A pilot study suggests the correspondence between SAR202 bacteria and dissolved organic matter in the late stage of a year-long microcosm incubation

SAR202 bacteria are abundant in the marine environment and they have been suggested to contribute to the utilization of recalcitrant organic matter (RDOM) within the ocean's biogeochemical cycle. However, this functional role has only been postulated by metagenomic studies. During a one-year microcosm incubation of an open ocean microbial community with lysed Synechococcus and its released DOM, SAR202 became relatively more abundant in the later stage (after day 30) of the incubation. Network analysis illustrated a high degree of negative associations between SAR202 and a unique group of molecular formulae (MFs) in phase 2 (day 30 to 364) of the incubation, which is empirical evidence that SAR202 bacteria are major consumers of the more oxygenated, unsaturated, and higher-molecular-weight MFs. Further investigation of the SAR202-associated MFs suggested that they were potentially secondary products arising from initial heterotrophic activities following the amendment of labile Synechococcus-derived DOM. This pilot study provided a preliminary observation on the correspondence between SAR202 bacteria and more resistant DOM, further supporting the hypothesis that SAR202 bacteria play important roles in the degradation of RDOM and thus the ocean's biogeochemical cycle.

The Predominance of Ammonia-Oxidizing Archaea in an Oceanic Microbial Community Amended with Cyanobacterial Lysate

When the oligotrophic microbial community was amended with Synechococcus-derived dissolved organic matter (SDOM) and incubated under the dark condition, archaea relative abundance was initially very low but made up more than 60% of the prokaryotic community on day 60, and remained dominant for at least 9 months. The archaeal sequences were dominated by Candidatus Nitrosopumilus, the Group I.1a Thaumarchaeota. The increase of Thaumarchaeota in the dark incubation corresponded to the period of delayed ammonium oxidation upon an initially steady increase in ammonia, supporting the remarkable competency of Thaumarchaeota in energy utilization and fixation of inorganic carbon in the ocean. IMPORTANCE Thaumarchaeota, which are ammonia-oxidizing archaea (AOA), are mainly chemolithoautotrophs that can fix inorganic carbon to produce organic matter in the dark. Their distinctive physiological traits and high abundance in the water column indicate the significant ecological roles they play in the open ocean. In our study, we found predominant Thaumarchaeota in the microbial community amended with cyanobacteria-derived lysate under the dark condition. Furthermore, Thaumarchaeota remained dominant in the microbial community even after 1 year of incubation. Through the ammonification process, dissolved organic matter (DOM) from cyanobacterial lysate was converted to ammonium which was used as an energy source for Thaumarchaeota to fix inorganic carbon into biomass. Our study further advocates the important roles of Thaumarchaeota in the ocean's biogeochemical cycle.

New Perspectives on the Marine Carbon Cycle-The Marine Dissolved Organic Matter Reactivity Continuum

This perspective challenges our current understanding of the marine carbon cycle, including an alternative explanation of bulk 14C-DOM measurements. We propose the adoption of the carbon reactivity continuum concept previously established for lakes and sediments for the oceans using kinetic data and term this the marine DOM reactivity continuum. We need to gain a fundamental understanding of the biogeochemical drivers of surface water DOM concentrations and reactivity, biological carbon pump efficiency, and the autotrophic communities that are the ultimate but variable sources of marine DOM. This perspective is intended to shift our focus to a more inclusive kinetic model and may lead us to a more accurate assessment of the active and dynamic role marine DOM plays in the global carbon cycle. Currently, the kinetic data to establish and validate such a marine DOM reactivity continuum model are still lacking, and their resolution depends on the discovery of new organic tracers that span large differences in reactivity and microbial degradation rates. We may need to refocus our efforts in deciphering the structure and reactivity of marine organic molecules in a kinetic context, including the microbial and physicochemical constraints on molecular reactivity that are present in the deep ocean.

Characterization of myeloid-derived suppressor cells and cytokines GM-CSF, IL-10 and MCP-1 in dogs with malignant melanoma receiving a GD3-based immunotherapy

Melanoma in humans and canines is an aggressive and highly metastatic cancer. The mucosal forms in both species share genetic and histopathologic features, making dogs a valuable spontaneous disease animal model. Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of cells of myeloid origin with immunosuppressive capabilities, which are increased in many human cancers and contribute to tumor immune evasion. They are a possible target to improve immunotherapy outcomes. Current information regarding MDSCs in canines is minimal, limiting their use as translational model for the study of MDSCs. The objective of this study was to characterize major MDSCs subsets (monocytic and polymorphonuclear) and the cytokines granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin 10 (IL-10) and monocyte chemoattractant protein-1 (MCP-1) in canines with malignant melanoma and to evaluate changes in MDSCs and the cytokines over time in response to a GD3-based active immunotherapy. Whole blood and serum collected from 30 healthy controls and 33 patients enrolled in the University of Florida melanoma vaccine trial were analyzed by flow cytometry with canine specific CD11b, MHCII and anti-human CD14 antibodies to assess ostensibly polymorphonuclear-MDSC (CD11b⁺ MHCII^- CD14^-) and monocytic-MDSC (CD11b⁺ MHCII^- CD14⁺) subsets. IL-10, MCP-1 and both MDSCs subsets were significantly elevated in melanoma dogs versus controls. Both MDSCs subsets decreased significantly following GD3-based immunotherapy administration but no significant changes in cytokines were seen over time. To our knowledge, this is the first report documenting increased monocytic-MDSCs in canine melanoma. This is consistent with human malignant melanoma data, supporting dogs as a valuable model for therapeutic intervention studies.

Brillouin light scattering measurement of the elastic properties of aligned multilamella lipid samples

Brillouin measurements of the elastic properties are presented for aligned multilamella samples of both pure dipalmitoyl phosphatidylcholine at various temperatures and water concentrations and for the same compound containing 33 mol% cholesterol at various temperatures and two water concentrations. For pure dipalmitoyl phosphatidylcholine the elastic moduli change significantly at the gel transition and the modulus for area compression of individual bilayers is inferred to be an order of magnitude larger below the gel transformation than above. The presence of cholesterol is shown to influence the elastic behavior of dipalmitoyl phosphatidylcholine.

