Conformational Dynamics of Dioxygenase AlkB and DNA in the Course of Catalytically Active Enzyme–Substrate Complex Formation

Russian Journal of Bioorganic Chemistry - Fe2+/2-ketoglutarate-dependent DNA-dioxygenase AlkB from Escherichia coli is able to restore the native structure of alkylated DNA bases. The enzymatic...     

Inactivation of DNA–Dependent Protein Kinase Promotes Heat–Induced Apoptosis Independently of Heat–Shock Protein Induction in Human Cancer Cell Lines

The inhibition of DNA damage response pathway seems to be an attractive strategy for cancer therapy. It was previously reported that in rodent cells exposed to heat stress, cell growth was promoted by the activity of DNA-dependent protein kinase (DNA-PK), an enzyme involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair. The absence of a functioning DNA-PK was associated with down regulation of heat shock protein 70 (HSP70). The objective of this study is thus to investigate the role of DNA-PK inhibition in heat-induced apoptosis in human cell lines. The inhibitors of phosphorylation of the DNA-PK catalytic subunit (DNA-PKcs) at Ser2056, such as NU7026 and NU7441, were utilized. Furthermore, knock down of DNA-PKcs was carried out using small interfering RNA (siDNA-PKcs). For heat exposure, cells were placed in water bath at 44°C for 60 min. Apoptosis was evaluated after 24 h incubation flow cytometrically. Proteins were extracted after 24 h and analyzed for HSP70 and HSP40 expression by Western blotting. Total RNA was extracted 6 h after treatment and analyzed using a GeneChip® microarray system to identify and select the up-regulated genes (≥1.5 fold). The results showed an enhancement in heat-induced apoptosis in absence of functioning DNA-PKcs. Interestingly, the expression levels of HSP70 and HSP40 were elevated in the absence of DNA-PKcs under heat stress. The results of genetic network analysis showed that HSPs and JUN genes were up-regulated independently of DNA-PKcs in exposed parent and knock out cells. In the presence of functioning DNA-PKcs, there was an observed up-regulation of anti-apoptotic genes, such as NR1D1, whereas in the absence of DNA-PKcs the pro-apoptotic genes, such as EGR2, were preferentially up-regulated. From these findings, we concluded that in human cells, the inactivation of DNA-PKcs can promote heat-induced apoptosis independently of heat-shock proteins.     

Formation and Rapid Export of the Monochlorobimane–Glutathione Conjugate in Cultured Rat Astrocytes

Monochlorobimane (MCB) is often used to visualize glutathione (GSH) levels in cultured cells, since it is quickly converted to a fluorescent GSH conjugate (GS–MCB). To test for consequences of MCB application on the GSH metabolism of astrocytes, we have studied rat astrocyte-rich primary cultures as model system. MCB caused a concentration dependent rapid decrease in the cellular GSH content. Simultaneously, a transient accumulation of GS–MCB in the cells was observed with a maximal content 5 min after MCB application. The cellular accumulation was followed by a rapid release of GS–MCB into the medium with a maximal initial export rate of 27.9 ± 6.5 nmol h⁻¹ mg protein⁻¹. Transporters of the family of multidrug resistance proteins (Mrps) are likely to be involved in this export, since the Mrp inhibitor MK571 lowered the export rate by 60%. These data demonstrate that, due to its rapid export from astrocytes, GS–MCB is only under well-defined conditions a reliable indicator of the cellular GSH concentration and that MK571 can be used to maintain maximal GS–MCB levels in astrocytes.     

α-Tocopherol Transfer Protein Expression in Rat Liver Exposed to Hyperoxia

&#102 -Tochopherol transfer protein ( &#102 TTP), a 32 kDa protein exclusively expressed in liver cytosol, has a high binding affinity for &#102 -tochopherol. The factors that regulate the expression of hepatic &#102 TTP are not clearly understood. In this study, we investigated whether or not exposure to hyperoxia (>95% O 2 for 48 h) could alter the expression of hepatic &#102 TTP. We also examined the association between the expression of antioxidant enzymes (hepatic glutathione peroxidase (GPX) and Mn-superoxide dismutase (Mn-SOD)) and the expression of hepatic &#102 TTP. The levels of thiobarbituric acid-reactive substances (TBARS) in both plasma and liver were significantly higher after rats were exposed to hyperoxia for 48 h when compared with the levels in control rats. Northern blotting showed a decrease in the expression of &#102 TTP messenger RNA (mRNA) after hyperoxia, although the &#102 TTP protein level remained constant. Expression of Mn-SOD mRNA and protein, as well as the expression of GPX mRNA, were stable after hyperoxia. These findings indicate that mRNA for hepatic &#102 TTP, rather than Mn-SOD or GPX, may be highly responsive to oxidative stress.     

