Effect of modification of cytochrome c on its reactions with superoxide and NADPH:cytochrome P-450 reductase

Acetylation and succinylation of cytochrome c decrease its rate of reaction with superoxide. The effect of succinylation is greater than that of acetylation. As predicted by the Brönsted-Debye-Hückel relationship, the effect of modification of cytochrome c is more pronounced at low ionic strength. Modification of cytochrome c causes a much greater decrease in its reaction with NADPH-cytochrome P-450 reductase, compared to its reaction with superoxide. This data forms the quantitative basis for the enhanced specificity of modified cytochrome c for superoxide detection previously described by other investigators. Additionally, a greatly simplified version of the trinitrobenzenesulfonic acid method for estimation of free amino groups is presented.     

Averaging interaction energies over homologs improves protein fold recognition in gapless threading.

Protein structure prediction is limited by the inaccuracy of the simplified energy functions necessary for efficient sorting over many conformations. It was recently suggested (Finkelstein, Phys Rev Lett 1998;80:4823-4825) that these errors can be reduced by energy averaging over a set of homologous sequences. This conclusion is confirmed in this study by testing protein structure recognition in gapless threading. The accuracy of recognition was estimated by the Z-score values obtained in gapless threading tests. For threading, we used 20 target proteins, each having from 20 to 70 homologs taken from the HSSP sequence base. The energy of the native structures was compared with the energy from 34 to 75 thousand of alternative structures generated by threading. The energy calculations were done with our recently developed Calpha atom-based phenomenological potentials. We show that averaging of protein energies over homologs reduces the Z-score from approximately -6.1 (average Z-score for individual chains) to approximately -8.1. This means that a correct fold can be found among 3 x 10(9) random folds in the first case and among 3 x 10(15) in the second. Such increase in selectivity is important for recognition of protein folds.     

Versican G3 domain enhances cellular adhesion and proliferation of bovine intervertebral disc cells cultured in vitro

The functional role of versican in influencing intervertebral disc cell adhesion and proliferation was analyzed in bovine intervertebral disc. We have previously demonstrated the C-terminal globular G3 (or selectin-like) domain of versican to influence mesenchymal chondrogenesis and fibroblast proliferation in vitro. For this study, a versican G3 expression construct was generated to examine the role of the G3 domain of versican. Nucleus pulposus and annulus fibrosus cells were isolated from adult bovine caudal discs using sequential enzymatic digestion and versican expression characterized by RT-PCR. In cell proliferation assays, we observed that there was greater cellular proliferation in the presence of versican G3 for both disc cell types. The higher proliferation rate of annulus fibrosus cells when compared to nucleus pulposus cells seeded in monolayer supports heterogeneity of intervertebral disc cell populations. The presence of versican G3 construct enhanced the adhesion of isolated nucleus pulposus and annulus fibrosus cells approximately 4 to 6 fold, respectively. Cellular adhesion was greater in the presence of versican G3 in a dose dependent manner. G3 product was purified using affinity columns, and the purified G3 also enhanced cell adhesion.     

Tec kinases regulate TCR-mediated recruitment of signaling molecules and integrin-dependent cell adhesion

T cells deficient in the Tec kinases Itk or Itk and Rlk exhibit defective TCR-stimulated proliferation, IL-2 production, and activation of phospholipase C-gamma. Evidence also implicates Tec kinases in actin cytoskeleton regulation, which is necessary for cell adhesion and formation of the immune synapse in T lymphocytes. In this study we show that Tec kinases are required for TCR-mediated up-regulation of adhesion via the LFA-1 integrin. We also demonstrate that the defect in adhesion is associated with defective clustering of LFA-1 and talin at the site of interaction of Rlk-/-Itk-/- and Itk-/- T cells with anti-TCR-coated beads. Defective recruitment of Vav1, protein kinase Ctheta, and Pyk2 was also observed in Rlk-/-Itk-/- and Itk-/- T cells. Stimulation with ICAM-2 in conjunction with anti-TCR-coated beads enhanced polarization of Vav1, protein kinase Ctheta, and Pyk2 in wild-type cells, demonstrating a role for integrins in potentiating the recruitment of signaling molecules in T cells. Increased recruitment of signaling molecules was most pronounced under conditions of low TCR stimulation. Under these suboptimal TCR stimulation conditions, ICAM-2 could also enhance the recruitment of signaling molecules in Itk-/-, but not Rlk-/-Itk-/- T cells. Thus, Tec kinases play key roles in regulating TCR-mediated polarization of integrins and signaling molecules to the site of TCR stimulation as well as the up-regulation of integrin adhesion.     