Active site structure of the catalase-peroxidases from Mycobacterium tuberculosis and Escherichia coli by extended X-ray absorption fine structure analysis

The catalase-peroxidase encoded by katG of Mycobacterium tuberculosis is a more effective activator of the antibiotic isoniazid than is the equivalent enzyme from Escherichia coli. The environment of the heme iron was investigated using X-ray absorption spectroscopy to determine if differences in this region were associated with the differences in reactivity. The variation in the distal side Fe-ligand distances between the two enzymes was the same within experimental error indicating that it was not the heme iron environment that produced the differences in reactivity. Analysis of variants of the E. coli catalase-peroxidase containing changes in active site residues Arg102 and His106 revealed small differences in Fe-water ligand distance including a shorter distance for the His106Tyr variant. The Arg102Leu variant was 5-coordinate, but His106Cys and Arg102Cys variants showed no changes within experimental error. These results are compared with those reported for other peroxidases.

Anatomy of an interview

Interviewing well is one of the most important skills that job seekers can possess. With the proper knowledge and preparation, anyone can interview more confidently. By looking at the anatomy of the interview process, you will know what is expected of you when you walk in the interviewer's door.

15N enrichment of ammonium, glutamine-amide and urea, measured via mass isotopomer analysis of hexamethylenetetramine

Ammonium is an important intermediate of protein metabolism and is a key component of acid-base balance. Investigations of the metabolism of NH(4)(+) in vivo using isotopic techniques are difficult because of the low concentration of NH(4)(+) in biological fluids and because of frequent artifactual isotopic dilution of the enrichment of NH(4)(+) during the assay. A new gas chromatographic mass spectrometric method was designed to monitor the (15)N enrichment and concentration of NH(4)(+) in vivo. These are both calculated from the mass isotopomer distribution of hexamethylenetetramine (HMT) formed by reacting NH(4)(+) with formaldehyde. The enrichment of NH(4)(+) is amplified four times since the HMT molecule contains four atoms of nitrogen derived from NH(4)(+). This allows the measurement of low (15)N enrichment of NH(4)(+), down to 0.1%. (15)N enrichment of urea and of the amide N of L-glutamine are measured by enzymatic release of NH(4)(+) and conversion of the latter to HMT. These new techniques facilitate in vivo investigations of the metabolism of NH(4)(+) and related compounds.

Escherichia coli primase zinc is sensitive to substrate and cofactor binding

The ligation state of the single zinc site in primase from Escherichia coli changes when various substrates and cofactors are added alone or in combination as determined by X-ray absorption spectroscopy. X-ray absorption spectroscopy (XAS) provides information about the local structure (approximately 5 A) of atoms surrounding the metal and has been widely used to characterize metalloproteins. The zinc site in native primase and in primase bound to low (30 mM) magnesium acetate was found to be tetrahedrally ligated by three sulfurs at an average distance of 2.36 +/- 0.02 A and one histidine nitrogen located at a distance of 2.15 +/- 0.03 A. When ATP, ATP and (dT)17, or ATP, low magnesium acetate and (dT)17 was added to primase, one (or two) additional nitrogen/oxygen ligands were coordinated to the zinc together with the histidine nitrogen at an average distance of 2.15 +/- 0.03 A. These additional ligands are likely from adjacent phosphates from ATP. Another structure was observed for the primase-(dT)17 complex in which an additional nitrogen/oxygen ligand likely from the phosphate backbone together with the histidine nitrogen was located at a significantly shorter average distance of 2.05 +/- 0.03 A. High magnesium acetate (300 mM) completely inactivates primase in a reversible manner such that the region near the zinc ligands becomes accessible to proteolytic digestion [Urlacher, T. M., and Griep, M. A. (1995) Biochemistry 34, 16708-16714]. In this inactive complex, additional oxygen/nitrogen ligands from acetate as well as the histidine nitrogen are located at a distance of 2.20 +/- 0.03 A from the zinc site. To test whether the catalytic magnesium was binding within approximately 5 A of the zinc, we incubated primase with high (300 mM) manganese acetate. The functional properties of magnesium and manganese are similar, but the larger atomic number of manganese enhances the X-ray backscattering, making it possible to identify. Since no significant difference was observed from the manganese-incubated sample, the catalytic metal-binding site is likely located >5 A from the zinc. These studies clearly show that primase zinc ligation changes upon binding substrates.

Fos expression in luteinizing hormone-releasing hormone neurons of guinea pigs, with knife cuts separating the preoptic area and the hypothalamus, demonstrating luteinizing hormone surges

LHRH neurons in guinea pigs, as in primates and other non-rodent species, are broadly distributed in the basal forebrain. In this study, knife cuts were made in the anterior hypothalamus, effectively separating more caudally positioned hypothalamic LHRH neurons from those in rostral preoptic areas. Guinea pigs with knife cuts displayed an LH surge in response to steroid administration. There was no significant difference in the number of LHRH neurons that expressed Fos in conjunction with an LH surge, although fewer total LHRH neurons were detected in the forebrain of knife-cut versus sham-cut animals. Knife-cut animals displayed a larger percentage of LHRH/Fos neurons in one region of the caudal hypothalamus than sham-cut animals. The area and perimeter of the LHRH reaction product within the cytoplasm of LHRH/Fos neurons were smaller than those of single-labeled LHRH neurons in sham-cut animals and in the caudal hypothalamus, but not the rostral preoptic area, of knife-cut animals. We conclude that caudal hypothalamic LHRH neurons separated from rostral preoptic regions are capable of sustaining an LH surge in guinea pigs. This finding is important, as LHRH neurons are present in the caudal hypothalamus, as well as in preoptic areas, of a large number of mammalian species, including humans.

