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1.
Sensors (Basel) ; 21(9)2021 May 07.
Article in English | MEDLINE | ID: mdl-34067137

ABSTRACT

In smartphone-based pedestrian navigation systems, detailed knowledge about user activity and device placement is a key information. Landmarks such as staircases or elevators can help the system in determining the user position when located inside buildings, and navigation instructions can be adapted to the current context in order to provide more meaningful assistance. Typically, most human activity recognition (HAR) approaches distinguish between general activities such as walking, standing or sitting. In this work, we investigate more specific activities that are tailored towards the use-case of pedestrian navigation, including different kinds of stationary and locomotion behavior. We first collect a dataset of 28 combinations of device placements and activities, in total consisting of over 6 h of data from three sensors. We then use LSTM-based machine learning (ML) methods to successfully train hierarchical classifiers that can distinguish between these placements and activities. Test results show that the accuracy of device placement classification (97.2%) is on par with a state-of-the-art benchmark in this dataset while being less resource-intensive on mobile devices. Activity recognition performance highly depends on the classification task and ranges from 62.6% to 98.7%, once again performing close to the benchmark. Finally, we demonstrate in a case study how to apply the hierarchical classifiers to experimental and naturalistic datasets in order to analyze activity patterns during the course of a typical navigation session and to investigate the correlation between user activity and device placement, thereby gaining insights into real-world navigation behavior.

2.
Int J Med Inform ; 150: 104453, 2021 06.
Article in English | MEDLINE | ID: mdl-33862508

ABSTRACT

OBJECTIVES: The European University Association (EUA) defines "employability" as a major goal of higher education. Therefore, competence-based orientation is an important aspect of education. The representation of a standardized job profile in the field of medical informatics, which is based on the most common labor market requirements, is fundamental for identifying and conveying the learning goals corresponding to these competences. METHODS: To identify the most common requirements, we extracted 544 job advertisements from the German job portal, STEPSTONE. This process was conducted via a program we developed in R with the "rvest" library, utilizing web crawling, web extraction, and text mining. After removing duplicates and filtering for jobs that required a bachelor's degree, 147 job advertisements remained, from which we extracted qualification terms. We categorized the terms into six groups: professional expertise, soft skills, teamwork, processes, learning, and problem-solving abilities. RESULTS: The results showed that only 45% of the terms are related to professional expertise, while 55% are related to soft skills. Studies of employee soft skills have shown similar results. The most prevalent terms were programming, experience, project, and server. Our second major finding is the importance of experience, further underlining how essential practical skills are. CONCLUSIONS: Previous studies used surveys and narrative descriptions. This is the first study to use web crawling, web extraction, and text mining. Our research shows that soft skills and specialist knowledge carry equal weight. The insights gained from this study may be of assistance in developing curricula for medical informatics.


Subject(s)
Medical Informatics , Curriculum , Data Mining , Humans , Learning
3.
Z Med Phys ; 31(1): 23-36, 2021 Feb.
Article in German | MEDLINE | ID: mdl-33092940

ABSTRACT

BACKGROUND: Currently there is an ever increasing interest in Lu-177 targeted radionuclide therapies, which target neuro-endocrine and prostate tumours. For a patient-specific treatment, an individual dosimetry based on SPECT/CT imaging is necessary. The aim of this study is to introduce a dosimetry method, where dose voxel kernels (DVK) are predicted by a neural network. METHODS: Kidneys are considered one of the most critical organs in any radionuclide therapy. Hence we chose kidneys of 26 patients, who underwent Lu-177-DOTATOC or PSMA therapy, as target organs for our dosimetric method. First of all, density kernels with a size of 9×9×9 voxels were considered, and the corresponding DVKs were calculated by Monte Carlo simulations. These kernels were used to train a neural network (NN), which received a density kernel as input and predicted a DVK at the output. To predict the dose distribution of an entire kidney, the organ had to be partitioned into a large number of density kernels. Afterwards the DVKs were predicted by a trained NN, and employed to reconstruct the whole-organ dose distribution by convolution with the activity distribution. This method was compared to the standard method where the activity distribution is convolved with a DVK based on a homogeneous soft tissue kernel. RESULTS: The number of training kernels amounted to 52,274 density kernels with corresponding MC-derived DVKs. The results serve as proof of principle of the newly proposed method and showed that the NN approach yielded superior results compared to the standard method with no additional computational effort. CONCLUSION: The NN approach is an accurate and highly competitive dosimetric method to precisely estimate absorbed radiation dose in critical organs like kidneys in clinical routine. To further improve the results, a larger number of DVKs needs to be computed by Monte Carlo simulations. An extension of the method to other organs is easily conceivable.


