Magnetic Resonance of Isotope Hybrid Flavoprotein <Superscript>2</Superscript>H-Flavoprotein (<Superscript>1</Superscript>-Flavin Mononucleotide)

FLAVOPROTEINS lend themselves particularly well to study by the combined techniques of magnetic resonance and isotope substitution^1–3. Recent electron spin resonance (ESR) and electron-nuclear double resonance (ENDOR) investigations have already indicated the utility of this approach to the study of the structure and function of flavin and flavoproteins^4–8. We have now prepared an unusual isotope hybrid flavoprotein that gives promise of great value for magnetic resonance studies. This substance is obtained by the introduction (by exchange) of an ¹H-flavin mononucleotide (¹H-FMN) prosthetic group into (fully deuterated) ²H-flavoprotein that can be isolated from the blue-green thermophilic alga Synechococcus lividus. This isotope hybrid protein makes it possible to apply in a unique way proton magnetic resonance (PMR) and ESR to the chemistry of protein-bound FMN.     

Isotopic signature (<Superscript>15</Superscript>N/<Superscript>14</Superscript>N and <Superscript>13</Superscript>C/<Superscript>12</Superscript>C) confirms similarity of trophic niches of millipedes (Myriapoda,diplopoda) in a temperate deciduous forest

The species composition, abundance, and isotopic signature of millipedes (Myriapoda, Diplopoda) were investigated in seven biotopes of Kaluzhskie Zaseki State Nature Reserve. Nine Diplopoda species were found in total, and the local species diversity (within a sampling plot) reached seven species. The Diplopoda tissues were similar to the plant litter in the isotopic composition of nitrogen (δ¹⁵N was by 0.4‰ higher, on average), but were strongly enriched in heavy carbon (δ¹³C was by 4‰ higher, on average). Removal of mineral carbon from the cuticle reduced δ¹³C of Diplopoda by about 1.4‰ on average. Differences in the δ¹⁵N and δ¹³C values between the species did not exceed 2.5‰. Differences in the isotopic compositions of the considered species were small, and, it is impossible to distinguish particular trophic guilds in the Diplopoda community. Analysis of the published data confirmed that isotopic differentiation of millipedes was much less pronounced than in other investigated groups of soil animals. Hence, millipedes of the deciduous forest form a uniform trophic group.     

<Superscript>137</Superscript>Cs, <Superscript>40</Superscript>K, <Superscript>238</Superscript>Pu, <Superscript>239+240</Superscript>Pu and <Superscript>90</Superscript>Sr in biological samples from King George Island (Southern Shetlands) in Antarctica

There are few data reported on radionuclide contamination in Antarctica. The aim of this paper is to report ¹³⁷Cs, ⁹⁰Sr and ^238,239+240Pu and ⁴⁰K activity concentrations measured in biological samples collected from King George Island (Southern Shetlands, Antarctica), mostly during 2001–2002. The samples included: bones, eggshells and feathers of penguin Pygoscelis papua, bones and feathers of petrel Daption capense, bones and fur of seal Mirounga leonina, algae Himantothallus grandifolius, Desmarestia anceps and Cystosphaera jacquinotii, fish Notothenia corriceps, sea invertebrates Amphipoda, shells of limpet Nacella concina, lichen Usnea aurantiaco-atra, vascular plants Deschampsia antarctica and Colobanthus quitensis, fungi Omphalina pyxidata, moss Sanionia uncinata and soil. The results show a large variation in some activity concentrations. Samples from the marine environment had lower contamination levels than those from terrestrial ecosystems. The highest activity concentrations for all radionuclides were found in lichen and, to a lesser extent, in mosses, probably because lichens take up atmospheric pollutants and retain them. The only significant correlation (except for that expected between ²³⁸Pu and ^239+240Pu) was noted for moss and lichen samples between plutonium and ⁹⁰Sr. A tendency to a slow decrease with time seems to be occurring. Analyses of the activity ratios show varying fractionation between various radionuclides in different organisms. Algae were relatively more highly contaminated with plutonium and radiostrontium, and depleted with radiocesium. Feathers had the lowest plutonium concentrations. Radiostrontium and, to a lesser extent, Pu accumulated in bones. The present low intensity of fallout in Antarctic has a lower ²³⁸Pu/^239+240Pu activity ratio than that expected for global fallout.     

<Superscript>1</Superscript>H, <Superscript>15</Superscript>N, <Superscript>13</Superscript>C resonance assignment of plant dehydrin early response to dehydration 10 (ERD10)

Early response to dehydration 10 protein (ERD10) is an intrinsically disordered protein from Arabidopsis thaliana. The protein is upregulated during stress however its mechanism of action at atomic level is not well understood. In the present work multidimensional NMR methodologies are used in order to facilitate the process of chemical shift assignment. The information provided here supports further NMR spectroscopy experiments aimed at elucidation of ERD10 behaviour during molecular recognition events with other proteins.     