The number of subunits comprising the channel formed by the T domain of diphtheria toxin.

In the presence of a low pH environment, the channel-forming T domain of diphtheria toxin undergoes a conformational change that allows for both its own insertion into planar lipid bilayers and the translocation of the toxin's catalytic domain across them. Given that the T domain contributes only three transmembrane segments, and the channel is permeable to ions as large as glucosamine(+) and NAD(-), it would appear that the channel must be a multimer. Yet, there is substantial circumstantial evidence that the channel may be formed from a single subunit. To test the hypothesis that the channel formed by the T domain of diphtheria toxin is monomeric, we made mixtures of two T domain constructs whose voltage-gating characteristics differ, and then observed the gating behavior of the mixture's single channels in planar lipid bilayers. One of these constructs contained an NH(2)-terminal hexahistidine (H6) tag that blocks the channel at negative voltages; the other contained a COOH-terminal H6 tag that blocks the channel at positive voltages. If the channel is constructed from multiple T domain subunits, one expects to see a population of single channels from this mixture that are blocked at both positive and negative voltages. The observed single channels were blocked at either negative or positive voltages, but never both. Therefore, we conclude that the T domain channel is monomeric.     

19F NMR study on the biodegradation of fluorophenols by various Rhodococcus species

Of all NMR observable isotopes 19F is the one perhaps most convenient for studies on biodegradation of environmental pollutants. The reasons underlying this potential of 19F NMR are discussed and illustrated on the basis of a study on the biodegradation of fluorophenols by four Rhodococcus strains. The results indicate marked differences between the biodegradation pathways of fluorophenols among the various Rhodococcus species. This holds not only for the level and nature of the fluorinated biodegradation pathway intermediates that accumulate, but also for the regioselectivity of the initial hydroxylation step. Several of the Rhodococcus species contain a phenol hydroxylase that catalyses the oxidative defluorination of ortho-fluorinated di- and trifluorophenols. Furthermore, it is illustrated how the 19F NMR technique can be used as a tool in the process of identification of an accumulated unknown metabolite, in this case most likely 5-fluoromaleylacetate. Altogether, the 19F NMR technique proved valid to obtain detailed information on the microbial biodegradation pathways of fluorinated organics, but also to provide information on the specificity of enzymes generally considered unstable and, for this reason, not much studied so far.     

Inability of choleragenoid-sensitized cells to induce T cell-mediated cytolysis.

Murine splenocytes and tumor cells bind cholera enterotoxoid (choleragenoid). Four hours after sensitization, choleragenoid-coated cells were lysed in the presence of anti-cholergenoid serum and complement, indicating that the binding was stable. Choleragenoid-coated cells were unable to sensitize spleen cells from normal or choleragenoid primed syngeneic mice into displaying a cytotoxic effect against choleragenoid-coated target cells in the T cell-mediated cytotoxicity assay. Cells coated with both choleragenoid and trinitrophenyl (TNP) groups did sensitize syngeneic spleen cells to display a cytotoxic effect against target cells bearing choleragenoid and TNP or TNP alone, but not choleragenoid alone. These data demonstrate that the mere binding of a foreign component to lymphoid cells is not sufficient to allow sensitization of cytotoxic T cells.     