Subject(s)
Neural Networks, Computer , Radiometry/methods , Radiation Dosage , Single Photon Emission Computed Tomography Computed Tomography
4.
Nuklearmedizin ; 59(5): 365-374, 2020 Sep.
Article in English | MEDLINE | ID: mdl-32663888

ABSTRACT

OBJECTIVE: Patients with advanced prostate cancer are suitable candidates for [177Lu]PSMA-617 therapy. Integrated SPECT/CT systems have the potential to improve the accuracy of patient-specific tumor dosimetry. We present a novel patient-specific Monte Carlo based voxel-wise dosimetry approach to determine organ and total tumor doses (TTD). METHODS: 13 patients with histologically confirmed metastasized castration-resistant prostate cancer were treated with a total of 18 cycles of [177Lu]PSMA-617 therapy. In each patient, dosimetry was performed after the first cycle of [177Lu]PSMA-617 therapy. Regions of interest were defined manually on the SPECT/CT images for the kidneys, spleen and all 295 PSMA-positive tumor lesions in the field of view. The absorbed dose to normal organs and to all tumor lesions were calculated by a three dimensional dosimetry method based on Monte Carlo Simulations. RESULTS: The average dose values yielded the following results: 2.59 ±â€Š0.63 Gy (1.67-3.92 Gy) for the kidneys, 0.79 ± 0.46 Gy (0.31-1.90 Gy) for the spleen and 11.00 ±â€Š11.97 Gy (1.28-49.10 Gy) for all tracer-positive tumor lesions. A trend towards higher TTD was observed in patients with Gleason Scores > 8 compared to Gleason Scores ≤ 8 and in lymph node metastases compared to bone metastases. A significant correlation was determined between the serum-PSA level before RLT and the TTD (r = -0.57, p < 0.05), as well as between the TTD with the percentage change of serum-PSA levels before and after therapy was observed (r = -0.57, p < 0.05). Patients with higher total tumor volumes of PSMA-positive lesions demonstrated significantly lower kidney average dose values (r = -0.58, p < 0.05). CONCLUSION: The presented novel Monte Carlo based voxel-wise dosimetry calculates a patient specific whole-body dose distribution, thus taking into account individual anatomies and tissue compositions showing promising results for the estimation of radiation doses of normal organs and PSMA-positive tumor lesions.


Subject(s)
Lutetium/metabolism , Monte Carlo Method , Prostate-Specific Antigen/metabolism , Prostatic Neoplasms, Castration-Resistant/metabolism , Prostatic Neoplasms, Castration-Resistant/pathology , Biological Transport , Humans , Lutetium/therapeutic use , Male , Middle Aged , Neoplasm Metastasis , Prostate-Specific Antigen/therapeutic use , Prostatic Neoplasms, Castration-Resistant/radiotherapy , Radiometry
5.
Eur Heart J Case Rep ; 4(1): 1-4, 2020 Feb.
Article in English | MEDLINE | ID: mdl-32128488