Tracing gluconeogenesis with deuterated water: measurement of low deuterium enrichments on carbons 6 and 2 of glucose

The contribution of gluconeogenesis to glucose production in vivo can be measured by enriching body water with 0.5% 2H2O and measuring the glucose labeling ratio C6/C2 (Landau et al., J. Clin. Invest. 95, 172-178, 1995). We present further refinements of the measurements of the 2H enrichments on C6 and C2 of glucose. The transfer of 2H from C6 of glucose to hexamethylenetetramine (HMT) and extraction in preparation for gas chromatography-mass spectrometry can be done in a single test tube, without distillation of the intermediate formaldehyde. In addition, extraction of small amounts of HMT is greatly improved by making a HMT-iodine adduct. For C2, glucose is reduced to sorbitol, and 2H on C2 is transferred enzymatically to [U-13C3]pyruvate, forming [U-13C3,2-2H]lactate. The latter is assayed by negative chemical ionization gas chromatography-mass spectrometry of the pentafluorobenzyl derivative. The natural enrichment of the [U-13C3]lactyl ion is only 0.4%, allowing measurements of 2H enrichment down to 0.1%. These techniques were used in dogs infused with 2H2O and in isolated rat livers perfused with buffer containing 1 to 5% 2H2O. Our data reveal a difference in the rate of labeling of C6 and C2 of glucose in vivo. Lastly, in cows infused with [6,6-2H2]glucose, we show that the turnover of glucose can be economically measured by assaying low tracer enrichment (down to 0.1%) via hexamethylenetetramine.

Stable isotope model for assessing production of short chain fatty acids from colon-derived sugar: application in pigs

Sugar reaching the colon because of intestinal maldigestion or malabsorption may be fermented to acetate and other short-chain fatty acids, resulting in stimulation of colonic water absorption and cell proliferation. To explore this phenomenon in more detail, we have developed a stable isotope model for estimating the fraction of colon-derived glucose or lactose that is fermented to acetate, propionate and butyrate. In an initial application of the model, [d3]-acetate and either [1-(13)C]-glucose or [D-1-(13)C]-lactose were infused into the cecum or colon of piglets, and plateau plasma acetate enrichment was monitored in the carotid artery. In acutely anesthetized piglets, the fractions of glucose and lactose fermented to acetate were 17.0 and 20.0%, respectively. In a chronically catheterized piglet, fermentation was higher (34.2%). When conducted in chronically catheterized animals or via a colostomy or ileostomy in infants, this model may be used to determine how age, previous surgery or antibiotic therapy affects the efficiency of colonic assimilation of carbohydrate.

Active site structure in cytochrome c peroxidase and myoglobin mutants: effects of altered hydrogen bonding to the proximal histidine

The globins and peroxidases, while performing completely different chemistry, share features of the iron heme active site: a protoporphyrin IX prosthetic group is linked to the protein by the proximal histidine residue. X-ray absorption spectroscopy provides a method to determine the local structure of iron heme active sites in proteins. Our previous studies using X-ray absorption spectroscopy revealed a significant difference in the Fe-N epsilon bond length between the peroxidases and the globins [for a review, see Powers, L. (1994) Molecular Electronics and Molecular Electronic Devices, Vol. 3, p 211 CRC Press Inc., Boca Raton, FL]. Globins typically have an Fe-N epsilon distance close to 2.1 A while the Fe-N epsilon distance in the peroxidases is closer to 1.9 A. We have proposed [Sinclair, R., Powers, L., Bumpus, J., Albo, A., & Brock, B. (1992) Biochemistry 31, 4892] that strong hydrogen bonding to the proximal histidine is responsible for the shorter bond length in the peroxidases. Here we use site-specific mutagenesis to eliminate the strong proximal hydrogen bonding in cytochrome c peroxidase and to introduce strong proximal hydrogen bonding in myoglobin. Consistent with our hypothesis, elimination of the Asp235-His175 hydrogen bond in CcP results in elongation of Fe-N epsilon from approximately 1.9 to approximately 2.1 A. Conversely, introduction of a similar strong proximal hydrogen bond in myoglobin shortens Fe-N epsilon from approximately 2.1 to approximately 1.9 A. These results correlate well with other biochemical data.

Formation of a porphyrin pi-cation radical in the fluoride complex of horseradish peroxidase

Horseradish peroxidase (HRP) was oxidized by IrCl6(2-) to a mixture of compounds I and II, the rate of oxidation and the ratio of the mixture being greatly affected by pH (Hayashi & Yamazaki, 1979). Oxidation of HRP by IrCl6(2-) in the presence of fluoride was significantly accelerated. This resulted in the formation of a new compound which is a ferric fluoride complex containing a porphyrin pi-cation radical. The spectrum of the new compound showed a decreased absorption band in the Soret region and a broad band at 570 nm; which was converted to that of the original ferric fluoride complex by addition of ascorbate or hydroquinone. Addition of cyanide slowed down the oxidation of HRP by IrCl6(2-), and the oxidation product was the same as that obtained in the absence of cyanide. Compound I was formed when H2O2 was added to HRP in the presence of fluoride or cyanide. The one-electron reduction potential (Eo') of the oxidized HRP-fluoride complex was measured at several pH values, the Eo' value at pH 7 being 861 +/- 4 mV. The ratio of delta Eo' to delta pH was 49 mV/pH unit.

X-ray absorption spectroscopy comparison of the active site structures of Phanerochaete chrysosporium lignin peroxidase isoenzymes H2, H3, H4, H5, H8, and H10

The iron heme and its immediate environment can provide information that is pivotal to our understanding of the structural and mechanistic features that confer unusual properties to the heme peroxidases. X-ray absorption spectroscopy (XAS), which is ideally suited for the investigation of the local environment and electronic structure of the heme iron of hemeproteins, has been used to characterize a variety of lignin peroxidase and manganese-dependent peroxidase isoenzymes produced by the white rot fungus Phanerochaete chrysosporium. The data suggest no differences within the error in the first coordination shell of iron for the isoenzymes H2, H3, H4, H5, H8, and H10 examined in this study. The pyrrole nitrogens are at a distance of 2.05 +/- 0.015 A, and the proximal histidine nitrogens are at 1.93 +/- 0.02 A, while the sixth ligands are located at 2.17 +/- 0.03 A. Significant differences are observed in higher coordination shells which may be related to conformational differences in the heme.

Enhancing the participation and independence of students with severe physical and multiple disabilities in performing community activities

The effectiveness of a multi-element approach derived from factors to increase self-determination of middle- and high-school-age students with physical and multiple disabilities was examined. The approach includes equipment and performance adaptations, brief in-school simulation training, and instruction and support for parents and home assistance providers. The intervention was instituted with 3 students; a multiple baseline design was used. Student participation and independence dramatically increased after the intervention. Results suggest that this approach may be one solution to providing students with both inclusive education and community skill and activity instruction. The impact of the intervention on student self-determination was discussed.