Threading with chemostructural restrictions method for predicting fold and functionally significant residues: application to dipeptidylpeptidase IV (DPP-IV)

We present a new method for more accurate modeling of protein structure, called threading with chemostructural restrictions. This method addresses those cases in which a target sequence has only remote homologues of known structure for which sequence comparison methods cannot provide accurate alignments. Although remote homologues cannot provide an accurate model for the whole chain, they can be used in constructing practically useful models for the most conserved-and often the most interesting-part of the structure. For many proteins of interest, one can suggest certain chemostructural patterns for the native structure based on the available information on the structural superfamily of the protein, the type of activity, the sequence location of the functionally significant residues, and other factors. We use such patterns to restrict (1) a number of possible templates, and (2) a number of allowed chain conformations on a template. The latter restrictions are imposed in the form of additional template potentials (including terms acting as sequence anchors) that act on certain residues. This approach is tested on remote homologues of alpha/beta-hydrolases that have significant structural similarity in the positions of their catalytic triads. The study shows that, in spite of significant deviations between the model and the native structures, the surroundings of the catalytic triad (positions of C(alpha) atoms of 20-30 nearby residues) can be reproduced with accuracy of 2-3 A. We then apply the approach to predict the structure of dipeptidylpeptidase IV (DPP-IV). Using experimentally available data identifying the catalytic triad residues of DPP-IV (David et al., J Biol Chem 1993;268:17247-17252); we predict a model structure of the catalytic domain of DPP-IV based on the 3D fold of prolyl oligopeptidase (Fulop et al., Cell 1998;94:161-170) and use this structure for modeling the interaction of DPP-IV with inhibitor.     

Individual and Aggregate Years‐of‐life‐lost Associated With Overweight and Obesity

This study presents nationally representative estimates of individual and aggregate years‐of‐life‐lost (YLLs) associated with overweight and three categories of obesity separately by age, race, smoking status, and gender strata. Using proportional hazards analysis and data from the National Health Interview Survey (NHIS) Linked Mortality Files, we estimated life expectancies for each BMI strata and quantified YLLs by comparing differences between each strata and the normal BMI reference group. Our results provide further evidence that overweight and mild obesity are not associated with a reduction in life expectancy. However, higher BMI categories are associated with lower expected survival. In aggregate, excess BMI is responsible for ～95 million YLLs. White females account for more than two‐thirds of the aggregate YLLs. Unless something is done to reduce the rising prevalence of those with BMIs >35, or to mitigate the impact of obesity or its correlates on YLLs, expected life expectancy for US adults may decrease in the future.     

Deficient innate immunity,thymopoiesis, and gene expression response to radiation in survivors of childhood acute lymphoblastic leukemia

Background: Survivors of childhood acute lymphoblastic leukemia (ALL) are at an increased risk of developing secondary malignant neoplasms. Radiation and chemotherapy can cause mutations and cytogenetic abnormalities and induce genomic instability. Host immunity and appropriate DNA damage responses are critical inhibitors of carcinogenesis. Therefore, we sought to determine the long-term effects of ALL treatment on immune function and response to DNA damage. Methods: Comparative studies on 14 survivors in first complete remission and 16 siblings were conducted. Results: In comparison to siblings on the cells that were involved in adaptive immunity, the patients had either higher numbers (CD19+ B cells and CD4+CD25+ T regulatory cells) or similar numbers (αβT cells and CD45RO+/RA? memory T cells) in the blood. In contrast, patients had lower numbers of all lymphocyte subsets involved in innate immunity (γδT cells and all NK subsets, including KIR2DL1+ cells, KIR2DL2/L3+ cells, and CD16+ cells), and lower natural cytotoxicity against K562 leukemia cells. Thymopoiesis was lower in patients, as demonstrated by less CD45RO?/RA+ naïve T cell and less SjTREC levels in the blood, whereas the Vβ spectratype complexity score was similar. Array of gene expression response to low-dose radiation showed that about 70% of the probesets had a reduced response in patients. One of these genes, SCHIP-1, was also among the top-ranked single nucleotide polymorphisms (SNPs) during the whole-genome scanning by SNP microarray analysis. Conclusion: ALL survivors were deficient in innate immunity, thymopoiesis, and DNA damage responses to radiation. These defects may contribute to their increased likelihood of second malignancy.