ABSTRACT

BACKGROUND: Antibody-mediated rejection (AMR) in cardiac transplantation may manifest early within the first weeks after transplantation but also late after months to years following transplantation resulting in mild heart failure to cardiogenic shock. While patients with early cardiac AMR are less affected and seem to have survival rates comparable to transplant recipients without AMR, late cardiac AMR is frequently associated with graft dysfunction, fulminant forms of cardiac allograft vasculopathy, and a high mortality rate. Nevertheless, AMR of cardiac allografts remains difficult to diagnose and to treat. CASE SUMMARY: We report the case of a 47-year-old male patient with late AMR of the cardiac allograft 3 years after heart transplantation. Antibody-mediated rejection was confirmed by endomyocardial biopsy and the presence of donor-specific antibodies (DSA). The patient was treated with high dose of prednisolone, plasmapheresis, intravenous Gamma Globulin, rituximab, immunoadsorption, and bortezomib. Under this treatment regimen left ventricular ejection fraction and pro B-type natriuretic peptide recovered, and the patient improved to New York Heart Association Class I. Currently, 3 years after the diagnosis of cardiac AMR, graft function continues to be nearly normal, and there is no evidence for transplant vasculopathy. DISCUSSION: This case illustrates that AMR can occur at any time after transplantation. Although graft function fully recovered after treatment in our patient, the level of DSA remained high, suggesting that DSA may not be a reliable parameter to determine the intensity and duration of the therapy.

6.
Urol Int ; 100(3): 288-293, 2018.
Article in English | MEDLINE | ID: mdl-29514140

ABSTRACT

BACKGROUND: The internet is an emerging source of information for prostate cancer (PCa) patients. Since little is known about the quality of information on PCa provided online, we investigated its accordance to the latest European Association of Urology (EAU) guidelines. METHODS: A total of 89 German web pages were included for analysis. A quality model classifying the provider of information and its expertise was introduced. Correctness of provided information was systematically compared to the EAU guidelines. RESULTS: Information was provided by medical experts (41%), media (11%), and pharmaceutical companies (6%). Certificates were found in 23% with a significantly higher rate if provided by medical experts (p = 0.003). The minority of web pages showed information in accordance with the EAU guidelines regarding screening (63%), diagnosis (32%), classification (39%), therapy (36%), complications (8%), and follow-up (27%). Web pages by medical experts as well as websites with any kind of certification showed a significantly higher guideline conformity regarding diagnosis (p = 0.027, p = 0.002), therapy (p = 0.010, p = 0.011), follow-up (p = 0.005, p < 0.001), and availability of references (p = 0.017, p = 0.003). CONCLUSIONS: The present study reveals that online health information on PCa lacks concordance to current guidelines. Certified websites or websites provided by medical experts showed a significantly higher quality and accordance with guidelines.


Subject(s)
Access to Information , Internet , Patient Education as Topic/standards , Prostatic Neoplasms/diagnosis , Prostatic Neoplasms/therapy , Urology/standards , Europe , Germany , Humans , Male , Neoplasm Recurrence, Local , Patient Education as Topic/methods , Practice Guidelines as Topic , Societies, Medical , Urology/methods
7.
IDCases ; 8: 84-86, 2017.
Article in English | MEDLINE | ID: mdl-28491815

ABSTRACT

Human infection with Leptospira interrogans can be life-threatening. Multiple organ involvement frequently presents with liver and kidney failure, less commonly including severe hemolysis and pulmonary hemorrhage syndrome. Here, we present a fulminant case of leptospirosis presenting with hemolysis and pulmonary hemorrhage. A formerly healthy 34 year old patient presented to a rural hospital with dyspnea and hemoptysis after a week of influenza-like symptoms. Initial assessment revealed severe sepsis, acute kidney failure and severe hemolysis. Within the next 29 h, a multi-organ failure developed, which could eventually not be reversed despite mechanical ventilation, venovenous extracorporeal membrane oxygenation, continuous renal replacement therapy, plasmapheresis and extracorporeal cytokine absorbent therapy. The diagnosis of leptospirosis was made after the patient died. The transmitting animal was a pet rat. Leptospirosis has to be considered in case of rapid multi-organ failure presenting with pulmonary hemorrhage.

