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Query: UNIPROT:P06889 (Mol)
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The Grand Canonical Monte Carlo method was used to analyse the phenomenon of adsorption of aromatic compounds (i.e. phenol, toluene, benzoic acid and salicylic acid) on the surface of the titania-silica (TiO2/SiO2) catalyst. We found that different types of interactions play important roles in the adsorption of molecules having polar and non-polar groups. Moreover, we found that the interactions between sorbate molecules are strong, and are the cause of multilayer adsorption occurring in the investigated temperature and pressure range.
J Mol Model 2007 Jul
PMID:Modeling the adsorption of aromatic compounds on the TiO2/SiO2 catalyst. 1734 Jan 10

Various aspects of energy metabolism and feed digestibility were evaluated in two reportedly improved strains of Nile tilapia (Oreochromis niloticus) namely GIFT (genetically improved farmed tilapia) and GMNT (genetically male Nile tilapia) and compared with those of CNT (conventional Nile tilapia). Fish were stocked individually in a computer-controlled respirometer system at 27+/-0.1 degrees C for 10 weeks. Metabolic rates were measured at three different feeding levels: starved, maintenance (3.0 g kg(-0.8) day(-1)) and growth (7.5 g kg(-0.8) day(-1)) using a fishmeal based feed containing TiO2 marker (41% crude protein, 9% crude lipid and 19 kJ (g DM)(-1) gross energy). The standard metabolic rate (SMR), measured at the beginning of the experiment (45.4+/-4.6, 52.4+/-7.7 and 46.8+/-4.6 mg O2 kg(-0.8) h(-1) respectively for GIFT, GMNT and CNT), did not differ significantly between the groups (p<0.05). Similarly, non-significant differences were also observed in the routine metabolic rates under starved, maintenance and growth conditions but the variability was higher in the case of GMNT and CNT than in GIFT. The latter group showed a significantly lower active metabolic rate (145 mg O2 kg(-0.8) h(-1)) compared to GMNT and CNT (232 and 253 mg O2 kg(-0.8) h(-1), respectively) at maintenance feeding level. The specific dynamic action (% offered feed energy) showed no significant differences among the groups. Digestibility coefficients of feed dry matter, protein, lipid and energy for the three tilapia groups also did not differ significantly. Therefore, we concluded that the genetic improvement or modification in the GIFT or GMNT might not upgrade the inherent physiological potential compared to CNT as far as energy metabolism and digestion efficiencies are concerned.
Comp Biochem Physiol A Mol Integr Physiol 2007 Sep
PMID:Comparison of metabolic rates and feed nutrient digestibility in conventional, genetically improved (GIFT) and genetically male (GMNT) Nile tilapia, Oreochromis niloticus (L.). 1755 97

Protein phosphorylation is a central cell signaling event that underlies a broad spectrum of key physiological processes. Advances in affinity chromatography and mass spectrometry are now providing the ability to identify and quantitate thousands of phosphorylation sites simultaneously. Comprehensive phosphoproteome analyses present sizable analytical challenges in view of suppression effects of phosphopeptides and the variable quality of MS/MS spectra. This work presents an integrated enzymatic and data mining approach enabling the comprehensive detection of native and putative phosphopeptides following alkaline phosphatase digestion of titanium dioxide (TiO2)-enriched cell extracts. The correlation of retention times of more than 750 phospho- and dephosphopeptide pairs from J774 macrophage cell extracts indicated that removal of the phosphate groups can impart a gain or a loss in hydrophobicity that is partly explained by the formation of a salt bridge with proximal amino groups. Dephosphorylation also led to an average 2-fold increase in MS sensitivity that facilitated peptide sequencing. More importantly, alkaline phosphatase digestion enhanced the overall population of putative phosphopeptides from TiO2-enriched cell extracts providing a unique approach to profile multiphosphorylated cognates that would have remained otherwise undetected. The application of this approach is demonstrated for differential phosphoproteome analyses of mouse macrophages exposed to interferon-gamma for 5 min. TiO2 enrichment enabled the identification of 1143 phosphopeptides from 432 different proteins of which 125 phosphopeptides showed a 2-fold change upon interferon-gamma exposure. The use of alkaline phosphatase nearly doubled the number of putative phosphopeptides assignments leading to the observation of key interferon-gamma signaling events involved in vesicle trafficking, production of reactive oxygen species, and mRNA translation.
Mol Cell Proteomics 2008 Apr
PMID:Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses: application to cell signaling events of interferon-gamma-stimulated macrophages. 1800 92

