Biomedical subjects

Zhigang Wang

Publications and source records attributed to Zhigang Wang.

At least 19 recordsLinked to original sources

PubMed2026

African swine fever virus A151R protein antagonizes the antiviral activity of barrier-to-autointegration factor (BAF) by targeting its dsDNA-binding activity.

Barrier-to-autointegration factor (BAF) is a ubiquitous double-stranded DNA-binding protein that compacts DNA and can restrict poxvirus replication in the cytoplasm. BAF antiviral DNA-binding activity is tightly regulated by dynamic phosphorylation mediated by viral and cellular enzymes. For example, vaccinia virus counteracts BAF by encoding the B1 kinase, which phosphorylates BAF and abrogates its DNA-binding activity. Some DNA viruses, such as African swine fever virus (ASFV), undergo cytoplasmic replication but appear to lack a B1-like kinase. Interestingly, ASFV encodes A151R, a viral protein recently found to stably interact with BAF. Here, we demonstrate that A151R is capable of counteracting the antiviral properties of BAF. Structural modeling indicates that A151R is not a protein kinase and does not phosphorylate BAF but instead directly targets its double-stranded DNA-binding interface. This interaction enhances genome replication and progeny production of a B1-deficient virus. Mechanistically, A151R markedly impairs BAF DNA binding and disrupts its dimerization, a key requirement for high-affinity DNA association. Importantly, disruption of the A151R-BAF interaction abolishes these effects and restores BAF antiviral function. In addition, expression of the unphosphorylatable BAF mutant, which normally exhibits strong chromatin association, was redistributed to the cytoplasm in the presence of A151R, further supporting phosphorylation-independent regulation of BAF-DNA association. In conclusion, our findings support a previously unrecognized mechanism by which ASFV A151R disables BAF antiviral activity by obscuring its DNA-binding interface and inhibiting DNA binding in a phosphorylation-independent manner.IMPORTANCEDNA viruses replicating in the cytoplasm must overcome host intrinsic defenses to ensure productive replication, yet the mechanisms underlying their antagonism of the DNA-binding antiviral factor BAF remain incompletely understood. Here, we identify African swine fever virus (ASFV) A151R as a novel viral regulator that disables BAF by targeting its double-stranded DNA-binding interface rather than altering its phosphorylation state. We demonstrate that A151R impairs BAF DNA binding, disrupts its dimerization, and promotes viral DNA accumulation and progeny production in a BAF-dependent manner. Importantly, this activity requires A151R-BAF interaction and is independent of BAF phosphorylation status. Our findings reveal a previously unrecognized strategy employed by ASFV to neutralize host DNA-binding restriction factors and expand the molecular framework of BAF-mediated antiviral defense.

A151R↗

PubMed2007

Tfb5 interacts with Tfb2 and facilitates nucleotide excision repair in yeast.

TFIIH is indispensable for nucleotide excision repair (NER) and RNA polymerase II transcription. Its tenth subunit was recently discovered in yeast as Tfb5. Unlike other TFIIH subunits, Tfb5 is not essential for cell survival. We have analyzed the role of Tfb5 in NER. NER was deficient in the tfb5 deletion mutant cell extracts, and was specifically complemented by purified Tfb5 protein. In contrast to the extreme ultraviolet (UV) sensitivity of rad14 mutant cells that lack any NER activity, tfb5 deletion mutant cells were moderately sensitive to UV radiation, resembling that of the tfb1-101 mutant cells in which TFIIH activity is compromised but not eliminated. Thus, Tfb5 protein directly participates in NER and is an accessory NER protein that stimulates the repair to the proficient level. Lacking a DNA binding activity, Tfb5 was found to interact with the core TFIIH subunit Tfb2, but not with other NER proteins. The Tfb5-Tfb2 interaction was correlated with the cellular NER function of Tfb5, supporting the functional importance of this interaction. Our results led to a model in which Tfb5 acts as an architectural stabilizer conferring structural rigidity to the core TFIIH such that the complex is maintained in its functional architecture.

Amino Acid Sequence↗

PubMed2006

Discovery of a new class of macrocyclic antagonists to the human motilin receptor.

A novel class of macrocyclic peptidomimetics was identified and optimized as potent antagonists to the human motilin receptor (hMOT-R). Well-defined structure-activity relationships allowed for rapid optimization of potency that eventually led to high affinity antagonists to hMOT-R. Potency and antagonist functional activity were confirmed both in functional and cell-based assays, as well as on isolated rabbit intestinal smooth muscle strips. Rapid access to this novel class of macrocyclic target structures was made possible through two efficient and complementary solid-phase parallel synthetic approaches, both of which are reported herein.