Synthesis and structures of Zn(C6H12OS2)2(ClO4)2 and Zn(C3H6NS2)2(C3H4N2)--model compounds for the Zn sites in RNA polymerase

Model compounds for the Zn sites of the beta' and the beta subunits in RNA polymerase [1] were synthesized. Single crystal structures and X-ray absorbtion spectroscopy measurements for these two model complexes are reported. In Zn(C6H12OS2)2(ClO4)2, the Zn is coordinated by four sulfur and two oxygen atoms. The average Zn-S bond length is 2.514 A and the Zn-O bond length is 2.089 A, which are similar to these bond distances reported for the Zn site in the beta' subunit of RNA polymerase. In Zn(C3H6NS2)2(C3H4N2), the Zn atom is coordinated by four sulfur atoms and one nitrogen atom of an imidazole group. The average of the Zn-S bond length is 2.469 A and the Zn-N bond length is 2.009 A, which are also similar to the Zn-S and Zn-N bonds in the beta subunits of RNA polymerase.

Metabolism of R-beta-hydroxypentanoate and of beta-ketopentanoate in conscious dogs

R-beta-Hydroxypentanoate and beta-ketopentanoate are homologues of physiological ketone bodies R-beta-hydroxybutyrate and acetoacetate. They derive from the oxidation in liver of the R-moiety of R,S-1,3-pentanediol, a potential nutrient. This report documents the metabolism of R-beta-hydroxypentanoate and beta-ketopentanoate in conscious dogs. Whether administered by bolus or constant infusion, the two substrates are interconverted and rapidly metabolized. When beta-ketopentanoate was infused at a rate corresponding to 75% of the dog's caloric requirement, the steady-state total plasma concentration of the two substrates was only 1.3 mM. Because the substrates are precursors of propionyl-CoA, we assayed the urinary concentrations of markers of propionic acidemia. Their accumulation was minor compared with what is observed in patients suffering from propionic acidemia. We conclude that, at least during short-term experiments, R-beta-hydroxypentanoate and beta-ketopentanoate are well metabolized in the dog without apparent intolerance to a large supply of propionyl-CoA.

Assay of the enantiomers of 1,2-propanediol, 1,3-butanediol, 1,3-pentanediol, and the corresponding hydroxyacids by gas chromatography-mass spectrometry

We developed gas chromatographic-mass spectrometric assays for the enantiomers of 1,2-propanediol, 1,3-butanediol, 1,3-pentanediol, and their corresponding hydroxyacids, lactate, beta-hydroxybutyrate, and beta-hydroxypentanoate (3-hydroxyvalerate) in biological fluids. The corresponding ketoacids, acetoacetate and beta-ketopentanoate, can be assayed simultaneously by pretreating the samples with NaB2H4. The assays involve spiking the samples with deuterated internal standards, deproteinization, ether extraction, and derivatization of the carboxyl groups with (R,S)-2-butanol/HCl and of the hydroxyl groups with chiral (S)-(+)-2-phenylbutyryl chloride. Mass spectrometric analysis is conducted under ammonia positive chemical ionization. We used these assays to follow the metabolism of diol enantiomers in dogs. For (R,S)-1,3-butanediol and (R,S)-1,3-pentanediol, the uptakes from dog plasma of the R and S enantiomer of each diol were identical. In contrast, the metabolism of (S)-1,2-propanediol was faster than that of (R)-1,2-propanediol. (R)-1,2-Propanediol is formed during acetone metabolism, while (R,S)-1,3-butanediol and (R,S)-1,3-pentanediol are potential nutrients. The assays developed will allow further investigations of the metabolisms of acetone, (R)-lactate, and artificial nutrients derived from the 1,3-butanediol and 1,3-pentanediol enantiomers.

Spontaneous fusions to prv43 can suppress the export defect of pseudorabies virus gIII signal peptide mutants

We have devised an enrichment scheme for the isolation of export-competent derivatives of pseudorabies virus glycoprotein gIII signal peptide mutants. Enrichment is based upon a growth advantage imparted upon gIII-containing virions compared with virions lacking the glycoprotein. Each of identified derivatives suppressed the gIII signal peptide defect by fusing the gIII gene in frame to the prv43 gene that lay immediately upstream; the result was the synthesis of a Prv43-gIII hybrid protein. The deduced Prv43 protein is predicted to span a membrane multiple times, and it appeared that the gIII portion of each hybrid used a hydrophobic domain of Prv43 protein to initiate its export. For at least two of the isolates, the hybrid protein was efficiently translocated across the endoplasmic reticulum membrane but appeared to be poorly exported out of the endoplasmic reticulum. Nonetheless, the prv43-gIII fusions encoded a gIII species that was localized to the virus envelope. Because the gIII portion of each hybrid protein must be exposed on the virion surface to provide a growth advantage, our results also suggest a preliminary membrane topology for wild-type Prv43 protein.

Comparative effects of the combination of digoxin and dl-sotalol therapy versus digoxin monotherapy for control of ventricular response in chronic atrial fibrillation. dl-Sotalol Atrial Fibrillation Study Group

To establish the value of adjuvant dl-sotalol to digoxin for control of the ventricular response in chronic atrial fibrillation, 60 patients were evaluated in a multicenter, randomized, double-blind, parallel, placebo-controlled study. Patients were evaluated with serial ambulatory ECG monitoring and exercise testing during stable digoxin dosing and then with the addition of either a placebo or dl-sotalol, 80 mg/day, or dl-sotalol, 160 mg/day. The combination of digoxin and dl-sotalol, at either 80 or 160 mg/day, resulted in a statistically significant reduction in heart rate at rest and with exercise during both exercise testing and ambulatory monitoring. No significant difference was observed between the two doses of dl-sotalol. There was no significant difference with regard to symptoms or side effects among the three groups. In summary, dl-sotalol was noted to be a safe and effective adjuvant to digoxin for control of the ventricular response in chronic atrial fibrillation.