8.
PLoS One ; 12(1): e0170037, 2017.
Article in English | MEDLINE | ID: mdl-28107462

ABSTRACT

Biogenesis of mitochondrial cytochrome c oxidase (COX) is a complex process involving the coordinate expression and assembly of numerous subunits (SU) of dual genetic origin. Moreover, several auxiliary factors are required to recruit and insert the redox-active metal compounds, which in most cases are buried in their protein scaffold deep inside the membrane. Here we used a combination of gel electrophoresis and pull-down assay techniques in conjunction with immunostaining as well as complexome profiling to identify and analyze the composition of assembly intermediates in solubilized membranes of the bacterium Paracoccus denitrificans. Our results show that the central SUI passes through at least three intermediate complexes with distinct subunit and cofactor composition before formation of the holoenzyme and its subsequent integration into supercomplexes. We propose a model for COX biogenesis in which maturation of newly translated COX SUI is initially assisted by CtaG, a chaperone implicated in CuB site metallation, followed by the interaction with the heme chaperone Surf1c to populate the redox-active metal-heme centers in SUI. Only then the remaining smaller subunits are recruited to form the mature enzyme which ultimately associates with respiratory complexes I and III into supercomplexes.


Subject(s)
Electron Transport Complex IV/biosynthesis , Metallochaperones/metabolism , Paracoccus denitrificans/metabolism , Electron Transport Complex IV/metabolism , Electrophoresis, Polyacrylamide Gel , Mass Spectrometry , Protein Binding
9.
PLoS One ; 11(12): e0167957, 2016.
Article in English | MEDLINE | ID: mdl-27936219

ABSTRACT

Lately, Ensemble Empirical Mode Decomposition (EEMD) techniques receive growing interest in biomedical data analysis. Event-Related Modes (ERMs) represent features extracted by an EEMD from electroencephalographic (EEG) recordings. We present a new approach for source localization of EEG data based on combining ERMs with inverse models. As the first step, 64 channel EEG recordings are pooled according to six brain areas and decomposed, by applying an EEMD, into their underlying ERMs. Then, based upon the problem at hand, the most closely related ERM, in terms of frequency and amplitude, is combined with inverse modeling techniques for source localization. More specifically, the standardized low resolution brain electromagnetic tomography (sLORETA) procedure is employed in this work. Accuracy and robustness of the results indicate that this approach deems highly promising in source localization techniques for EEG data.


Subject(s)
Brain/physiology , Electroencephalography/methods , Task Performance and Analysis , Tomography/methods , Adult , Brain/diagnostic imaging , Brain Mapping/methods , Data Collection , Evoked Potentials , Female , Humans , Male , Young Adult
10.
Biochim Biophys Acta ; 1847(10): 1093-100, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26009016

ABSTRACT

Oxygen reduction by cytochrome ba3 oxidase from Thermus thermophilus was studied by stopped-flow and microsecond freeze-hyperquenching analyzed with UV-Vis and EPR spectroscopy. In the initial phase, the low-spin heme b560 is rapidly and almost completely oxidized (kobs>33,000s(-1)) whereas CuA remains nearly fully reduced. The internal equilibrium between CuA and heme b560 with forward and reverse rate constants of 4621s(-1) and 3466s(-1), respectively, indicates a ~7.5mV lower midpoint potential for CuA compared to heme b560. The formation of the oxidized enzyme is relatively slow (693s(-1)). In contrast to the Paracoccus denitrificans cytochrome aa3 oxidase, where in the last phase of the oxidative half cycle a radical from the strictly conserved Trp272 is formed, no radical is formed in the cytochrome ba3 oxidase. Mutation of the Trp229, the cytochrome ba3 oxidase homologue to the Trp272, did not abolish the activity, again in contrast to the Paracoccus cytochrome aa3 oxidase. Differences in the proton pumping mechanisms of Type A and Type B oxidases are discussed in view of the proposed role of the strictly conserved tryptophan residue in the mechanism of redox-linked proton pumping in Type A oxidases. In spite of the differences between the Type A and Type B oxidases, we conclude that protonation of the proton-loading site constitutes the major rate-limiting step in both catalytic cycles.