Animals↗

PubMed2006

Characterization of a high-throughput screening assay for inhibitors of elongation factor p and ribosomal peptidyl transferase activity.

Elongation Factor P (EF-P) is an essential component of bacterial protein synthesis, enhancing the rate of translation by facilitating the addition of amino acids to the growing peptide chain. Using purified Staphylococcus aureus EF-P and a reconstituted Escherichia coli ribosomal system, an assay monitoring the addition of radiolabeled N-formyl methionine to biotinylated puromycin was developed. Reaction products were captured with streptavidin-coated scintillation proximity assay (SPA) beads and quantified by scintillation counting. Data from the assay were used to create a kinetic model of the reaction scheme. In this model, EF-P binding to the ribosome essentially doubled the rate of the ribosomal peptidyl transferase reaction. As described here, EF-P bound to the ribosomes with an apparent K(a) of 0.75 microM, and the substrates N-fMet-tRNA and biotinylated puromycin had apparent K(m)s of 19 microM and 0.5 microM, respectively. The assay was shown to be sensitive to a number of antibiotics known to target ribosomal peptide bond synthesis, such as chloramphenicol and puromycin, but not inhibitors that target other stages of protein synthesis, such as fusidic acid or thiostrepton.

Anti-Bacterial Agents↗

PubMed2006

Nanoliter-scale reactor arrays for biochemical sensing.

A general approach is described for array-based biochemical sensing that uses contact-free dispersal of compounds into addressable microfabricated reactors. The arrays are composed of 1 to 100 nL volume open reactors that have been microfabricated on quartz substrates using lithography. The open architecture of these reactors allows them to be addressed in parallel or individually with an ink-jet arrayer that is capable of distributing 0.004 to 1 nL volumes of reagents. A seven-step biochemical assay has been conducted on a small array of reactors to demonstrate how they can be integrated with an ink-jet arrayer and optical detector. This nanoreactor assay format appears to overcome several limitations that chip-based microarray technology currently imposes on protein assays: the arrays can be created in a manner that does not expose the biochemical reagents to osmotic stress, independent reactions can be conducted in individual reactors, and the conditions in all of the reactors (e.g., concentration and pH) can be rapidly scanned. We believe that these nanoreactor arrays will be useful for biochemical sensing that involves delicate proteins and protein assemblies.

Biosensing Techniques↗

PubMed2006

Interplay between two phase transitions: crystallization and liquid-liquid phase separation in a polyolefin blend.

The interplay between liquid-liquid phase separation (LLPS) and crystallization at several compositions in statistical copolymer blends of poly(ethyleneco-hexene) and poly(ethylene-cobutene) has been examined by optical microscopy (OM), atomic force microscopy (AFM), and differential scanning calorimetry (DSC). The phase contrast optical microscopy shows interconnected bicontinuous structures for deeply quenched LLPS, characteristic of spinodal decomposition. After a second quench to a temperature below the melting point, an overwhelming change in crystallization kinetics has been clearly observed, which is caused by the increase of the nucleation rate assisted by concentration fluctuations due to the spontaneous spinodal LLPS. We propose a new mechanism of "fluctuation assisted nucleation" in the crystallization process for such interactive process in a blend system. The experimental results from OM, AFM, and DSC measurements at various conditions are all consistent with the fluctuation assisted nucleation model.

Journal Article↗

PubMed2006

Synthesis and photoelectron spectroscopic studies of N(CH2CH2NMe)3P=E (E = O, S, NH, CH2).