Characterization of the prv43 gene of pseudorabies virus and demonstration that it is not required for virus growth in cell culture

We have determined the complete DNA sequence of the prv43 gene of a swine herpesvirus, pseudorabies virus. prv43 is 1119 bp in length with a G+C content of 74.5% and is predicted to encode a multiply hydrophobic protein with a molecular mass of 38 kDa. prv43 is colinear with the herpes simplex virus type 1 UL43 locus, and the prv43 and UL43 gene products are predicted to be 47% similar and 23% identical. prv43 is an early gene, producing a 1.2-kb transcript that is easily detected at 2 hr postinfection but not at 6 hr postinfection. We have constructed a prv43 deletion mutant that does not express a prv43 transcript. This mutant did not appear to be defective for viral growth and demonstrated that the gene is nonessential for virus growth in cell culture.

Structure of the binuclear heme iron-copper site in the quinol-oxidizing cytochrome aa3 from Bacillus subtilis

Cytochrome aa3-600 is a terminal quinol oxidase of Bacillus subtilis, belonging to the large family of structurally and functionally related respiratory enzymes to which the mitochondrial cytochrome c oxidase also belongs. However, the CuA center typical of the cytochrome c oxidases is lacking from cytochrome aa3-600. The presence of only one copper, viz. CuB of the binuclear heme iron-copper site, makes cytochrome aa3-600 especially suitable for XAS analysis of this structure. Cu and Fe XAS data for fully oxidized cytochrome aa3-600 indicate a structure for the binuclear site similar to that previously reported for mitochondrial cytochrome c oxidase (see Powers et al. (1981) Biophys. J. 34, 465-468). Heme Fea3 has a proximal histidine nitrogen ligand 2.10 +/- 0.02 A from the iron, and a distal S or Cl ligand at 2.36 +/- 0.03 A. The latter is also a ligand of CuB (2.21 +/- 0.02 A), and apparently forms a bridge between the two metals which are 3.70 +/- 0.06 A apart. CuB has two more close-lying ligands at 1.95 +/- 0.02 A, which are likely histidine nitrogens. The similarity between EXAFS of CuB and type 1 'blue' copper is contrasted to EPR and optical spectroscopic properties of CuB, and the nature of the bridging ligand is discussed.

Ranitidine is effective therapy for erosive esophagitis

Two ranitidine dosages were compared for the treatment of erosive esophagitis in a multicenter, double-blind, randomized, parallel-group, placebo-controlled study. Adults with endoscopically verified erosive esophagitis were treated with either ranitidine 150 mg four times daily (n = 106), ranitidine 300 mg four times daily (n = 106), or placebo (n = 116) for up to 12 wk. Patients were also encouraged to adhere to lifestyle modifications (e.g., to elevate the head of bed, etc). Erosive esophagitis healing, determined by endoscopy, was achieved in 69% and 62% of ranitidine-treated patients by 8 wk and in 79% and 74% by 12 wk (150 mg and 300 mg, respectively) compared with 28% of placebo-treated patients by 8 wk and 40% by 12 wk (p < 0.001 ranitidine vs. placebo). Onset of heartburn relief occurred within 24 h of initiating either ranitidine dosage, and relief was maintained throughout the 12-wk study. Both ranitidine dosages displayed safety profiles similar to that of placebo. We conclude that ranitidine 150 mg or 300 mg administered four times daily is effective for healing erosive esophagitis and relieving its symptoms.

An extended X-ray absorption fine structure investigation of the structure of the active site of lactoperoxidase

Native lactoperoxidase, compound III, and the reduced forms (at pH 6 and 9) were studied using X-ray absorption spectroscopy (XAS). Native lactoperoxidase has four pyrrole nitrogen ligands at an average distance of 2.04 +/- 0.01 A, a proximal ligand at 1.91 +/- 0.02 A, and a sixth (distal) ligand at 2.16 +/- 0.03 A. Lactoperoxidase native enzyme has a first coordination shell structure that is similar to that of native lignin peroxidase [Sinclair, R., Yamazaki, I., Bumpus, J., Brock, B., Chang, C.-S., Albo, A., & Powers, L. (1992) Biochemistry 31, 4892-4900] and different from that of horseradish peroxidase [Chance, B., Powers, L., Ching, Y., Poulos, T., Schonbaum, G., Yamazaki, I., & Paul, K. (1984) Arch. Biochem. Biophys. 235, 596-611]. Similarly, lactoperoxidase compound III resembles lignin peroxidase compound III. The five-coordinated ferrous form was stable at pH 9, but at pH 6 it was rapidly converted to the six-coordinated form with a distal ligand at 2.18 +/- 0.03 A. No evidence typical of changes in spin state was obtained at the different pH values.

pH dependence of the active site of horseradish peroxidase compound II

Using X-ray absorption spectroscopy, we investigated the active site of horseradish peroxidase (HRP) compound II at two different pH values. The results indicate that the bond length of the sixth coordinated ligand of the active site was 1.90 +/- 0.02 A at pH 7, decreasing to 1.72 +/- 0.02 A at pH 10. The average iron-to-pyrrole nitrogen and the proximal ligand bond lengths showed no significant changes. The position of higher coordination shells around the iron center changed, implying that some movement or deformation of nearby amino acid residues and/or of the heme occurred. Results of this study suggest that the decrease of the Fe-O bond length of HRP compound II at the higher pH might be attributed to the loss of a hydrogen bond which is present between the oxygen ligand and an amino acid residue in the heme pocket at pH 7.

The structure of the zinc sites of Escherichia coli DNA-dependent RNA polymerase

X-ray absorption spectroscopy is ideally suited for the investigation of the electronic structure and the local environment (approximately 5 A) of specific atoms in biomolecules. While the edge region provides information about the valence state of the absorbing atom, the chemical identity of neighboring atoms, and the coordination geometry, the extended x-ray absorption fine structure region contains information about the number and average distance of neighboring atoms and their relative disorder. The development of sensitive detection methods has allowed studies using near physiological concentrations (as low as approximately 100 microM). RNA polymerase from Escherichia coli contains two zinc atoms: one tightly bound in the beta' subunit, the subunit that participates in template binding, and the other loosely bound in the beta subunit, the subunit that participates in substrate binding. X-ray absorption studies of these zinc sites in the native protein and of the zinc site in the beta' subunit after removal of the zinc in the beta subunit site by p-(hydroxymercuri)benzenesulfonate (Giedroc, D. P., and Coleman, J. E. (1986) Biochemistry 25, 4969-4978) indicate that both zinc sites have octahedral coordination. The zinc in the beta' subunit site has four sulfur ligands at an average distance of 2.36 +/- 0.02 A and two oxygen (or nitrogen) ligands at an average distance of 2.23 +/- 0.02 A. The beta subunit zinc site has five sulfur ligands at an average distance of 2.38 +/- 0.01 A and one histidine nitrogen ligand at 2.14 +/- 0.02 A. These results are in general agreement with earlier biochemical and spectroscopic studies.