11.
Soft Matter ; 11(15): 2906-2908, 2015 Apr 21.
Article in English | MEDLINE | ID: mdl-25763882

ABSTRACT

As a surrogate of live cells, proteo-lipobeads are presented, encapsulating functional membrane proteins in a strict orientation into a lipid bilayer. Assays can be performed just as on live cells, for example using fluorescence measurements. As a proof of concept, we have demonstrated proton transport through cytochrome c oxidase.


Subject(s)
Electron Transport Complex IV/chemistry , Lipid Bilayers/chemistry , Sepharose/chemistry , Biomimetics , Fluorescence , Fluorescent Dyes/chemistry
12.
FEBS Lett ; 589(5): 565-8, 2015 Feb 27.
Article in English | MEDLINE | ID: mdl-25637325

ABSTRACT

Two different pathways through which protons access cytochrome c oxidase operate during oxygen reduction from the mitochondrial matrix, or the bacterial cytoplasm. Here, we use electrocatalytic current measurements to follow oxygen reduction coupled to proton uptake in cytochrome c oxidase isolated from Paracoccus denitrificans. Wild type enzyme and site-specific variants with defects in both proton uptake pathways (K354M, D124N and K354M/D124N) were immobilized on gold nanoparticles, and oxygen reduction was probed electrochemically in the presence of varying concentrations of Zn(2+) ions, which are known to inhibit both the entry and the exit proton pathways in the enzyme. Our data suggest that under these conditions substrate protons gain access to the oxygen reduction site via the exit pathway.


Subject(s)
Electrochemistry/methods , Electron Transport Complex IV/metabolism , Enzymes, Immobilized/metabolism , Paracoccus denitrificans/enzymology , Protons , Electron Transport , Enzyme Activation/drug effects , Gold/chemistry , Metal Nanoparticles/chemistry , Zinc/pharmacology
13.
Langmuir ; 31(8): 2511-6, 2015 Mar 03.
Article in English | MEDLINE | ID: mdl-25670233

ABSTRACT

An artificial bilayer lipid membrane system is presented, featuring the oriented encapsulation of membrane proteins in a functionally active form. Nickel nitrilo-triacetic acid-functionalized silica nanoparticles, of a diameter of around 25 nm, are used to attach the proteins via a genetically engineered histidine tag in a uniform orientation. Subsequently, the proteins are reconstituted within a phospholipid bilayer, formed around the particles by in situ dialysis to form so-called proteo-lipobeads (PLBs). With a final size of about 50 nm, the PLBs can be employed for UV/vis spectroscopy studies, particularly of multiredox center proteins, because the effects of light scattering are negligible. As a proof of concept, we use cytochrome c oxidase (CcO) from P. denitrificans with the his tag genetically engineered to subunit I. In this orientation, the P side of CcO is directed to the outside and hence electron transfer can be initiated by reduced cytochrome c (cc). UV/vis measurements are used in order to determine the occupancy by CcO molecules encapsulated in the lipid bilayer as well as the kinetics of electron transfer between CcO and cc. The kinetic data are analyzed in terms of the Michaelis-Menten kinetics showing that the turnover rate of CcO is significantly decreased compared to that of solubilized protein, whereas the binding characteristics are improved. The data demonstrate the suitability of PLBs for functional cell-free bioassays of membrane proteins.