<Superscript>1</Superscript>H, <Superscript>13</Superscript>C and <Superscript>15</Superscript>N chemical shift assignment of lissencephaly-1 homology (LisH) domain homodimer of human two-hybrid-associated protein 1 with RanBPM (Twa1)

The CTLH complex is a large, highly conserved eukaryotic complex composed of eight proteins that has been associated to several cellular functions, more often described as an E3 ubiquitin ligase complex involved in protein degradation through ubiquitination but also via vacuole-dependent degradation. A common feature observed in several components of this complex is the presence of the domains lissencephaly-1 homology (LisH) and C-terminal to LisH (CTLH). The LisH domain is found in several proteins involved in chromosome segregation, microtubule dynamics, and cell migration. Also, this domain participates in protein dimerization, besides affecting protein half-life, and influencing in specific cellular localization. Among the proteins found in the CTLH complex, Twa1 (Two-hybrid-associated protein 1 with RanBPM), also known as Gid8 (glucose-induced degradation protein 8 homolog) is the smallest, being a good model for structural studies by NMR. In this work we report the chemical shift assignments of the homodimeric LisH domain of Twa1, as a first step to determine its solution structure.     

TNK cells (NKG2D<Superscript>+</Superscript> CD8<Superscript>+</Superscript> or CD4<Superscript>+</Superscript> T lymphocytes) in the control of human tumors

Innate and adaptive immune responses have many interactions that are regulated by the balance of signals initiated by a variety of activatory and inhibitory receptors. Among these, the NKG2D molecule was identified as expressed by T lymphocytes, including most CD8⁺ cells and a minority of CD4⁺ cells, designated TNK cells in this paper. Tumor cells may overexpress the stress-inducible NKG2D ligands (NKG2DLs: MICA/B, ULBPs) and the NKG2D signaling has been shown to be involved in lymphocyte-mediated anti-tumor activity. Aberrant expression of NKG2DLs by cancer cells, such as the release of soluble form of NKG2DLs, can lead to the impairment of these immune responses. Here, we discuss the significance of NKG2D in TNK-mediated anti-tumor activity. Our studies demonstrate that NKG2D⁺ T cells (TNK) are commonly recruited at the tumor site in melanoma patients where they may exert anti-tumor activity by engaging both TCR and NKG2D. Moreover, NKG2D and TCR triggering was also observed by peripheral blood derived T lymphocyte- or T cell clone-mediated tumor recognition, both in melanoma and colorectal cancer (CRC) patients. Notably, heterogeneous expression of NKG2DLs was found in melanoma and CRC cells, with a decrease of these molecules along with tumor progression. Therefore, through the mechanisms that govern NKG2D engagement in anti-tumor activity and the expression of NKG2DLs by tumor cells that still need to be dissected, we showed that NKG2D expressing TNK cells are a relevant T cell subtype for immunosurveillance of tumors and we propose that new immunotherapeutic interventions for cancer patients should be aimed also at enhancing NKG2DLs expression by tumor cells. This paper is a focused research review based on a presentation given at the sixth annual meeting of the Association for Immunotherapy of Cancer (CIMT), held in Mainz, Germany, 15–16 May 2008.     

An intraresidual i(HCA)CO(CA)NH experiment for the assignment of main-chain resonances in <Superscript>15</Superscript>N, <Superscript>13</Superscript>C labeled proteins

An improved pulse sequence, intraresidual i(HCA)CO(CA)NH, is described for establishing solely ¹³C′(i), ¹⁵N(i), ¹H^N(i) connectivities in uniformly ¹⁵N/¹³C-labeled proteins. In comparison to the “out-and-back” style intra-HN(CA)CO experiment, the new pulse sequence offers at least two-fold higher experimental resolution in the ¹³C′ dimension and on average 1.6 times higher sensitivity especially for residues in α-helices. Performance of the new experiment was tested on a small globular protein ubiquitin and an intrinsically unfolded 110-residue cancer/testis antigen CT16/PAGE5. Use of intraresidual i(HCA)CO(CA)NH experiment in combination with the established HNCO experiment was crucial for the assignment of highly disordered CT16.     

