Exploring the mechanisms of the reductase activity of neuroglobin by site-directed mutagenesis of the heme distal pocket.

Neuroglobin (Ngb) is a six-coordinate globin that can catalyze the reduction of nitrite to nitric oxide. Although this reaction is common to heme proteins, the molecular interactions in the heme pocket that regulate this reaction are largely unknown. We have shown that the H64L Ngb mutation increases the rate of nitrite reduction by 2000-fold compared to that of wild-type Ngb [Tiso, M., et al. (2011) J. Biol. Chem. 286, 18277-18289]. Here we explore the effect of distal heme pocket mutations on nitrite reduction. For this purpose, we have generated mutations of Ngb residues Phe28(B10), His64(E7), and Val68(E11). Our results indicate a dichotomy in the reactivity of deoxy five- and six-coordinate globins toward nitrite. In hemoglobin and myoglobin, there is a correlation between faster rates and more negative potentials. However, in Ngb, reaction rates are apparently related to the distal pocket volume, and redox potential shows a poor relationship with the rate constants. This suggests a relationship between the nitrite reduction rate and heme accessibility in Ngb, particularly marked for His64(E7) mutants. In five-coordinate globins, His(E7) facilitates nitrite reduction, likely through proton donation. Conversely, in Ngb, the reduction mechanism does not rely on the delivery of a proton from the histidine side chain, as His64 mutants show the fastest reduction rates. In fact, the rate observed for H64A Ngb (1120 M(-1) s(-1)) is to the best of our knowledge the fastest reported for a heme nitrite reductase. These differences may be related to a differential stabilization of the iron-nitrite complexes in five- and six-coordinate globins.

Rapid determination of globin chains in red blood cells by capillary electrophoresis using INSTCoated fused-silica capillary.

A laboratory-made INSTCoated fused-silica capillary has been newly used for CE separation of four mixtures of proteins in sodium phosphate BGEs at pH 3.0 and 2.5, respectively. The obtained separation efficiencies range from 145,000 theoretical plates per meter for myoglobin to 1,216,000 m(-1) for lysozyme. A total of 49-89% of the number of theoretical plates was obtained in a commercial polyvinyl alcohol coated capillary compared to the INSTCoated capillary under the same experimental conditions, 0-86% was obtained in a laboratory polyacrylamide-coated capillary, and only 0-6% was obtained in an uncoated fused-silica capillary. The RSD values for the intraday repeatability for an INSTCoated capillary were 0.1-1.0% (migration time) and 0.3-2.4% (peak area); RSD values for the interday repeatability in the same capillary are 0.6-1.4% (migration time) and 2.4-5.5% (peak area); RSD values for interday repeatability between different capillaries equaled 1.7-2.1% (migration time) and 2.8-10.9% (peak area). The INSTCoated capillary has been further used for rapid determination of globin chains isolated from red blood cells. A separation of α and ß chains prepared from adult blood has been completed in 3 min with a peak resolution of 1.3, and the separation of α and (G)γ chains prepared from newborn blood took 3 min with a peak resolution of 3.6.

Cloning, expression and purification of Atlantic salmon (Salmo salar, L.) neuroglobin.

Neuroglobin (Ngb) exists only in small amounts in salmon brain. In order to study the protein in more detail salmon neuroglobin (sNgb) was cloned, heterologously expressed in Escherichia coli and purified. The protein had red color and showed the characteristic peaks at 411nm (metNgb), 415nm (carboxyNgb) and 424nm (deoxyNgb). Western analysis showed that sNgb reacted weakly against a rabbit anti human neuroglobin (hNgb) and strongly to a sNgb specific antibody. Our 3D-homology model of the sNgb indicated modifications adjacent to and in the O(2)/CO binding site. This may correlate to differences in substrate affinities for the sNgb compared to the hNgb. Also sNgb contained shorter helixes and longer interhelical loops typical for psychrophilic proteins.

Gene expression profiling of human whole blood samples with the Illumina WG-DASL assay.