Structure of the active site of lignin peroxidase isozyme H2: native enzyme, compound III, and reduced form

The wood-degrading fungus Phanerochaete chrysosporium secretes a number of extracellular enzymes called lignin peroxidases which are involved in the degradation of both lignin and a number of persistent environmental pollutants. Lignin peroxidase isozyme H2, a glycosylated protein of approximately 40 kDa, contains a single heme. X-ray absorption spectroscopy (XAS) has been used to probe the local environment of the iron in the active site of resting enzyme, reduced enzyme, and compound III. For the native and reduced forms, respectively, the average Fe-pyrrole nitrogen distances are 2.055 and 2.02 A (+/- 0.015 A); the Fe-proximal nitrogen distance is 1.93 and 1.91 A (+/- 0.02 A) while the Fe-distal ligand distance is 2.17 and 2.10 A (+/- 0.03 A). Although the results are not as well-defined, the active-site structure of compound III is largely 2.02 +/- 0.015 A for the average Fe-pyrrole nitrogen distance, 1.90 +/- 0.02 for the Fe-proximal nitrogen, and 1.74 +/- 0.03 A for the Fe-distal ligand distance. The heme iron-pyrrole nitrogen distance is more expanded in ligninase H2 than in other peroxidases. The possible significance of this is discussed in relation to other heme proteins.

EXAFS studies of the isolated bovine heart Rieske [2Fe-2S]1+(1+,2+) cluster

Recently the involvement of one or, more likely, two nitrogen-ligands in the Rieske-type [2Fe-2S] cluster has been reported based on the chemical assay and various spectroscopic analyses, such as EPR, Mössbauer, ENDOR, and resonance Raman, of isolated Thermus thermophilus HB-8 protein by Fee and his collaborators. Similarly, the presence of at least one nitrogen ligand was shown in the mitochondrial Rieske [2Fe-2S] cluster. We have conducted EXAFS studies of the Rieske [2Fe-2S] protein isolated from the cytochrome bc1 complex of bovine heart mitochondria. Standard analysis could not distinguish one or two nitrogen ligands per cluster. However, one nitrogen and three cysteine ligands per cluster was found to be, possibly, a better solution in more comprehensive analysis procedures.

Comparison of the data, analysis, and results of X-ray absorption studies of cytochrome c oxidase

Differences in the methods of analysis of X-ray absorption data used by Powers et al. [Powers, L., Blumberg, W. E., Chance, B., Barlow, C., Leigh, J., Jr., Smith, J., Yonetani, T., Vik, S., & Peisach, J. (1979) Biochim. Biophys. Acta 547, 520-538; Powers, L., Chance, B., Ching, Y., & Angiolillo, P. (1981) Biophys. J. 34, 465-498] and Scott et al. [Scott, R., Schwartz, J., & Cramer S. (1986) Biochemistry 25, 5546-5555] are clarified. In addition, we compare the X-ray absorption data and results for resting cytochrome c oxidase reported by both groups using the same analysis method and conclude apart from any assumptions that the data are not identical.

X-ray absorption spectroscopic study of the active copper sites in dopamine beta-hydroxylase

X-ray absorption spectroscopy has been used to investigate the local environment of the copper sites in bovine dopamine beta-hydroylase, the enzyme that catalyzes the conversion of dopamine to norepinephrine in the adrenal medulla and noradrenergic nerve cells. The marked similarity of the x-ray absorption edge features of the oxidized and ascorbate-reduced forms of the enzyme with those of the corresponding Cu(imidazole)4 complexes suggests that the ligation in both cases is very similar. Furthermore, this similarity is found for the extended x-ray absorption fine structure data, and analysis shows only nitrogen (or oxygen) ligation for both enzyme forms. Thus, four nitrogen atoms provide the best fit to the data at an average distance of 1.97 +/- 0.02 A for the oxidized enzyme and four nitrogen atoms at 2.05 +/- 0.02 A for the ascorbate-reduced form. The present data analysis also indicates that there is little change in the average copper ligand environment upon reduction of the enzyme-bound copper from Cu(II) to the Cu(I). The data for the oxidized form of the enzyme are in agreement with previous spin-echo EPR experiments that show three to four imidazole nitrogen ligands for each copper (McCracken, J., Desai, P. R., Papadopoulos, N. J., Villafranca, J. J., and Peisach, J. (1988) Biochemistry 27, 4133-4137). In addition, the data do not indicate the presence of any heavy atom (sulfur or chlorine) ligation to the ascorbate-reduced form of the enzyme as reported by Scott et al. (Scott, R. A., Sullivan, R. J., DeWolf, W. E., Jr., Dolle, R. E., and Kruse, L. I. (1988) Biochemistry 27, 5411-5417).

On the environment of zinc in beef heart cytochrome c oxidase: an x-ray absorption study

The role of zinc in beef heart cytochrome c oxidase has been studied by using x-ray absorption spectroscopy, zinc depletion and secondary structure predictions of subunits of beef heart cytochrome c oxidase. The stoichiometry of zinc in cytochrome oxidase has been determined in 35 different preparations and found to be one-half of copper (Cu:Zu = 2:1). Zinc is tightly bound to this enzyme and cannot be removed by dialysis against EDTA. However, zinc could be partially (up to 50%) depleted by treating the enzyme with either dipicolinic acid or by trypsin digestion. This partial depletion of zinc does not change the O2 uptake rate. X-ray absorption spectroscopy shows that the atom is in a distorted tetrahedral environment with mostly sulfur ligands. Since subunit VIa removed by the digestion removes about one-half the zinc, a possible binding site involves the two S sites present in that subunit with an appropriate folding in a structural role.

Does the peroxide compound of cytochrome oxidase contain a ferryl iron?