The synthesis and the crystal and molecular structure of N(CH(2)CH(2)NMe)(3)P=CH(2) is reported. The P-N(ax) distance is rather long in N(CH(2)CH(2)NMe)(3)P=CH(2). The ylide N(CH(2)CH(2)NMe)(3)P=CH(2) proved to be a stronger proton acceptor than proazaphosphatrane N(CH(2)CH(2)NMe)(3)P, since it was shown to deprotonate N(CH(2)CH(2)NMe)(3)PH(+). The extremely strong basicity of the ylide is in accordance with its low ionization energy (6.3 eV), which is the lowest in the presently investigated series N(CH(2)CH(2)NMe)(3)P=E (E: CH(2), NH, lone pair, O and S), and to the best of our knowledge it is the smallest value observed for a non-conjugated phosphorus ylide. Computations reveal the existence of two bond strech isomers, and the stabilization of the phosphorus centered cation by electron donation from the equatorial and the axial nitrogens. Similar stabilizing effects operate in the case of protonation of E. A fine balance of these different interactions determines the P-N(ax) distance, which is thus very sensitive to the level of the theory applied. According to the quantum mechanical calculations, methyl substitution at the equatorial nitrogens flattens the pyramidality of this atom, increasing its electron donor capability. As a consequence, the PN(ax) distance in the short-transannular bonded protonated systems and the radical cations is longer by about 0.5 A in the N(eq)(Me) than in the N(eq)(H) systems. Accordingly, isodesmic reaction energies show that a stabilization of about 25 and 10 kcal/mol is attributable to the formation of the transannular bond in case of N(eq)(H) and the experimentally realizable N(eq)(Me) species, respectively.

Journal Article↗

PubMed2006

Poleta, Polzeta and Rev1 together are required for G to T transversion mutations induced by the (+)- and (-)-trans-anti-BPDE-N2-dG DNA adducts in yeast cells.

Benzo[a]pyrene is an important environmental mutagen and carcinogen. Its metabolism in cells yields the mutagenic, key ultimate carcinogen 7R,8S,9S,10R-anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide, (+)-anti-BPDE, which reacts via its 10-position with N2-dG in DNA to form the adduct (+)-trans-anti-BPDE-N2-dG. To gain molecular insights into BPDE-induced mutagenesis, we examined in vivo translesion synthesis and mutagenesis in yeast cells of a site-specific 10S (+)-trans-anti-BPDE-N(2)-dG adduct and the stereoisomeric 10R (-)-trans-anti-BPDE-N2-dG adduct. In wild-type cells, bypass products consisted of 76% C, 14% A and 7% G insertions opposite (+)-trans-anti-BPDE-N2-dG; and 89% C, 4% A and 4% G insertions opposite (-)-trans-anti-BPDE-N2-dG. Translesion synthesis was reduced by approximately 26-37% in rad30 mutant cells lacking Poleta, but more deficient in rev1 and almost totally deficient in rev3 (lacking Polzeta) mutants. C insertion opposite the lesion was reduced by approximately 24-33% in rad30 mutant cells, further reduced in rev1 mutant, and mostly disappeared in the rev3 mutant strain. The insertion of A was largely abolished in cells lacking either Poleta, Polzeta or Rev1. The insertion of G was not detected in either rev1 or rev3 mutant cells. The rad30 rev3 double mutant exhibited a similar phenotype as the single rev3 mutant with respect to translesion synthesis and mutagenesis. These results show that while the Polzeta pathway is generally required for translesion synthesis and mutagenesis of the (+)- and (-)-trans-anti-BPDE-N2-dG DNA adducts, Poleta, Polzeta and Rev1 together are required for G-->T transversion mutations, a major type of mutagenesis induced by these lesions. Based on biochemical and genetic results, we present mechanistic models of translesion synthesis of these two DNA adducts, involving both the one-polymerase one-step and two-polymerase two-step models.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

PubMed2006

Enhanced gene delivery into skeletal muscles with ultrasound and microbubble techniques.

RATIONALE AND OBJECTIVES: This experiment was directed to explore the effects of ultrasound microbubbles on gene structure in vitro and green fluorescent protein (GFP) plasmid transfer into skeletal muscles in vivo. By establishing a rat ischemic hind limb model, the effects of ultrasound-mediated microbubble destruction on vascular endothelial growth factor (VEGF) gene transfection to skeletal muscles were also studied in vivo. MATERIALS AND METHODS: Ultrasound irradiation was applied on the mixture of microbubbles and GFP plasmid in vitro. Gel electrophoresis was used to detect the effects of ultrasound and microbubbles on GFP plasmid. For in vivo experiments, ultrasound irradiation was applied on the hind limb after directly injecting microbubbles into the hind limb of Wistar rats. Directly after treatment, the skeletal muscles were harvested to observe the microstructure. We also studied the transfer rate of GFP plasmid DNA into the skeletal muscles of rats by applying ultrasound and microbubble technique. Furthermore, a naked VEGF plasmid was applied to study the feasibility of angiogenesis by using rats ischemia models. RESULTS: Gel electrophoresis of plasmid DNA showed that there was no difference between the groups. By studying the hematoxylin and eosin stained pictures of the skeletal muscles, we found that ultrasound irradiation of skeletal muscle after injection of microbubbles could cause the exudation of the red blood cells, whereas it had no effects on the microstructure of muscle fibers. In vivo experiments showed that an ultrasound microbubble could enhance the transfer of plasmid DNA to the skeletal muscles. CONCLUSIONS: The ultrasound-mediated microbubble technique provides an effective noninvasive method for gene therapy.