Subject(s)
Electron Transport Complex IV/chemistry , Lipid Bilayers/chemistry , Membrane Proteins/chemistry , Nanoparticles/chemistry , Phospholipids/chemistry , Silicon Dioxide/chemistry , Electron Transport Complex IV/metabolism , Lipid Bilayers/chemical synthesis , Models, Molecular , Paracoccus denitrificans/enzymology , Particle Size , Phospholipids/chemical synthesis , Surface Properties
14.
Biochemistry ; 54(4): 1144-50, 2015 Feb 03.
Article in English | MEDLINE | ID: mdl-25565128

ABSTRACT

Lipids of cytochrome c oxidase (COX) of Paracoccus denitrificans have been identified by MALDI-TOF MS direct analyses of isolated protein complexes, avoiding steps of lipid extraction or chromatographic separation. Two different COX preparations have been considered in this study: the enzyme core consisting of subunits I and II (COX 2-SU) and the complete complex comprising all four subunits (COX 4-SU). In addition, MALDI-TOF MS lipid profiles of bacterial COX are also compared with those of the isolated mitochondrial COX and bacterial bc1 complex. We show that the main lipids associated with bacterial COX 4-SU are phosphatidylglycerol (PG) and phosphatidylcholine (PC), and minor amounts of cardiolipin (CL). PG and PC are absent in the COX 2-SU preparation lacking subunits III and IV, whereas CL is still present. Quantitative analyses indicate that at variance from mitochondrial COX, cardiolipin is present in substoichiometric amounts in bacterial COX, at a CL:COX molar ratio of ∼1:10. We conclude that bacterial COX does not require CL for structure or its activity.


Subject(s)
Cardiolipins/analysis , Electron Transport Complex IV/analysis , Lipids/analysis , Oxidoreductases/analysis , Paracoccus denitrificans/enzymology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
15.
Biochim Biophys Acta ; 1847(2): 202-211, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25445316

ABSTRACT

The biogenesis of the mitochondrial cytochrome c oxidase is a complex process involving the stepwise assembly of its multiple subunits encoded by two genetic systems. Moreover, several chaperones are required to recruit and insert the redox-active metal centers into subunits I and II, two a-type hemes and a total of three copper ions, two of which form the CuA center located in a hydrophilic domain of subunit II. The copper-binding Sco protein(s) have been implicated with the metallation of this site in various model organisms. Here we analyze the role of the two Sco homologues termed ScoA and ScoB, along with two other copper chaperones, on the biogenesis of the cytochrome c oxidase in the bacterium Paracoccus denitrificans by deleting each of the four genes individually or pairwise, followed by assessing the functionality of the assembled oxidase both in intact membranes and in the purified enzyme complex. Copper starvation leads to a drastic decrease of oxidase activity in membranes from strains involving the scoB deletion. This loss is shown to be of dual origin, (i) a severe drop in steady-state oxidase levels in membranes, and (ii) a diminished enzymatic activity of the remaining oxidase complex, traced back to a lower copper content, specifically in the CuA site of the enzyme. Neither of the other proteins addressed here, ScoA or the two PCu proteins, exhibit a direct effect on the metallation of the CuA site in P. denitrificans, but are discussed as potential interaction partners of ScoB.


Subject(s)
Carrier Proteins/physiology , Copper/metabolism , Electron Transport Complex IV/chemistry , Molecular Chaperones/physiology , Paracoccus denitrificans/enzymology , Base Sequence , Binding Sites , Molecular Sequence Data
16.
FEBS J ; 282(3): 537-49, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25420759

ABSTRACT

Biogenesis of the mitochondrial cytochrome c oxidase (COX) is a complex process due to its numerous subunits encoded by two genomes, as well as the localization of redox centers deep within the membrane. Here, we have assessed the biogenesis of the homologous aa3-type oxidase of the soil bacterium Paracoccus denitrificans. First, protein partners were analyzed using various membrane solubilization strategies to show interactions between COX and CtaG, a chaperone implicated in CuB site metallation. Using an unbiased MS approach after immunological pull-down from untreated or cross-linked membranes, we then extend our view towards a hypothetical 'biogenesis complex' by identifying two further metal-inserting chaperones, Surf1c and Sco, together with enzymes catalyzing heme a synthesis. Our study also tentatively supports previous speculation regarding the existence of a predominantly co-translational mechanism for cofactor insertion during COX biogenesis.


