic sequence analyses, N-terminal sequencing, peptide mass fingerprinting and mass spectrometry analysis on entire subunits, we conclude that the B-type enzyme from this bacterium is a three-subunit complex. It is composed of subunit I (encoded by coxA2) of 59000 Da, subunit II (encoded by coxB2) of 16700 Da and subunit IIa which contain 12, 1 and 1 transmembrane helices respectively. A structural model indicates that the structural organization of the complex strongly resembles that of the ba3 cytochrome c oxidase from the bacterium Thermus thermophilus, the IIa helical subunit being structurally the lacking N-terminal transmembrane helix of subunit II present in the A-type oxidases. Analysis of the genomic context of genes encoding oxidases indicates that this third subunit is present in many of the bacterial oxidases from B-family, enzymes that have been described as two-subunit complexes
Predicting Progression of IgA Nephropathy: New Clinical Progression Risk Score
IgA nephropathy (IgAN) is a common cause of end-stage renal disease (ESRD) in Asia. In this study, based on a large cohort of Chinese patients with IgAN, we aim to identify independent predictive factors associated with disease progression to ESRD. We collected retrospective clinical data and renal outcomes on 619 biopsy-diagnosed IgAN patients with a mean follow-up time of 41.3 months. In total, 67 individuals reached the study endpoint defined by occurrence of ESRD necessitating renal replacement therapy. In the fully adjusted Cox proportional hazards model, there were four baseline variables with a significant independent effect on the risk of ESRD. These included: eGFR [HRâ=â0.96(0.95â0.97)], serum albumin [HRâ=â0.47(0.32â0.68)], hemoglobin [HRâ=â0.79(0.72â0.88)], and SBP [HRâ=â1.02(1.00â1.03)]. Based on these observations, we developed a 4-variable equation of a clinical risk score for disease progression. Our risk score explained nearly 22% of the total variance in the primary outcome. Survival ROC curves revealed that the risk score provided improved prediction of ESRD at 24th, 60th and 120th month of follow-up compared to the three previously proposed risk scores. In summary, our data indicate that IgAN patients with higher systolic blood pressure, lower eGFR, hemoglobin, and albumin levels at baseline are at a greatest risk of progression to ESRD. The new progression risk score calculated based on these four baseline variables offers a simple clinical tool for risk stratification
An Observational Cohort Study of the Kynurenine to Tryptophan Ratio in Sepsis: Association with Impaired Immune and Microvascular Function
Both endothelial and immune dysfunction contribute to the high mortality rate in human sepsis, but the underlying mechanisms are unclear. In response to infection, interferon-Îł activates indoleamine 2,3-dioxygenase (IDO) which metabolizes the essential amino acid tryptophan to the toxic metabolite kynurenine. IDO can be expressed in endothelial cells, hepatocytes and mononuclear leukocytes, all of which contribute to sepsis pathophysiology. Increased IDO activity (measured by the kynurenine to tryptophan [KT] ratio in plasma) causes T-cell apoptosis, vasodilation and nitric oxide synthase inhibition. We hypothesized that IDO activity in sepsis would be related to plasma interferon-Îł, interleukin-10, T cell lymphopenia and impairment of microvascular reactivity, a measure of endothelial nitric oxide bioavailability. In an observational cohort study of 80 sepsis patients (50 severe and 30 non-severe) and 40 hospital controls, we determined the relationship between IDO activity (plasma KT ratio) and selected plasma cytokines, sepsis severity, nitric oxide-dependent microvascular reactivity and lymphocyte subsets in sepsis. Plasma amino acids were measured by high performance liquid chromatography and microvascular reactivity by peripheral arterial tonometry. The plasma KT ratio was increased in sepsis (median 141 [IQR 64â235]) compared to controls (36 [28â52]); p<0.0001), and correlated with plasma interferon-Îł and interleukin-10, and inversely with total lymphocyte count, CD8+ and CD4+ T-lymphocytes, systolic blood pressure and microvascular reactivity. In response to treatment of severe sepsis, the median KT ratio decreased from 162 [IQR 100â286] on day 0 to 89 [65â139] by day 7; pâ=â0.0006) and this decrease in KT ratio correlated with a decrease in the Sequential Organ Failure Assessment score (p<0.0001). IDO-mediated tryptophan catabolism is associated with dysregulated immune responses and impaired microvascular reactivity in sepsis and may link these two fundamental processes in sepsis pathophysiology
National Institutes of HealthâSponsored Clinical Islet Transplantation Consortium Phase 3 Trial: Manufacture of a Complex Cellular Product at Eight Processing Facilities
Eight manufacturing facilities participating in the National Institutes of Healthâsponsored Clinical Islet Transplantation (CIT) Consortium jointly developed and implemented a harmonized process for the manufacture of allogeneic purified human pancreatic islet (PHPI) product evaluated in a phase 3 trial in subjects with type 1 diabetes. Manufacturing was controlled by a common master production batch record, standard operating procedures that included acceptance criteria for deceased donor organ pancreata and critical raw materials, PHPI product specifications, certificate of analysis, and test methods. The process was compliant with Current Good Manufacturing Practices and Current Good Tissue Practices. This report describes the manufacturing process for 75 PHPI clinical lots and summarizes the results, including lot release. The results demonstrate the feasibility of implementing a harmonized process at multiple facilities for the manufacture of a complex cellular product. The quality systems and regulatory and operational strategies developed by the CIT Consortium yielded product lots that met the prespecified characteristics of safety, purity, potency, and identity and were successfully transplanted into 48 subjects. No adverse events attributable to the product and no cases of primary nonfunction were observed
Vibrational resonances and Cu B displacement controlled by proton motion in cytochrome c oxidase
Cytochrome c oxidase (CcO), found in the inner mitochondrial membranes or in many bacteria, catalyzes the four-electron reduction of molecular oxygen to water. Four protons are pumped across the inner mitochondrial membrane through CcO. In this study, quantum mechanics/molecular mechanics and molecular dynamics calculations are used to probe the spectroscopic characteristics of the ferryl intermediates in the aa 3 CcO/O 2 reaction. These highly elaborate calculations, supported by several calculations on smaller model systems, demonstrate the sensitivity of vibrational frequencies on the Coulombic field of heme a 3 and their dependence on the distance of the adjacent Cu B to the heme a 3-Fe atom. This distance seems to be associated with the protonation state of the heme a 3 propionate A, and we propose that it plays a crucial role on the mechanism of action of CcO. In detail, we link proton pumping activity in CcO enzyme (a) to a multiple (1:1:2) resonance among the frequencies of FeIV=O bond stretching, the breathing mode of Histidine 411, and a bending mode of the His411-FeIV=O species (aa 3 from Paracoccus denitrificans numbering) and (b) to Cu B displacement by electrostatic interactions toward the heme a 3 iron. We find that the vibrations of the His411-FeIV=O unit become highly coupled depending on the protonation state of the heme a 3 ring A propionate/Asp399 pair, and we propose a mechanism for the resonance Raman enhancement of the bending mode ÎŽ(His411-FeIV=O). Calculations on model systems demonstrate that the position of Cu B in relation to heme a 3 iron-oxo plays a crucial role in regulating that resonance. We also discuss the origin of the coupling between bending, ÎŽ(His411- FeIV=O) and v(Fe=O) stretching modes, and the role played by such vibrational coupling interactions or CuB position in controlling functional properties of the enzyme, including electron/proton coupling as well as experimental spectr
Climate and Demography Dictate the Strength of Predator-Prey Overlap in a Subarctic Marine Ecosystem
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