The reaction of peroxide with cytochrome oxidase generates a peroxide compound having a Soret maximum at 428 nm. X-ray absorption spectroscopy analysis of the local structure of the active site iron shows marked similarity to that of the cytochrome c peroxidase intermediate Compound ES, which contains a short iron to proximal nitrogen distance compared to globins. Reductive titration of the 580 nm band of this compound indicates that the iron is one oxidizing equivalent above the resting oxidized form. These results support the presence of a ferryl iron (Fe(IV) = O) in the peroxide compound similar to that found for the peroxidases.

Kinetic, structural, and spectroscopic identification of geminate states of myoglobin: a ligand binding site on the reaction pathway

Elementary steps or geminate states in the reaction of gaseous ligands with transport proteins delineate the trajectory of the ligand and its rebinding to the heme. By use of kinetic studies of the 765-nm optical "conformation" band, three geminate states were identified for temperatures less than approximately 100 K. MbCO, which is accumulated by photolysis between 1.2 and approximately 10 K, was characterized by our previous optical and X-ray absorption studies [Chance, B., Fischetti, R., & Powers, L. (1983) Biochemistry 22, 3820-3829]. Between 10 and approximately 100 K, geminate states that are also identified that have recombination rates of approximately 10(3) s-1 and approximately 10(-5) s-1 (40 K). Thus, it is possible to maintain a steady-state nearly homogeneous population of the slowest recombining geminate state, Mb, by regulated continuous illumination (optical pumping). Both X-ray absorption and resonance Raman studies under similar conditions of optical pumping show that the heme structure around the iron in Mb is similar to that of MbCO. In both geminate states, the iron-proximal histidine distance remains unchanged (+/- 0.02 A) from that of MbCO while the iron to pyrrole nitrogen average distance has not fully relaxed to that of the deoxy state. In MbCO the CO remains close to iron but not bound, and the Fe...CO angle, which is bent in MbCO (127 +/- 4 degrees C), is decreased by approximately 15 degrees [Powers, L., Sessler, J. L., Woolery, G. L., & Chance, B. (1984) Biochemistry 23, 5519-5523]. The CO molecule in Mb, however, has moved approximately 0.7 A further from iron. Computer graphics modeling of the crystal structure of MbCO places the CO in a crevice in the heme pocket that is just large enough for the CO molecule end-on. Above approximately 100 K resonance Raman studies show that this structure relaxes to the deoxy state.

The transmembrane helices of beef heart cytochrome oxidase

The locations of the transmembrane helices in the 12 subunits of beef heart cytochrome oxidase were predicted with a modified form of the von Heijne-Blomberg hydrophobicity scale. Based on ∼20 residues per transmembrane helix, about 480 of the estimated 660 helical residues (36.8% of 1,793 total residues) are expected to be in transmembrane helices that have their axes tilted by a small angle α from the normal to the plane of the membrane. This angle is calculated to be ∼30°, based on the observed overall tilt angle θ of 39° obtained from circular dichroism (CD) measurements on multilamellar films, or about 25°, based on the observed tilt angle θ of 36° obtained from the infrared linear dichroism of films. For 21 residues per transmembrane helix, the calculated values of α become 32° and 28°, respectively, depending upon the value of θ used. Thus, a transmembrane helical tilt angle of ∼30° accounts for the predicted transmembrane stretches in cytochrome oxidase if 20-21 residues are sufficient to span the membrane. Additional helical residues in the lipid head region may deviate by a larger angle from the normal to the plane of the membrane in cytochrome oxidase.

Structure of the copper sites in membrane-bound cytochrome c oxidase

The structures of membrane proteins are difficult to obtain by crystallography and may be altered by the detergents used in their extraction. X-ray absorption spectroscopy has been used to identify the structures of the copper atoms of the membrane-bound enzyme in mitochondria and in submitochondrial particles at respective concentrations of 100 and 200 micron of molar copper. To within the experimental error, the x-ray absorption spectra of the copper atoms of the membrane-bound and the Yonetani (Yonetani, T. (1961) J. Biol. Chem. 236, 1680-1688) purified oxidase are identical; all detectable shells of the active site indicate no alteration of structural parameters. Significant differences are found when compared to the Hartzell-Beinert (Hartzell, R. C., and Beinert, H. (1974) Biochim. Biophys. Acta 368, 318-338) preparation. Extended x-ray absorption fine structure technology is now adequate for the direct studies of membrane proteins in situ in their natural environment.

Structure of the copper cluster in canine hepatic metallothionein using X-ray absorption spectroscopy

The metal binding site in the lysosomal copper metallothionein from canine liver (LyCuLP) was examined with X-ray edge and extended X-ray absorption fine structure (EXAFS) spectroscopies. The k-absorption edge spectrum of LyCuLP was consistent with the coordination of univalent copper. The Fourier transform of the EXAFS data showed four resolved shells of backscattering atoms. Comparisons between the phase and amplitude functions derived from the isolated shells to those of Cu-Cu, Cu-S, and Cu-N model compounds showed that each copper was coordinated by four sulfur atoms at a distance of 2.27 +/- 0.02 A. Analysis of the outer shell data indicated backscattering copper atoms at 2.74 +/- 0.05, 3.32 +/- 0.05, and 3.88 +/- 0.05 A. Interatomic distances determined from the EXAFS data were compared to the distances observed by X-ray crystallographic analysis of adamantane-like clusters containing four and five copper atoms and a cubic cluster containing four copper atoms, structurally similar to the 4Fe-4S clusters in some ferredoxins. The results of these comparisons suggest that the copper complexed in LyCuLP is arranged in an adamantane-like cluster. The structure derived for this protein may be conserved in other copper metallothioneins.

Cytochrome c peroxidase compound ES is identical with horseradish peroxide compound I in iron-ligand distances

X-ray absorption studies of compound ES of cytochrome c peroxidase show a short iron-oxygen distance of 1.67 +/- 0.04 A, an iron-histamine distance of 1.91 +/- 0.03 A, and an iron-pyrrole nitrogen average distance of 2.02 +/- 0.02 A. This is identical within the error with the reported structure of horseradish peroxidase compound I [Chance, B., Powers, L., Ching, Y., Poulos, T., Yamazaki, I., & Paul, K. G. (1984) Arch. Biochem. Biophys. 235, 596-611]. Comparisons of the structures of myoglobin peroxide [Chance, M., Powers, L., Kumar, C., & Chance, B. (1986) Biochemistry (preceding paper in this issue)], compound ES, and the intermediates of horseradish peroxidase reveal the possible mechanisms for the stabilization of the free radical species generated during catalysis. The proximal histidine regulates the structure and function of the pyrrole nitrogens and the heme, allowing for the formation and maintenance of the characteristic intermediates.