Simultaneous <Superscript>1</Superscript>H- or <Superscript>2</Superscript>H-, <Superscript>15</Superscript>N- and multiple-band-selective <Superscript>13</Superscript>C-decoupling during acquisition in <Superscript>13</Superscript>C-detected experiments with proteins and oligonucleotides

Significant resolution improvement in ¹³C,¹³C-TOCSY spectra of uniformly deuterated and ¹³C, ¹⁵N-labeled protein and ¹³C,¹⁵N-labeled RNA samples is achieved by introduction of multiple-band-selective ¹³C-homodecoupling applied simultaneously with ¹H- or ²H- and ¹⁵N-decoupling at all stages of multidimensional experiments including signal acquisition period. The application of single, double or triple band-selective ¹³C-decoupling in 2D-[¹³C,¹³C]-TOCSY experiments during acquisition strongly simplifies the homonuclear splitting pattern. The technical aspects of complex multiple-band homonuclear decoupling and hardware requirements are discussed. The use of this technique (i) facilitates the resonance assignment process as it reduces signal overlap in homonuclear ¹³C-spectra and (ii) possibly improves the signal-to-noise ratio through multiplet collapse. It can be applied in any ¹³C-detected experiment.     

Detection of hepatitis C virus (HCV) negative strand RNA and NS3 protein in peripheral blood mononuclear cells (PBMC): CD3<Superscript>+</Superscript>, CD14<Superscript>+</Superscript> and CD19<Superscript>+</Superscript>

Background

Although hepatitis C virus (HCV) is primarily hepatotropic, markers of HCV replication were detected in peripheral blood mononuclear cells (PBMC) as well as in ex vivo collected tissues and organs. Specific strains of HCV were found to be capable to infect cells of the immune system: T and B cells and monocytes/macrophages as well as cell lines in vitro. The direct invasion of cells of the immune system by the virus may be responsible for extrahepatic consequences of HCV infection: cryoglobulinemia and non-Hodgkin’s lymphoma.The aim of the present study was to determine the prevalence of markers of HCV infection: negative strand HCV RNA and non-structural NS3 protein in PBMC subpopulations: CD3⁺, CD14⁺ and CD19⁺. The presence of virus and the proportion of affected cells within a particular PBMC fraction could indicate a principal target cell susceptible for HCV.

Methods

PBMC samples were collected from 26 treatment-free patients chronically infected with HCV. PBMC subpopulations: CD3⁺, CD14⁺, CD19⁺ were obtained using positive magnetic separation. The presence of negative strand RNA HCV and viral NS3 protein were analyzed by strand-specific RT-PCR and NS3 immunocytochemistry staining.

Results

Negative strand HCV RNA was detectable in 7/26 (27%), whereas NS3 protein in 15/26 (57.6%) of PBMC samples. At least one replication marker was found in 13/26 (50%) of CD3⁺ cells then in 8/26 (30.8%) of CD14⁺ and CD19⁺ cells. The highest percentage of cells harboring viral markers in single specimen was also observed in CD3⁺ (2.4%), then in CD19⁺ (1.2%), and much lower in CD14⁺ (0.4%) cells.

Conclusions

Our results indicate that CD3⁺ cells are a dominant site for extrahepatic HCV replication, although other PBMC subpopulations may also support virus replication.

     

Immobilized redox mediators for electrochemical NAD(P)<Superscript>+</Superscript> regeneration

The applicability of dissolved redox mediators for NAD(P)⁺ regeneration has been demonstrated several times. Nevertheless, the use of mediators in solutions for sensor applications is not a very convenient strategy since the analysis is not reagentless and long stabilization times occur. The most important drawbacks of dissolved mediators in biocatalytic applications are interferences during product purification, limited reusability of the mediators, and their cost-intensive elimination from wastewater. Therefore, the use of immobilized mediators has both economic and ecological advantages. This work critically reviews the current state-of-art of immobilized redox mediators for electrochemical NAD(P)⁺ regeneration. Various surface modification techniques, such as adsorption polymerization and covalent linkage, as well as the corresponding NAD(P)⁺ regeneration rates and the operational stability of the immobilized mediator films, will be discussed. By comparison with other existing regeneration systems, the technical potential and future perspectives of biocatalytic redox reactions based on electrochemically fed immobilized mediators will be assessed.     

<Superscript>1</Superscript>H, <Superscript>15</Superscript>N, <Superscript>13</Superscript>C resonance assignment of human osteopontin

Osteopontin (OPN) is a 33.7 kDa intrinsically disordered protein and a member of the SIBLING family of proteins. OPN is bearing a signal peptide for secretion into the extracellular space, where it exerts its main physiological function, the control of calcium biomineralization. It is often involved in tumorigenic processes influencing proliferation, migration and survival, as well as the adhesive properties of cancer cells via CD44 and integrin signaling pathways. Here we report the nearly complete NMR chemical shift assignment of recombinant human osteopontin.     