Amphiphysin I (amphI) is dephosphorylated by calcineurin during nerve terminal depolarization and synaptic vesicle endocytosis (SVE). Some amphI phosphorylation sites (phosphosites) have been identified with in vitro studies or phosphoproteomics screens. We used a multifaceted strategy including 32P tracking to identify all in vivo amphI phosphosites and determine their relative abundance and potential relevance to SVE. AmphI was extracted from 32P-labeled synaptosomes, phosphopeptides were isolated from proteolytic digests using TiO2 chromatography, and mass spectrometry revealed 13 sites: serines 250, 252, 262, 268, 272, 276, 285, 293, 496, 514, 539, and 626 and Thr-310. These were distributed into two clusters around the proline-rich domain and the C-terminal Src homology 3 domain. Hierarchical phosphorylation of Ser-262 preceded phosphorylation of Ser-268, -272, -276, and -285. Off-line HPLC separation and two-dimensional tryptic mapping of 32P-labeled amphI revealed that Thr-310, Ser-293, Ser-285, Ser-272, Ser-276, and Ser-268 contained the highest 32P incorporation and were the most stimulus-sensitive. Individually Thr-310 and Ser-293 were the most abundant phosphosites, incorporating 16 and 23% of the 32P. The multiple phosphopeptides containing Ser-268, Ser-276, Ser-272, and Ser-285 had 27% of the 32P. Evidence for a role for at least one proline-directed protein kinase and one non-proline-directed kinase was obtained. Four phosphosites predicted for non-proline-directed kinases, Ser-626, -250, -252, and -539, contained low amounts of 32P and were not depolarization-responsive. At least one alternatively spliced amphI isoform was identified in synaptosomes as being constitutively phosphorylated because it did not incorporate 32P during the 1-h labeling period. Multiple phosphosites from amphI-co-migrating synaptosomal proteins were also identified, including SGIP (Src homology 3 domain growth factor receptor-bound 2 (Grb2)-like (endophilin)-interacting protein 1), AAK1, eps15R, MAP6, alpha/beta-adducin, and HCN1. The results reveal two sets of amphI phosphosites that are either dynamically turning over or constitutively phosphorylated in nerve terminals and improve understanding of the role of individual amphI sites or phosphosite clusters in synaptic SVE.
Mol Cell Proteomics 2008 Jun
PMID:The in vivo phosphorylation sites in multiple isoforms of amphiphysin I from rat brain nerve terminals. 1834 31

An improved method of detection of multiphosphorylated peptides by RPLC-MS/MS analysis under low pH conditions (pH approximately 1.7, 3% formic acid) is demonstrated for the model phosphoproteins, bovine alpha- and beta-casein. Changes in the pH conditions from normal (pH approximately 3.0, 0.1% formic acid) to low (pH approximately 1.7, 3% formic acid) significantly improved the detection limit of multiphosphorylated peptides carrying negative (-) solution charge states. In particular, bovine beta-casein tetraphosphorylated peptide, was detected with a loading amount of only 50 fmol of trypsin-digested bovine beta-casein under low pH conditions, which is 200 times lower than necessary to detect the peptide under normal pH conditions. In order to understand the low pH effect, various loading amounts of trypsin-digested bovine alpha- and beta-caseins were analyzed by RPLC-MS/MS analyses under two different pH conditions. The question of whether the low pH condition improves the detection of multiphosphorylated peptides by increasing ionization efficiencies could not be proven in this study because synthetic multiphosphorylated peptides could not be easily obtained by peptide synthesis. Interestingly, increased hydrophilicity resulting from multiple phosphorylation events is shown to negatively affect the peptide retention on reversed-phase column material. It was also demonstrated that the low pH condition could effectively enhance the retention of multiphosphorylated peptides on reversed-phase column material. The usefulness of low pH RPLC analysis was tested using an actual phosphopeptide-enriched sample prepared from mouse brain tissues. Previously, low pH solvents have been used in SCX fractionation and TiO2 enrichment processes to selectively enrich phosphopeptides during the phosphopeptide enrichment procedure, but the improved detection of multiphosphorylated peptides in RPLC-MS/MS analysis under low pH conditions has not been reported before (Ballif, B. A.; Villen, J.; Beausoleil, S. A.; Schwartz, D.; Gygi, S. P. Mol. Cell. Proteomics 2004, 3, 1093-1101. Villen, J.; Beausoleil, S. A.; Gerber, S. A.; Gygi, S. P. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1488-1493. Schlosser, A.; Vanselow, J. T.; Kramer, A. Anal. Chem. 2005, 77, 5243-5250.).
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PMID:Detection of multiphosphorylated peptides in LC-MS/MS analysis under low pH conditions. 1834 89