Animals↗

PubMed2006

Controlled expression of recombinant genes and preparation of cell-free extracts in yeast.

Biochemistry is an important experimental tool in the study of protein functions. Biochemical studies frequently involve overexpression of a cloned gene and purification of the recombinant protein. The yeast Saccharomyces cerevisiae provides an effective system for expression and purification of recombinant proteins owing to the ease of applying molecular techniques and obtaining large quantities of cells with a low cost. Additionally, complex biochemical processes such as transcription and DNA repair can be studied in yeast cell-free extracts in vitro, which benefit greatly from a large collection of well-defined mutant strains. Controlled gene expression and preparation of cell-free extracts are important techniques in the yeast system. Two commonly used inducible gene expression systems, the GAL1 promoter and the CUP1 promoter, are described. Protocols of preparing yeast whole cell extracts and nuclear extracts are presented, each of which is designed for specific applications.

Cell Fractionation↗

PubMed2005

An efficient method to express and refold a truncated human procaspase-9: a caspase with activity toward Glu-X bonds.

A truncated form of human procaspase-9 missing the first 111 amino acids, and a variety of mutants derived therefrom, have been expressed in Escherichia coli inclusion bodies. Upon refolding to active enzymes, Delta(1-111) procaspase-9 and mutants were recovered at purity greater than 95% and with a final yield of 20-35 mg/L cell culture. Our active procaspase-9 retains its pro-segment, while undergoing major auto processing at Asp315 and a minor (20%) cleavage at Glu306. This unusual cleavage at a Glu-X bond also took place in the D315E mutant, and we describe herein the inhibitor Z-VAE-fmk that shows enhanced inactivation of procaspase-9 over caspases-3. The bond at Asp330, not processed by procaspase-9, is cleaved by caspase-3 and the resulting procaspase-9 variant, missing the 316-330 bridge, is six times as active as the non-mutated Delta(1-111) proenzyme. A deletion mutant lacking residues 316-330 underwent auto activation by cleavage at Asp315-Ala331 bond. Moreover, substitution of Glu306 by an Asp residue in this mutant led to rapid removal of the peptide spanning Ser307 to Asp330, and resulted in an enzyme that was 7.6 times as active as the non-mutated Delta(1-111) procaspase-9. Finally, replacing both Asp315 and Glu306 with Ala generated a procaspase-9 mutant incapable of auto processing. This single chain procaspase-9 was fully as active as the non-mutated Delta(1-111) enzyme processed at Asp315 or Glu306. Our demonstration that unprocessed procaspase-9 mutants are active as proteases with caspase-type specificity suggests that the role of procaspase-9 in cascade activation of executioner caspases might, in some circumstances, be carried out alone and without association of the apoptosome.

Amino Acid Metabolism, Inborn Errors↗

PubMed2005

The p-benzoquinone DNA adducts derived from benzene are highly mutagenic.

Benzene is a human leukemia carcinogen, resulting from its cellular metabolism. A major benzene metabolite is p-benzoquinone (pBQ), which can damage DNA by forming the exocyclic base adducts pBQ-dC, pBQ-dA, and pBQ-dG in vitro. To gain insights into the role of pBQ in benzene genotoxicity, we examined in vitro translesion synthesis and in vivo mutagenesis of these pBQ adducts. Purified REV1 and Polkappa were essentially incapable of translesion synthesis in response to the pBQ adducts. Opposite pBQ-dA and pBQ-dC, purified human Poliota was capable of error-prone nucleotide insertion, but was unable to perform extension synthesis. Error-prone translesion synthesis was observed with Poleta. However, DNA synthesis largely stopped opposite the lesion. Consistent with in vitro results, replication of site-specifically damaged plasmids was strongly inhibited by pBQ adducts in yeast cells, which depended on both Polzeta and Poleta. In wild-type cells, the majority of translesion products were deletions at the site of damage, accounting for 91%, 90%, and 76% for pBQ-dA, pBQ-dG, and pBQ-dC, respectively. These results show that the pBQ-dC, pBQ-dA, and pBQ-dG adducts are strong blocking lesions, and are highly mutagenic by predominantly inducing deletion mutations. These results are consistent with the lesion structures predicted by molecular dynamics simulation. Our results led to the following model. Translesion synthesis normally occurs by directly copying the lesion site through base insertion and extension synthesis. When the lesion becomes incompatible in accommodating a base opposite the lesion in DNA, translesion synthesis occurs by a less efficient lesion loop-out mechanism, resulting in avoiding copying the damaged base and leading to deletion.