BACKGROUND: Microarray-based gene expression analysis of peripheral whole blood is a common strategy in the development of clinically relevant biomarker panels for a variety of human diseases. However, the results of such an analysis are often plagued by decreased sensitivity and reliability due to the effects of relatively high levels of globin mRNA in whole blood. Globin reduction assays have been shown to overcome such effects, but they require large amounts of total RNA and may induce distinct gene expression profiles. The Illumina whole genome DASL assay can detect gene expression levels using partially degraded RNA samples and has the potential to detect rare transcripts present in highly heterogeneous whole blood samples without the need for globin reduction. We assessed the utility of the whole genome DASL assay in an analysis of peripheral whole blood gene expression profiles. RESULTS: We find that gene expression detection is significantly increased with the use of whole genome DASL compared to the standard IVT-based direct hybridization. Additionally, globin-probe negative whole genome DASL did not exhibit significant improvements over globin-probe positive whole genome DASL. Globin reduction further increases the detection sensitivity and reliability of both whole genome DASL and IVT-based direct hybridization with little effect on raw intensity correlations. Raw intensity correlations between total RNA and globin reduced RNA were 0.955 for IVT-based direct hybridization and 0.979 for whole genome DASL. CONCLUSIONS: Overall, the detection sensitivity of the whole genome DASL assay is higher than the IVT-based direct hybridization assay, with or without globin reduction, and should be considered in conjunction with globin reduction methods for future blood-based gene expression studies.

Improvements in monitoring the N-terminal valine adduct in human globin after exposure to sulfur mustard and synthesis of reference chemicals.

The N-terminal valine adduct (HETE-Val) in globin is believed to behave as a long-lived biomarker after exposure to sulfur mustard (HD). Development of a highly sensitive method for monitoring HETE-Val, particularly at low HD exposure levels or for retrospective detection, would be a significant achievement. In this study, by improving the sample preparation method, a sensitive NCI-GC/MS method was established for the analysis of HETE-Val in globin after HD exposure. To optimize and investigate the sample preparation method, all the relevant HETE-Val chemicals were synthesized, purified, and characterized. By carrying out optimized solid phase extraction (SPE) cleanup followed by modified Edman degradation results in a low detection level and clean baseline. The minimum detectable exposure level of human blood (in vitro) to HD is 20 nmol/L (S/N>3). The interday and intraday precisions of the proposed method were found to be acceptable with less than a 15% relative standard deviation (RSD). A nearly linear dose-effect relationship was observed between HETE-Val and a HD exposure concentration range of 0.1-120 µmol/L. The percentage of HD that reacted with N-terminal valine in globin obtained from human blood (in vitro) was quantified using the proposed method.

Globin-mediated nitric oxide detoxification in the foodborne pathogenic bacterium Campylobacter jejuni proceeds via a dioxygenase or denitrosylase mechanism.

Nitric oxide (NO(·)) is a toxin, but bacteria have evolved various strategies to detoxify this harmful radical to nitrate, the best known mechanism being the dioxygenase reaction of bacterial flavohaemoglobins. In addition, globins can form oxoferryl (Fe(IV)=O) species through the reaction of the ferric haem with hydrogen peroxide: these species can also detoxify NO(·) to nitrite and nitrate. During infection, Campylobacter is exposed to both NO(·) and hydrogen peroxide. A question therefore arises: does Campylobacter jejuni utilize its single domain globin (Cgb) to detoxify NO(·) via the oxoferryl route, or via the more conventional dioxygenase or denitroxylase routes? The data herein demonstrate that the reaction between Cgb and hydrogen peroxide is much slower than for other globins, and subsequent reaction between the oxoferryl species and NO(·) is unfavourable. Furthermore, NO(·) may bind to Cgb in the oxyferrous, ferrous and ferric states. The ample opportunity for NO(·) to interact with ferrous and ferric Cgb, and the unfavourable reaction of ferric Cgb with hydrogen peroxide, suggests that NO(·) detoxification in C. jejuni proceeds via a dioxygenase or denitroxylase route requiring the haem iron to exist only in the Fe(II) or Fe(III) redox states.

Multicenter clinical sample collection for microarray analysis.