X-ray absorption studies of myoglobin peroxide reveal functional differences between globins and heme enzymes

X-ray absorption studies of myoglobin peroxide show that although it is not identical with compound I or II of horseradish peroxidase [Chance, B., Powers, L., Ching, Y., Poulos, T., Yamazaki, I., & Paul, K. G. (1984) Arch. Biochem. Biophys. 235, 596-611], it has some structural features in common with both. As seen in compound I, the Fe-O distance is short, but the iron-pyrrole nitrogen distance is contracted with a longer iron-histidine distance like compound II. The iron has a higher oxidation state than Fe3+, suggesting an oxyferryl ion type species. Comparison of the structures of various peroxidase and myoglobin compounds points out systematic differences that may explain the catalytic activity of the pi cation radical as well as some of the differences between globins and heme enzymes.

Multiple structures and functions of cytochrome oxidase

X-ray absorption studies have been used to investigate the structure of the four redox centers (2Fe, 2Cu) of the terminal enzyme in the respiratory chain, cytochrome c oxidase in the resting oxidized form as well as in the functional intermediates that are freeze-trapped. Methods of x-ray fluorescence detection for these low-concentration samples together with low-temperature cryostats and simultaneous optical monitoring were developed to ensure good signal-to-noise data and sample integrity. The resting oxidized form contains a sulfur bridge between the copper and iron of the active site which are separated by approximately 3.8 A. This separation of the active site metal atoms was uniquely identified by comparison of both the iron and copper EXAFS data and iron EXAFS of the copper-depleted enzyme. In the reduced state, the CO or O2 is bound to the active site iron having a structure identical to CO or oxy hemoglobin while the sulfur remains with the active site copper. Little change in structure is observed for the other iron and copper. It is the sulfur bridged active site form that is isolated by the Yonetani and Caughy methods with greater than or equal to 85% homogeneity but not the Hartzell-Beinert or similar methods. Another form observed in the redox cycle is also fully oxidized but lacks the sulfur bridged active site with the iron of the active site having a structure identical to that of the peroxidases. This form exhibits peroxidase as well as oxidase activity, and a stable intermediate is formed with hydrogen and ethylhydrogen peroxide in which the iron of the active site is structurally similar to that of the peroxidase intermediate. The active site copper, however, does not participate in the peroxidatic role and the structures of the other iron and copper are identical to those of the sulfur bridged resting oxidized form. Thus this unique enzyme has peroxidase activity which may serve to safeguard its main oxidase function.

Structure and reactivity of multiple forms of cytochrome oxidase as evaluated by X-ray absorption spectroscopy and kinetics of cyanide binding

The extended X-ray absorption fine structure (EXAFS) data show differences between the active site structures of different cytochrome oxidase preparations. In the resting (as isolated) state of the Yonetani preparation, the bridging atom between Fe3+a3 and Cu2+a3 is present [Powers, L., Chance, B., Ching, Y., & Angiolillo, P. (1981) Biophys. J. 34, 465], whereas in another preparation (e.g., Hartzell-Beinert), this atom seems to be bound only to Fe3+a3 in a significant fraction of the molecules. Both preparations bind cyanide in a multiphasic fashion, suggesting that the resting cytochrome oxidase is not homogeneous but rather is a mixture of several forms. The proportion of these forms as detected by cyanide binding kinetics differs for different preparations. However, upon reduction and reoxidation (conversion to the "oxygenated" form) the cyanide binding kinetics become monophasic and all preparations of the oxygenated form bind cyanide at the same rate. Thus, a combination of structural and kinetic approaches seems necessary for evaluation of the nature of the active site of cytochrome oxidase in its various forms.

X-ray absorption studies of intermediates in peroxidase activity

The structures of the enzyme-substrate compounds of peroxidases and catalase determined by X-ray absorption spectroscopy are presented. The valence state of the iron in Compounds I and II is determined from the edge to be higher than Fe+3. A short Fe-Ne (proximal histidine) distance is observed in all forms except Compound II, forcing the Fe-Np average distance to be long, a result which differentiates the peroxidases from the oxygen transport hemoproteins and plays a pivotal role in the mechanism. A correlation is shown between the ratio of peaks in the low k (ligand field indicator ratio) region, the Fe-Np (heme pyrrole nitrogen) average distance, and the magnetic susceptibility, which provides a sensitive indicator of spin state. The mechanism of H2O2 reduction is shown by analysis of the structural changes observed in the intermediates. Possible relationship of these compounds to that of the peroxidatic form of cytochrome oxidase is suggested by these results.

CO bond angle changes in photolysis of carboxymyoglobin

Previous studies [Chance, B., Fischetti, B., & Powers, L. (1983) Biochemistry 22, 3820-3829] of the local structure changes around the iron in carboxymyoglobin on photolysis at 4 K revealed that the iron-carbon distance increased approximately 0.05 A but was accompanied by a lengthening of the iron-pyrrole nitrogen bonds of the heme (approximately 0.03 A) that was not as large as that found in the deoxy form. Further analysis of these data together with comparison to model compounds indicates that the Fe-C-O bond angle in carboxymyoglobin is bent (127 +/- 4 degrees), having a structure identical, within the error, with the "pocket" porphyrin model compound FePocPiv(1-MeIm)(CO) [Collman, J. P., Brauman, J. I., Collins, T. J., Iverson, B. L., Lang, G., Pettman, R., Sessler, J. L., & Walters, M. A. (1983) J. Am. Chem Soc. 105, 3038-3052]. On photolysis, this angle decreases by 5-10 degrees. In addition, correlation is observed between the increase in the length of the Fe-C bond and the decrease of the Fe-C-O angle. These results suggest that the rate-limiting step in recombination is the thermal motion of CO in the pocket to achieve an appropriate bonding angle with respect to the iron. These changes constitute the first molecular picture of the photolysis process, as well as the structure of the geminate state, and are important in clarifying nuclear tunneling parameters.