<Superscript>13</Superscript>C-<Superscript>13</Superscript>C NOESY: A constructive use of <Superscript>13</Superscript>C-<Superscript>13</Superscript>C spin-diffusion

¹³C-¹³C NOESY experiments were performed under long mixing time conditions on reduced human superoxide dismutase (32 kDa, ¹⁵N, ^13C and 70% ²H labeled). ¹³C-¹³C couplings were successfully eliminated through post-processing of in-phase-anti-phase (IPAP) data. It appears that at mixing time _m of 3.0 s the spin diffusion mechanism allows the detection of 96% of the two-bond correlations involving C and C. The interpretation was confirmed by simulations. This approach broadens the range of applicability of ¹³C-¹³C NOESY spectroscopy.     

<Superscript>1</Superscript>H, <Superscript>13</Superscript>C and <Superscript>15</Superscript>N resonance assignment of human guanylate kinase

Human guanylate kinase (hGMPK) is a critical enzyme that, in addition to phosphorylating its physiological substrate (d)GMP, catalyzes the second phosphorylation step in the conversion of anti-viral and anti-cancer nucleoside analogs to their corresponding active nucleoside analog triphosphates. Until now, a high-resolution structure of hGMPK is unavailable and thus, we studied free hGMPK by NMR and assigned the chemical shift resonances of backbone and side chain ¹H, ¹³C, and ¹⁵N nuclei as a first step towards the enzyme’s structural and mechanistic analysis with atomic resolution.     

(3, 2)D <Superscript>1</Superscript>H, <Superscript>13</Superscript>C BIRD<Superscript>r,X</Superscript>-HSQC-TOCSY for NMR structure elucidation of mixtures: application to complex carbohydrates

Overlap of NMR signals is the major cause of difficulties associated with NMR structure elucidation of molecules contained in complex mixtures. A 2D homonuclear correlation spectroscopy in particular suffers from low dispersion of ¹H chemical shifts; larger dispersion of ¹³C chemical shifts is often used to reduce this overlap, while still providing the proton–proton correlation information e.g. in the form of a 2D ¹H, ¹³C HSQC-TOCSY experiment. For this methodology to work, ¹³C chemical shift must be resolved. In case of ¹³C chemical shifts overlap, ¹H chemical shifts can be used to achieve the desired resolution. The proposed (3, 2)D ¹H, ¹³C BIRD^r,X-HSQC-TOCSY experiment achieves this while preserving singlet character of cross peaks in the F₁ dimension. The required high-resolution in the ¹³C dimension is thus retained, while the cross peak overlap occurring in a regular HSQC-TOCSY experiment is eliminated. The method is illustrated on the analysis of a complex carbohydrate mixture obtained by depolymerisation of a fucosylated chondroitin sulfate isolated from the body wall of the sea cucumber Holothuria forskali.     

Interactions fulvate-metal (Zn<Superscript>2+</Superscript>, Cu<Superscript>2+</Superscript> and Fe<Superscript>2+</Superscript>): theoretical investigation of thermodynamic,structural and spectroscopic properties

The use of theoretical calculation to determine structural properties of fulvate-metal complex (zinc, copper and iron) is here related. The species were proposed in the ratio 1:1 and 2:1 for which the molecular structure was obtained through the semi-empirical method PM6. The calculation of thermodynamic stability (\(\Delta H_{(aq.)}^{0}\)) predicted that the iron complex were more exo-energetic. Metallic ions were coordinated to the phtalate groups of the model-structure of fulvic acid Suwannee River and the calculations of vibrational frequencies suggested that hydrogen bonds may help on the stability of the complex formation.     

Affordable uniform isotope labeling with <Superscript>2</Superscript>H, <Superscript>13</Superscript>C and <Superscript>15</Superscript>N in insect cells

For a wide range of proteins of high interest, the major obstacle for NMR studies is the lack of an affordable eukaryotic expression system for isotope labeling. Here, a simple and affordable protocol is presented to produce uniform labeled proteins in the most prevalent eukaryotic expression system for structural biology, namely Spodoptera frugiperda insect cells. Incorporation levels of 80 % can be achieved for ¹⁵N and ¹³C with yields comparable to expression in full media. For ²H,¹⁵N and ²H,¹³C,¹⁵N labeling, incorporation is only slightly lower with 75 and 73 %, respectively, and yields are typically twofold reduced. The media were optimized for isotope incorporation, reproducibility, simplicity and cost. High isotope incorporation levels for all labeling patterns are achieved by using labeled algal amino acid extracts and exploiting well-known biochemical pathways. The final formulation consists of just five commercially available components, at costs 12-fold lower than labeling media from vendors. The approach was applied to several cytosolic and secreted target proteins.