In this chapter, we describe numerous methods to extract RNA, DNA, and protein from tissue, represented by kidney transplant biopsies, and from peripheral blood cells collected at various clinical sites. Gene expression profiling and SNP-based genome-wide association studies are done using various microarray platforms. In addition, protocols that enable simultaneous protein purification from these clinical samples, enable additional strategies for understanding of the molecular processes involved in organ transplantation, immunosuppressive drug regimens, and the elements determining allograft success and failure. Successfully establishing a multicenter clinical study was essential to meet our objectives for subject enrollment and transplant outcomes. This chapter focuses on our experience setting up and coordinating clinical sample collection from multiple transplant centers for the purpose of microarray analysis.

High-level production of recombinant Arenicola marina globin chains in Escherichia coli: a new generation of blood substitute.

This work reports for the first time the expression of a soluble B2 globin chain that is part of the extracellular hexagonal-bilayer haemoglobin from Arenicola marina. Two recombinant B2 globins were produced, one fused with gluthatione S-tranferase (B2-GST) and the other without a fusion tag (RecB2) and requiring a different purification procedure. We also describe a new method for the expression of globin that uses Studier's auto-induction medium together with the heme precursor delta-aminolevulinic acid. Media supplementation with the heme precursor delta-aminolevulinic acid in the culture increased heme synthesis by E. coli leading to the expression of the recombinant B2 globins in their active form. RecB2 and B2-GST were expressed with a yield of up to 105 mg/l of E. coli culture. Our approach is rapid and requires only one chromatographic purification step for B2-GST and three purification steps for RecB2. The overall results on RecB2 and B2-GST show that the recombinant globins exhibit similar properties to those of Arenicola marina native HBL-Hb with a great stability and a strong oxygen binding. The results and methodologies described in this paper are the beginning of a work aiming at reconstituting a recombinant HBL-Hb by genetic engineering in order to produce an innovative oxygen carrier for therapeutic applications.

Acrylamide: a dietary carcinogen formed in vivo?

Acrylamide, a chemical formed during heating of human foods, reacts with N-terminal valine in hemoglobin (Hb) and forms stable reaction products (adducts). These adducts to N-terminal valine in Hb have been used to estimate daily intake of acrylamide. Daily intake of acrylamide estimated from Hb adduct levels was higher than daily intake estimated from dietary questionnaires, possibly indicating other sources of exposures. Therefore, in this study the possible endogenous formation of acrylamide was investigated by treating mice with FeSO 4, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-hydrochloric acid (MPTP), or methamphetamine (METH). Acrylamide Hb adducts were determined, and a significant increase ( p < 0.05) in acrylamide Hb adduct levels was observed 24 h following treatment with FeSO 4 and 72 h following treatment with MPTP or METH. The results of this study show that acrylamide Hb adduct levels are increased in mice treated with compounds known to induce free radicals, thus suggesting the endogenous production of acrylamide.

Expression, purification, and crystallization of neuro- and cytoglobin.

Neuroglobin and cytoglobin, members of the globin family, are present in vertebrate cells at very low concentrations. As the function of both proteins is still a matter of debate, it is very important to be able to produce and purify these proteins, and in general all members of the globin family, to homogeneity. For this purpose, this chapter describes the expression of neuro- and cytoglobin by E. coli and its preparative purification. These proteins are then used in crystallization experiments. Also an analytical purification strategy is discussed in detail.

Inferring evolution of fish proteins: the globin case study.

Because hemoglobins (Hbs) of all animal species have the same heme group, differences in their properties, including oxygen affinity, electrophoretic mobility, and pH sensitivity, must result from the interaction of the prosthetic group with specific amino acid residues in the primary structure. For this reason, fish globins have been the object of extensive studies in the past few years, not only for their structural characteristics but also because they offer the possibility to investigate the evolutionary history of Hbs in marine and freshwater species living in a large variety of environmental conditions. For such a purpose, phylogenetic analysis of globin sequences can be combined with knowledge of the phylogenetic relationships between species. In addition, Type I functional-divergence analysis is aimed toward predicting the amino acid residues that are more likely responsible for biochemical diversification of different Hb families. These residues, mapped on the three-dimensional Hb structure, can provide insights into functional and structural divergence.

Alpha and beta chains of hemoglobin inhibit production of Staphylococcus aureus exotoxins.