Titanium dioxide nanoparticles (nano-TiO2) are widely used as a photocatalyst in air and water remediation. These nanoparticles are known to induce toxicity; however, their cytotoxic mechanism is not fully understood. In this study, we investigated the underlying mechanism of nano-TiO2-induced cytotoxicity in peripheral blood lymphocytes. We examined the genotoxic effects of nano-TiO2 in lymphocytes using alkaline single-cell gel electrophoresis (Comet) and cytokinesis-block micronucleus (CBMN) assays. Lymphocytes treated with nano-TiO2 showed significantly increased micronucleus formation and DNA breakage. Western-blot analysis to identify proteins involved in the p53-mediated response to DNA damage revealed the accumulation of p53 and activation of DNA damage checkpoint kinases in nano-TiO2-treated lymphocytes. However, p21 and bax, downstream targets of p53, were not affected, indicating that nano-TiO2 does not stimulate transactivational activity of p53. The generation of reactive oxygen species (ROS) in nano-TiO2-treated cells was also observed, andN-acetylcysteine (NAC) supplementation inhibited the level of nano-TiO2-induced DNA damage. Given that ROS-induced DNA damage leads to p53 activation in the DNA damage response, our results suggest that nano-TiO2 induces ROS generation in lymphocytes, thereby activating p53-mediated DNA damage checkpoint signals.
Environ Mol Mutagen 2008 Jun
PMID:Titanium dioxide nanoparticles trigger p53-mediated damage response in peripheral blood lymphocytes. 1841 68

Molecular structures and vibrational spectra of the CO species adsorbed on the Pt/TiO2, Pt/CeO2 and FeOx/Pt/CeO2 have been investigated by means of density functional theory (DFT) calculation and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). The geometrical structures and vibrational frequencies were obtained at the MPW1PW91/SDD level. Theoretical calculation shows that the calculated IR spectra were in good agreement with the experimental results. The calculated results clarify the assignment of the adsorbed CO species on the surface of Pt/TiO2, Pt/CeO2 and FeOx/Pt/CeO2.
Spectrochim Acta A Mol Biomol Spectrosc 2008 Dec 15
PMID:DRIFTS investigation and DFT calculation of the adsorption of CO on Pt/TiO2, Pt/CeO2 and FeOx/Pt/CeO2. 1855 Apr 22

Rhodococcus ruber GIN1 (formally Rh. strain GIN1) was previously isolated on the basis of its strong adherence to coal fly ash (CFA) and titanium dioxide particles from CFA sedimentation ponds of an electrical power plant in Israel. The interaction of the bacterium with oxides has been shown to be mediated by a cell surface protein designated TiBP (titanium binding protein) involving primarily strong, non-electrostatic forces. In this work, we set forward to identify this unique exocellular protein. Sequence analysis of the purified protein by mass spectrometry (LC/MS/MS) following trypsinization revealed 11 peptides. All of them showed >90% amino acid residues identity with sequences of one of the orthologs (dldh1) of the cytosolic enzyme dihydrolipoamide dehydrogenase (DLDH), based on the genome sequence of Rhodococcus strain RHA1. This genome was selected as a reference since currently it is the only sequenced Rhodococcal genome. Altogether, these peptides covered over 25% of the 52 kDa protein molecule. N- and C-termini primers were prepared and used to sequence the paralog gene from Rh. ruber GIN1 after polymerase chain reaction (PCR) amplification. All 11 peptides showed 100% identity with the sequence of this gene. The homology of TiBP with the supposedly cytosolic DLDH raised the question of whether the exocellular TiBP possesses DLDH activity. Indeed, intact late logarithmic phase Rh. ruber GIN1 cells, previously shown to express TiBP, were found to possess such activity, while very low activity was associated with stationary phase cells which possess diminished TiBP expression on their surface. Further evidence for the exocellular location of TiBP/DLDH was achieved using specific anti-TiBP polyclonal antibodies by whole cell and protein enzyme-linked immunosorbent assay (ELISA), showing high reactivity of the logarithmic phase cell surface and substantially lower reactivity with the stationary phase cells. As expected, logarithmic phase spheroplasts were not recognized by these antibodies. Similar results were obtained by fluorescence and scanning electron microscopy. Our postulation that DLDH is located on the surface of Rh. ruber GIN1, serving as a TiO2 binding protein, is in accordance with literary evidence on DLDH in other organisms, Bacteria, Archea, and Eukaryots that suggests it is associated with the outer membranes or cell surfaces. As an exocellular protein DLDH assumes various tasks which are not related to its classical role as a 2-oxoacid dehydrogenase, including serving as an adhesion/binding protein in certain bacteria.
J Mol Recognit
PMID:The titanium binding protein of Rhodococcus ruber GIN1 (NCIMB 40340) is a cell-surface homolog of the cytosolic enzyme dihydrolipoamide dehydrogenase. 1895 42