Comparative Bioavailability of Mineral-enriched Gluconates and Yeast in Rat Liver After Depletion–Repletion Feeding

There are many forms of mineral supplements currently available. Among these mineral-enriched gluconates and yeast are considered two of the more biologically available supplements. The purpose of this study was to use zinc (Zn)- or copper (Cu)-deficient rats to determine whether the organically bound mineral in yeast or the salt gluconate form was more bioavailable, i.e., is absorbed and found in a greater concentration in liver. It was demonstrated that Zn-enriched yeast was 3.7 times more bioavailable than the Zn gluconate and that Cu-enriched yeast was 1.4 times more bioavailable than the Cu gluconate.     

Dynamics of PLCγ and Src Family Kinase 1 Interactions during Nuclear Envelope Formation Revealed by FRET-FLIM

The nuclear envelope (NE) breaks down and reforms during each mitotic cycle. A similar process happens to the sperm NE following fertilisation. The formation of the NE in both these circumstances involves endoplasmic reticulum membranes enveloping the chromatin, but PLCγ-dependent membrane fusion events are also essential. Here we demonstrate the activation of PLCγ by a Src family kinase (SFK1) during NE assembly. We show by time-resolved FRET for the first time the direct in vivo interaction and temporal regulation of PLCγ and SFK1 in sea urchins. As a prerequisite for protein activation, there is a rapid phosphorylation of PLCγ on its Y783 residue in response to GTP in vitro. This phosphorylation is dependent upon SFK activity; thus Y783 phosphorylation and NE assembly are susceptible to SFK inhibition. Y783 phosphorylation is also observed on the surface of the male pronucleus (MPN) in vivo during NE formation. Together the corroborative in vivo and in vitro data demonstrate the phosphorylation and activation of PLCγ by SFK1 during NE assembly. We discuss the potential generality of such a mechanism.     

Analysis of DNA–Protein Contacts in a Complex between Methyltransferase SsoII and a Promoter Region of the SsoII Restriction–Modification Genes

Heterocyclic bases and phosphate groups involved in the DNA–methyltransferase SsoII (M·SsoII) interaction were identified in the regulatory DNA region localized within the promoter region of the SsoII restriction–modification genes by footprinting with the use of formic acid, hydrazine, dimethyl sulfate, and N-ethyl-N-nitrosourea as modifying agents. It has been established that the enzyme interacts with three guanines, one adenine, two thymines, and three phosphate groups of each strand of the DNA duplex. These heterocyclic bases and phosphate groups are disposed symmetrically within the 15-mer inverted repeat of the regulatory DNA region. It has been demonstrated by footprinting with dimethyl sulfate that the C7 atoms of guanines interacting with the enzyme are exposed to the DNA major groove. Two theoretical models were built describing the contacts in a complex between M·SsoII and the regulatory DNA region.     

Repair of DNA–Protein Cross-links in Mammalian Cells

DNA–protein cross-links are generated by both endogenous and exogenous DNA damaging agents, as intermediates during normal DNA metabolism, and during abortive base excision repair. Cross-links are relatively common lesions that are lethal when they block progression of DNA polymerases. DNA–protein cross-links may be broadly categorized into four groups by the DNA and protein chemistries near the cross-link and by the source of the cross-link: DNA–protein cross-links may be found (1) in nicked DNA at the 3' end of one strand (topo I), (2) in nicked DNA at the 5' end of one strand (pol beta), (3) at the 5' ends of both strands adjacent to nicks in close proximity (topo II; Spo 11), and (4) in one strand of duplex DNA (UV irradiation; bifunctional carcinogens and chemotherapeutic agents). Repair mechanisms are reasonably well-defined for groups 1 and 3, and suggested for groups 2 and 4. Our work is focused on the recognition and removal of DNA–protein cross-links in duplex DNA (group 4).     

Predicting the Impact of Single-Nucleotide Polymorphisms in CDK2–Flavopiridol Complex by Molecular Dynamics Analysis

Cyclic-dependent kinase 2 (CDK2) is one of the primary protein kinases involved in the regulation of cell cycle progression. Flavopiridol is a flavonoid derived from an indigenous plant act as a potent antitumor drug showing increased inhibitory activity toward CDK2. The presence of deleterious variations in CDK2 may produce different effects in drug-binding adaptability. Studies on nsSNPs of CDK2 gene will provide information on the most likely variants associated with the disease. Furthermore, investigating the relationship between deleterious variants and its ripple effect in the inhibitory action with drug will provide fundamental information for the development of personalized therapies. In this study, we predicted four variants Y15S, V18L, P45L, and V69A of CDK2 as highly deleterious. Occurrence of these variations seriously affected the normal binding capacity of flavopiridol with CDK2. Analysis of 10-ns molecular dynamics (MD) simulation trajectories indicated that the predicted deleterious variants altered the CDK2 stability, flexibility, and surface area. Notably, we noticed the decrease in number of hydrogen bonds between CDK2 and flavopiridol mutant complexes in the whole dynamic period. Overall, this study explores the possible relationship between the CDK2 deleterious variants and the drug-binding ability with the help of molecular docking and MD approaches.     

Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests

Identifying interaction sites in proteins provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Although there are numerous papers on the prediction of interaction sites using information derived from structure, there are only a few case reports on the prediction of interaction residues based solely on protein sequence. Here, a sliding window approach is combined with the Random Forests method to predict protein interaction sites using (i) a combination of sequence- and structure-derived parameters and (ii) sequence information alone. For sequence-based prediction we achieved a precision of 84% with a 26% recall and an F-measure of 40%. When combined with structural information, the prediction performance increases to a precision of 76% and a recall of 38% with an F-measure of 51%. We also present an attempt to rationalize the sliding window size and demonstrate that a nine-residue window is the most suitable for predictor construction. Finally, we demonstrate the applicability of our prediction methods by modeling the Ras–Raf complex using predicted interaction sites as target binding interfaces. Our results suggest that it is possible to predict protein interaction sites with quite a high accuracy using only sequence information.     

Protein–Protein Interactions in DNA Base Excision Repair

The system of base excision repair (BER) ensures correction of the most abundant DNA damages in mammalian cells and plays an important role in maintaining genome stability. Enzymes and protein factors participate in the multistage BER in a coordinated fashion, which ensures repair efficiency. The suggested coordination mechanisms are based on formation of protein complexes stabilized via either direct or indirect DNA-mediated interactions. The results of investigation of direct interactions of the proteins participating in BER with each other and with other proteins are outlined in this review. The known protein partners and sites responsible for their interaction are presented for the main participants as well as quantitative characteristics of their affinity. Information on the mechanisms of regulation of protein–protein interactions mediated by DNA intermediates and posttranslational modification is presented. It can be suggested based on all available data that the multiprotein complexes are formed on chromatin independent of the DNA damage with the help of key regulators of the BER process – scaffold protein XRCC1 and poly(ADP-ribose) polymerase 1. The composition of multiprotein complexes changes dynamically depending on the DNA damage and the stage of BER process.     

Base recognition of gap sites in DNA–DNA and DNA–RNA duplexes by short oligonucleotides

To increase base recognition capability and sensitivity, we propose the separation of a commonly used single-probe system for oligonucleotide analysis into a set of three probes: a fluorophore-labeled probe, a promoter probe, and a short probe. In this study, we found that the probes of only 4 nt in length can selectively bind the corresponding gap site on complexes consisting of the target, fluorophore-labeled probe, and promoter probe, exhibiting a more than 14-fold difference in ligation between the matched and mismatched sequences. Moreover, we demonstrated that the immobilized short probes accurately recognized the sequences of the gap sites.     

Guanosine 3′-Diphosphate,a Stimulant of Glucocorticoidal Tyrosine Aminotransferase Induction in Isolated Rat Liver Cells

Zein, an associate of two heterogeneous subunits, was fractionated into monomer, dimer and polymer (a mixture of the trimer and higher polymers) fractions. Sulfhydryl group analysis showed that almost all cysteine residues of the dimer and the polymer were involved in formation of intermolecular disulfide bonds. In the monomer, however, intramolecular disulfide bonds existed. To clarify in more detail the state of cysteine residues in the monomer, an experiment was carried out using a Thiopropyl-Sepharose 6B column. The possibility was shown that some of the cysteine residues were blocked or substituted. A model was presented to explain the state of cysteine residues in the monomer.     

Prevention of CCAAT/Enhancer-binding Protein �� DNA Binding by Hypoxia during Adipogenesis

Upon exposure to adipogenesis-inducing hormones, confluent 3T3-L1 preadipocytes express C/EBPβ (CCAAT/enhancer binding protein β). Early induced C/EBPβ is inactive but, after a lag period, acquires its DNA-binding capability by sequential phosphorylation. During this period, preadipocytes pass the G₁/S checkpoint synchronously. Thr¹⁸⁸ of C/EBPβ is phosphorylated initially to prime the factor for subsequent phosphorylation at Ser¹⁸⁴ or Thr¹⁷⁹ by GSK3β, which translocates into the nuclei during the G₁/S transition. Many events take place during the G₁/S transition, including reduction in p27^Kip1 protein levels, retinoblastoma (Rb) phosphorylation, GSK3β nuclear translocation, and C/EBPβ binding to target promoters. During hypoxia, hypoxia-inducible factor-1α (HIF-1α) is stabilized, thus maintaining expression of p27^Kip1, which inhibits Rb phosphorylation. Even under normoxic conditions, constitutive expression of p27^Kip1 blocks the nuclear translocation of GSK3β and DNA binding capability of C/EBPβ. Hypoxia also blocks nuclear translocation of GSK3β and DNA binding capability of C/EBPβ in HIF-1α knockdown 3T3-L1 cells that fail to induce p27^Kip1. Nonetheless, under hypoxia, these cells can block Rb phosphorylation and the G₁/S transition. Altogether, these findings suggest that hypoxia prevents the nuclear translocation of GSK3β and the DNA binding capability of C/EBPβ by blocking the G₁/S transition through HIF-1α-dependent induction of p27^Kip1 and an HIF-1α/p27-independent mechanism.