Prior studies suggest Staphylococcus aureus exotoxins are not produced when the organism is cultured in human blood. Human blood was fractionated into plasma and water-lysed red blood cells, and it was demonstrated that mixtures of alpha and beta globins of hemoglobin (as low as 1 mug/mL) inhibited S. aureus exotoxin production while increasing production of protein A and not affecting bacterial growth. Pepsin but not trypsin digestion destroyed the ability of alpha and beta globin to inhibit exotoxin production. Exotoxin production by both methicillin-resistant and methicillin-susceptible organisms was inhibited. Production of streptococcal pyrogenic exotoxin A by Streptococcus pyogenes was unaffected by alpha and beta globin chains but was inhibited when produced in S. aureus. Use of isogenic S. aureus strains suggested the targets of alpha and beta globin chains, leading to inhibition of staphylococcal exotoxins, included the two-component system SrrA-SrrB. delta hemolysin production was also inhibited, suggesting the two-component (and quorum sensing) system AgrA-AgrC was targeted. The alpha and beta globin chains represent promising molecules to interfere with the pathogenesis of serious staphylococcal diseases.

Evaluation of effects from repeated inhalation exposure of F344 rats to high concentrations of propylene.

Chronic exposure to propylene does not result in any increased incidence of tumors, yet does increase N7-hydroxypropylguanine (N7-HPGua) adducts in tissue DNA. To investigate any potential for genotoxicity (mutagenicity or clastogenicity), male F344 rats were exposed via inhalation to up to 10,000 ppm propylene for 1, 3, or 20 days (6 h/day, 5 days/week). The endpoints examined included gene (Hprt, splenocytes) and chromosomal (bone marrow micronucleus [MN]) mutations, hemoglobin (hydroxypropylvaline, HPVal) adducts in systemic blood, and DNA adducts (N7-HPGua) in several tissues. Similarly exposed female and male F344 rats, implanted with bromodeoxyuridine (BrdU) minipumps, were evaluated for nasal effects (irritation via histopathology and cell proliferation via BrdU). Internal dose measures provided clear evidence for propylene exposure, with HPVal increased for all exposures; N7-HPGua was increased in all tissues from rats exposed for more than 1 day (except lymphocytes). Saturation of propylene conversion to propylene oxide was apparent from the adduct dose-response curves. There were no biologically significant genotoxic effects demonstrated at any exposure level, with no increase in Hprt mutant frequency or in bone marrow MN formation. In addition, no histopathological changes were noted in rodent nasal tissues nor any induction of cell proliferation in nasal tissues. These results demonstrate that repeated exposure of rats to high concentrations of propylene (< or = 10,000 ppm) does not produce evidence of local nasal cavity toxicity or evidence of systemic genotoxicity to hematopoietic tissue, despite the formation of N7-HPGua adducts. In addition, these data indicate that formation of N7-HPGua does not correlate with any measure of genotoxic effect, neither mutagenic nor clastogenic.

A combined micro-resonance Raman and absorption set-up enabling in vivo studies under varying physiological conditions: The nerve globin in the nerve cord of Aphrodite aculeata.

We hereby report on the design of a set-up combining micro-resonance Raman and absorption spectroscopy with a microfluidic system. The set-up enabled us to study the nerve globin of Aphrodite aculeata in the functional isolated nerve cord under varying physiological conditions for extended periods of time. The oxygenation cycle of the organism was triggered by utilizing the microfluidic system that allowed for a fast switch between aerobic and anaerobic conditions. The nerve globin was found to very easily shift from a penta-coordinated high spin ferrous form to the oxy state upon a change from anaerobic to aerobic conditions. The observed fast reaction to varying O(2) concentrations supports an oxygen-carrying and/or -storing function of the nerve globin. In addition, by combining resonance Raman and absorption spectroscopy, the physiological response could be distinguished from light-induced effects.

Absence of increased alpha1-microglobulin in IgA nephropathy proteinuria.