Human mesothelial cells (LP9/TERT-1) were exposed to low and high (15 and 75 microm(2)/cm(2) dish) equal surface area concentrations of crocidolite asbestos, nonfibrous talc, fine titanium dioxide (TiO2), or glass beads for 8 or 24 hours. RNA was then isolated for Affymetrix microarrays, GeneSifter analysis and QRT-PCR. Gene changes by asbestos were concentration- and time-dependent. At low nontoxic concentrations, asbestos caused significant changes in mRNA expression of 29 genes at 8 hours and of 205 genes at 24 hours, whereas changes in mRNA levels of 236 genes occurred in cells exposed to high concentrations of asbestos for 8 hours. Human primary pleural mesothelial cells also showed the same patterns of increased gene expression by asbestos. Nonfibrous talc at low concentrations in LP9/TERT-1 mesothelial cells caused increased expression of 1 gene Activating Transcription Factor 3 (ATF3) at 8 hours and no changes at 24 hours, whereas expression levels of 30 genes were elevated at 8 hours at high talc concentrations. Fine TiO2 or glass beads caused no changes in gene expression. In human ovarian epithelial (IOSE) cells, asbestos at high concentrations elevated expression of two genes (NR4A2, MIP2) at 8 hours and 16 genes at 24 hours that were distinct from those elevated in mesothelial cells. Since ATF3 was the most highly expressed gene by asbestos, its functional importance in cytokine production by LP9/TERT-1 cells was assessed using siRNA approaches. Results reveal that ATF3 modulates production of inflammatory cytokines (IL-1 beta, IL-13, G-CSF) and growth factors (VEGF and PDGF-BB) in human mesothelial cells.
Am J Respir Cell Mol Biol 2009 Jul
PMID:Alterations in gene expression in human mesothelial cells correlate with mineral pathogenicity. 1909 84

Nano-TiO2 and superoxide dismutase (SOD, EC 1.15.1.1) have been added to cosmetics and used to prevent injury of skin from UV-radiation, which might be related to the decrease of oxidative damage of skin. In previous studies we had proven that nano-anatase could increase the activity of SOD and decrease the oxidative damage in vivo. The mechanisms by which nano-anatase promoted SOD activity, however, are still not clearly understood. In the present work, nano-anatase in various concentrations was added to SOD from rat erythrocytes in vitro to gain insight into the mechanism of molecular interactions between nano-anatase and SOD by various spectral methods, suggesting that the reaction between SOD and nano-anatase was two-order, which meant that the SOD activity was greatly increased by low concentration of nano-anatase and inhibited by high concentration of nano-anatase. The spectroscopic assays suggested that the nano-anatase was determined to directly bind to SOD; the binding site of nano-anatase to SOD was 0.256 and the binding constants were 6.54 x 10(5) and 3.6 x 10(5)Lmol(-1); Ti was bound with three oxygen or nitrogen atoms and a sulfur atoms of amino acid residues at the Ti-O(N) and Ti-S bond lengths of 1.86 and 2.37 A, respectively, the binding nano-anatase entirely altered the secondary structure of SOD. It implied that the nano-anatase coordination created a new metal ion-active site form in SOD, thus leading to an enhancement in SOD activity.
Spectrochim Acta A Mol Biomol Spectrosc 2009 Jul 15
PMID:Direct evidence for interaction between nano-anatase and superoxide dismutase from rat erythrocytes. 1934 6


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