Subject(s)
Bacterial Proteins/metabolism , Electron Transport Complex IV/metabolism , Paracoccus denitrificans/metabolism , Protein Binding
17.
J Bacteriol ; 196(2): 472-82, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24214947

ABSTRACT

The cbb3-type cytochrome c oxidases (cbb3-CcOs) are members of the heme-copper oxidase superfamily that couple the reduction of oxygen to translocation of protons across the membrane. The cbb3-CcOs are present only in bacteria and play a primary role in microaerobic respiration, being essential for nitrogen-fixing endosymbionts and for some human pathogens. As frequently observed in Pseudomonads, Pseudomonas stutzeri contains two independent ccoNO(Q)P operons encoding the two cbb3 isoforms, Cbb3-1 and Cbb3-2. While the crystal structure of Cbb3-1 from P. stutzeri was determined recently and cbb3-CcOs from other organisms were characterized functionally, less emphasis has been placed on the isoform-specific differences between the cbb3-CcOs. In this work, both isoforms were homologously expressed in P. stutzeri strains from which the genomic version of the respective operon was deleted. We purified both cbb3 isoforms separately by affinity chromatography and increased the yield of Cbb3-2 to a similar level as Cbb3-1 by replacing its native promoter. Mass spectrometry, UV-visible (UV-Vis) spectroscopy, differential scanning calorimetry, as well as oxygen reductase and catalase activity measurements were employed to characterize both cbb3 isoforms. Differences were found concerning the thermal stability and the presence of subunit CcoQ. However, no significant differences between the two isoforms were observed otherwise. Interestingly, a surprisingly high turnover of at least 2,000 electrons s(-1) and a high Michaelis-Menten constant (Km ~ 3.6 mM) using ascorbate-N,N,N',N'-tetramethyl-p-phenylenediamine dihydrochloride (TMPD) as the electron donor were characteristic for both P. stutzeri cbb3-CcOs. Our work provides the basis for further mutagenesis studies of each of the two cbb3 isoforms specifically.


Subject(s)
Electron Transport Complex IV/metabolism , Pseudomonas stutzeri/enzymology , Calorimetry , Catalase/metabolism , Chromatography, Affinity , Electron Transport Complex IV/chemistry , Electron Transport Complex IV/genetics , Electron Transport Complex IV/isolation & purification , Enzyme Stability , Gene Expression , Hydrogen-Ion Concentration , Kinetics , Mass Spectrometry , Oxidoreductases/metabolism , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Isoforms/isolation & purification , Protein Isoforms/metabolism , Pseudomonas stutzeri/genetics , Spectrophotometry, Ultraviolet , Temperature
18.
J Biol Chem ; 288(28): 20261-6, 2013 Jul 12.
Article in English | MEDLINE | ID: mdl-23723073

ABSTRACT

Identification of the intermediates and determination of their structures in the reduction of dioxygen to water by cytochrome c oxidase (CcO) are particularly important to understanding both O2 activation and proton pumping by the enzyme. In this work, we report the products of the rapid reaction of O2 with the mixed valence form (CuA(2+), heme a(3+), heme a3(2+)-CuB(1+)) of the enzyme. The resonance Raman results show the formation of two ferryl-oxo species with characteristic Fe(IV)=O stretching modes at 790 and 804 cm(-1) at the peroxy oxidation level (PM). Density functional theory calculations show that the protein environment of the proximal H-bonded His-411 determines the strength of the distal Fe(IV)=O bond. In contrast to previous proposals, the PM intermediate is also formed in the reaction of Y167F with O2. These results suggest that in the fully reduced enzyme, the proton pumping ν(Fe(IV)=O) = 804 cm(-1) to ν(Fe(IV)=O) = 790 cm(-1) transition (P→F, where P is peroxy and F is ferryl) is triggered not only by electron transfer from heme a to heme a3 but also by the formation of the H-bonded form of the His-411-Fe(IV)=O conformer in the proximal site of heme a3. The implications of these results with respect to the role of an O=Fe(IV)-His-411-H-bonded form to the ring A propionate of heme a3-Asp-399-H2O site and, thus, to the exit/output proton channel (H2O) pool during the proton pumping P→F transition are discussed. We propose that the environment proximal to the heme a3 controls the spectroscopic properties of the ferryl intermediates in cytochrome oxidases.