To search for biomarkers of IgA nephropathy, protein profiles of urine samples from patients with IgA nephropathy and normal volunteers were compared using two-dimensional DIGE. Most of the 172 spots identified in the urine were serum proteins, and their amounts in IgA nephropathy urine were much higher than those in normal urine; this can be explained as proteinuria caused by glomerular dysfunction. However, only alpha(1)-microglobulin, also one of the major serum proteins, in IgA nephropathy urine was not higher in amount than that in normal urine. We confirmed using ELISA analysis that the amounts of transferrin and albumin in IgA nephropathy and diabetic nephropathy urine were much higher than those in normal urine, whereas the amount of alpha(1)-microglobulin in IgA nephropathy urine was not higher than that in normal urine and was much lower than that in diabetic nephropathy urine. Approximately 50% of alpha(1)-microglobulin forms a complex with IgA in serum. These results suggest that alpha(1)-microglobulin in IgA nephropathy urine is a characteristic protein and might be a biomarker for IgA nephropathy and that alpha(1)-microglobulin might have a relationship with IgA nephropathy pathology.

Efecto de la fijación en la calidad del ADN: estudio controlado con cinco fijadores / Effect of fixation on DNA quality: controlled study with five fixatives

Antecedentes: Los tejidos fijados y embebidos en parafina son una fuente importante de material para diagnóstico e investigación. La amplificación de ADN desde este tipo de tejidos, mediante reacción en cadena de la polimerasa (PCR), es afectada por el tipo de fijador y los tiempos de fijación empleados. Para determinar el parámetro que mejor se adecue a las condiciones de trabajo de nuestro laboratorio de Patología Molecular, evaluamos el efecto de cinco fijadores sobre la calidad del ADN bajo condiciones controladas. Material y Método: Muestras de mucosa gástrica fueron fijadas, embebidas en parafina y luego procesadas para extracción de ADN empleando un protocolo basado en digestión con proteinasa K. La calidad del ADN se evaluó mediante amplificación de tres fragmentos del gen β-globina (268, 536 y 989 pb). Resultados: No observamos mayores diferencias entre fijadores ni tiempos de fijación en la amplificación de ADN de 268 y 536 pb. No obstante, la amplificación del fragmento mayor (981 pb) se vio alterada al aumentar el tiempo de fijación, a excepción de aquellas muestras fijadas en etanol 70% que presentaron una banda de similar intensidad a la obtenida para muestras control (tejido fresco congelado). Conclusiones: Estos resultados nos proporcionan una pauta para el diseño de experimentos de acuerdo a la calidad del material archivado, optimizando recursos humanos e insumos

Background: Fixed and paraffin-embedded tissues from pathological archives are an important source for research. DNA amplification by polymerase chain reaction (PCR) from those materials is affected by fixatives and fixation time. In order to determine the best condition for our laboratory work, we evaluated the effect of five different fixatives on DNA quality under controlled conditions. Material and Method: Gastric mucosa samples from two patients were fixed, embedded in paraffin and then processed for DNA extraction using a routine method based on proteinase K digestion. DNA quality was evaluated by amplifying three Beta-globin gene fragments (268, 536 and 989 bp). Results: We did not observe major differences among fixatives nor fixation times for 268 and 536 bp fragments but the amplification of the greatest fragment was altered by increasing the fixation time, by excepting those samples fixed in 70% ethanol which present a similar band intensity than control samples (snap-frozen tissue). Conclusions: These results give us a good guideline to design experiments considering the quality of our archival material

Purification of placenta-eluted gamma globulins and their strong effect against graft-versus-host reactions in vitro and in vivo.

In the 1980s, attempts were made to use placenta-eluted gamma globulins (PEGG) in patients with graft-versus-host disease (GVHD) after bone marrow transplantation (BMT). Because production of PEGG had been discontinued for many years, we aimed to reestablish a method of production and further explore the mechanisms of the effect of these globulins on GVHD. PEGG were prepared by elution at acid pH from extensively washed human placenta followed by precipitation with saturated ammonium sulfate and absorption on a protein A Sepharose column. In vitro study showed PEGG significantly inhibited both the proliferative response of T-cells to phytohemagglutinin (PHA) and the mixed lymphocyte reaction (MLR). Results of flow cytometric analysis indicated that PEGG down-regulated the expression of CD25 and CD69 on T-cells stimulated by PHA. Cytokine quantification in MLR supernatant showed that PEGG decreased secretion of interferon 3 (IFN-3) but increased production of interleukin 4. In a murine GVHD model, we investigated the preventive effect of PEGG on lethal GVHD in irradiated recipients of allogeneic bone marrow cells and spleen cell transplants by in vivo administration. Compared with controls, recipients treated with PEGG had a markedly increased survival rate with less histopathological evidence of GVHD. These results suggest that PEGG may be a potent therapeutic agent for GVHD.