Subject(s)
Bacterial Proteins/chemistry , Copper/chemistry , Electron Transport Complex IV/chemistry , Heme/chemistry , Iron/chemistry , Oxygen/chemistry , Bacterial Proteins/metabolism , Copper/metabolism , Electron Transport Complex IV/metabolism , Heme/metabolism , Histidine/chemistry , Histidine/metabolism , Hydrogen Bonding , Iron/metabolism , Oxidation-Reduction , Oxygen/metabolism , Oxygen Isotopes , Paracoccus denitrificans/enzymology , Peroxides/chemistry , Peroxides/metabolism , Spectrum Analysis, Raman
19.
Biochim Biophys Acta ; 1827(3): 319-27, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23103386

ABSTRACT

The four subunit (SU) aa(3) cytochrome c oxidase (CcO) from Paracoccus denitrificans is one of the terminal enzymes of the respiratory chain. Its binuclear active center, residing in SU I, contains heme a(3) and Cu(B). Apart from its oxygen reductase activity, the protein possesses a peroxidase and a catalase activity. To compare variants and the wild type (WT) protein in a more stringent way, a recombinant (rec.) WT strain was constructed, carrying the gene for SU I on a low copy number plasmid. This rec. WT showed no difference in oxygen reductase activity compared to the American Type Culture Collection (ATCC) WT CcO but surprisingly its catalase activity was increased by a factor of 20. The potential over-production of SU I might impair the correct insertion of heme a(3) and Cu(B) because of a deficiency in metal inserting chaperones. An altered distance between heme a(3) and Cu(B) and variations in protein structure are possible reasons for the observed increased catalase activity. The availability of chaperones was improved by cloning the genes ctaG and surf1c on the same plasmid as the SU I gene. The new rec. WT CcO showed in fact a reduced catalase activity. Using differential scanning calorimetry no significant difference in thermal stability between the ATCC WT CcO and the rec. WT CcO was detected. However, upon aging the thermal stability of the rec. WT CcO was reduced compared to that of the ATCC WT CcO pointing to a decreased structural stability of the rec. WT CcO.


Subject(s)
Catalase/metabolism , Electron Transport Complex IV/metabolism , Paracoccus denitrificans/enzymology , Calorimetry, Differential Scanning , Cloning, Molecular , Kinetics , Recombinant Proteins/metabolism
20.
J Lipid Res ; 53(7): 1417-25, 2012 Jul.
Article in English | MEDLINE | ID: mdl-22556215

ABSTRACT

A simple and fast method of lipid analysis of isolated intact mitochondria by means of MALDI-TOF mass spectrometry is described. Mitochondria isolated from bovine heart and yeast have been employed to set up and validate the new method of lipid analysis. The mitochondrial suspension is directly applied over the target and, after drying, covered by a thin layer of the 9-aminoacridine matrix solution. The lipid profiles acquired with this procedure contain all peaks previously obtained by analyzing the lipid extracts of isolated mitochondria by TLC and/or mass spectrometry. The novel procedure allows the quick, simple, precise, and accurate analysis of membrane lipids, utilizing only a tiny amount of isolated organelle; it has also been tested with intact membranes of the bacterium Paracoccus denitrificans for its evolutionary link to present-day mitochondria. The method is of general validity for the lipid analysis of other cell fractions and isolated organelles.


Subject(s)
Lipids/analysis , Mitochondria/chemistry , Saccharomyces cerevisiae/chemistry , Saccharomyces cerevisiae/cytology , Animals , Cattle , Mitochondria, Heart/chemistry , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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