Mutations associated with beta-thalassemia intermedia in Kuwait.

OBJECTIVE: To identify the beta-globin gene mutations associated with beta-thalassemia (beta-thal) intermedia in Kuwait. SUBJECTS AND METHODS: Eighteen patients from 13 unrelated families, mean age 12.7 +/- 8.1 years, range 4-31 years, were involved in the study. They did not require regular blood transfusion. Complete blood count and cation exchange high-performance liquid chromatography hemoglobin quantitation were carried out using standard techniques. Beta-thal mutations were identified with a combination of PCR amplification, allele- specific oligonucleotide hybridization or direct DNA sequencing. The patients were also screened for the alpha2-globin gene (-3.7 kb) deletion. RESULTS: Of the 13 families, 4 were homozygous for the IVS-I-II (G-->A) and 4 for the IVS-I-6 (T-->C) mutations, while 1 each was a compound heterozygote for the following mutation combinations: CD 8 (-AA) and -101 (C-->T); IVS-I-6 (T-->C) and CD 19 (A-->G); IVS-II-1 (G-->A) and -28 (A-->C); IVS-I-110 (G-->A) and deltabeta0 deletion. Therefore, homozygosity for two typically mild mutations (IVS-II-1 and IVS-I-6) accounted for 61% of the genotypes in our patients. CONCLUSION: Our results indicate that screening should commence with these two common alleles in Kuwaiti patients presenting with beta-thal syndrome. Early identification of intermedia patients will avoid the complications following an unnecessary hypertransfusion program.

Effect of glucose concentration on formation of AGEs in erythrocytes in vitro.

Posttranslational modifications, such as advanced glycoxidation and lipoxidation end products (AGE/ALEs), are implicated in the pathogenesis of diabetic complications and atherosclerosis. Recent studies have demonstrated that AGE/ALEs are generated not only in extracellular matrix proteins, but also in intracellular proteins from metabolic intermediates. In this study we investigate the effect of glucose concentration on the formation of the AGE/ALEs, Nepsilon-(carboxymethyl)lysine (CML), Nepsilon-(carboxyethyl)lysine (CEL), S-(carboxymethyl)cysteine (CMC), and S-(2-succinyl)cysteine (2SC) in erythrocytes as a function of glucose concentration. Human erythrocytes (10% hematocrit) were incubated in Dulbecco's modified Eagle's medium (DMEM) containing 5 mM or 30 mM glucose for 5 days at 37 degrees C. Globin was recovered by precipitation with 0.25 M HCl in acetone. Following acid hydrolysis, amino acids were converted to their trifluoroacetyl methyl ester derivatives and analyzed by GC/MS/MS. The CML and CEL content of globin increased in a time- and glucose-dependent manner and also increased 1.3- and 1.8-fold, respectively, in incubations containing 30 mM glucose; whereas CMC and 2SC content did not change during the five-day incubations. Furthermore, CEL content of globin in erythrocytes incubated with 30 mM was the highest in the other AGEs, indicating that methylglyoxal may play a major role in AGE formation in erythrocytes. The erythrocyte system should be useful for cellular screening of the efficacy of inhibitors of AGE/ALE formation.

Removing peroxide impurities from ether improves the quality of globin chains for biosynthetic studies.

The diagnosis of the different forms of thalassemia is one of the important applications of analysis of globin chains. These analyses are done by high performance liquid chromatography (HPLC) using a MONO-S cation exchange column and ether is used for washing the globin powder in the final step. The presence of peroxide impurities in ether could change the structure of the globin chains. In the chromatograms, these modified globins appear as separated peaks next to the unmodified globin peaks. In these cases, the alpha/beta ratio exceed by artifact the correct value. Our study demonstrates that diagnostic centers should ensure that the ether they use is pure.