Benzene↗

PubMed2005

Mesoporous membrane device for asymmetric biosensing.

An array of micron size reactors has been designed and fabricated on a mesoporous membrane to create a platform for asymmetric biochemical sensing. Fabrication of this device required that a technique be developed to integrate the mesoporous alumina membrane with a polymeric layer that maintains the integrity of the membrane surface and permeability. This device was used to control an enzyme reaction at the surface of the membrane through the diffusion of the substrates from the opposite sides of the membrane. Asymmetric reactions promise new modes of sensing, enhanced stability of delicate biomolecular systems, and enhanced sensitivity and speed in sensing.

Aluminum Oxide↗

PubMed2005

A path from I(h) to C1 symmetry for C20 cage molecule.

The symmetry of the C20 cage is studied based on the intrinsical relationship among point groups (Bradley, C. J.; Cracknell, A. P. The Mathematical Theory of Symmetry in Solids; Claredon Press: Oxford, 1972). The structure of the C20 cage with I(h) symmetry is constructed, as are eight other structures with subgroup symmetry. A path from I(h) symmetry to C1 symmetry is obtained for the closed-shell electronic state, and the structure with D2h symmetry is the most stable on this path. Using the D2h structure the correlation energy correction is studied on the condition of restricted excitation space at the CCSD(T) level. We obtain curves on the relation between the orbital numbers and the total energy at the CCSD(T), CCSD, and MP2 level, respectively. The results of these curves obtained from MP2 and CCSD(T) methods have the same tendency, while the results of CCSD gradually diverge with an increase in orbital numbers. When the orbitals used in the calculation reach 460, the total energy is -759.644 hartree at MP2 level and is -759.721 hartree by the CCSD(T) method. From the calculation results, we find that a large basis set can improve the reliability of the MP2 method, and to restrict excitation space is necessary when using the CCSD(T) method.

Journal Article↗

PubMed2005

Multiple losses of neutral C14H14 in the tandem mass spectrometry of several perbenzyl ether intermediates in the synthesis of green tea constituents.

Electrospray and matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS/MS) experiments were used to investigate an unusual fragmentation in collision-induced dissociation (CID) of sodiated and potassiated perbenzyl ether intermediates obtained in the total synthesis of gallate ester constituents of green tea. Prominent fragments correspond to multiple sequential losses of neutral C14H14 that were not observed in the protonated and ammoniated species, that instead present fragment ion series in which members are separated by C7H6. High-resolution MALDI quadrupole time-of-flight (Q-TOF) and electrospray-Fourier transform mass spectrometry (FTMS) were used to confirm elemental compositions of these and related ions.

Esters↗

PubMed2004

Roles of Rad23 protein in yeast nucleotide excision repair.

Nucleotide excision repair (NER) removes many different types of DNA lesions. Most NER proteins are indispensable for repair. In contrast, the yeast Rad23 represents a class of accessory NER proteins, without which NER activity is reduced but not eliminated. In mammals, the complex of HR23B (Rad23 homolog) and XPC (yeast Rad4 homolog) has been suggested to function in the damage recognition step of NER. However, the precise function of Rad23 or HR23B in NER remains unknown. Recently, it was suggested that the primary function of RAD23 protein in NER is its stabilization of XPC protein. Here, we tested the significance of Rad23-mediated Rad4 stabilization in NER, and analyzed the repair and biochemical activities of purified yeast Rad23 protein. Cellular Rad4 was indeed stabilized by Rad23 in the absence of DNA damage. Persistent overexpression of Rad4 in rad23 mutant cells, however, largely failed to complement the ultraviolet sensitivity of the mutant. Consistently, deficient NER in rad23 mutant cell extracts could not be complemented by purified Rad4 protein in vitro. In contrast, partial complementation was observed with purified Rad23 protein. Specific complementation to the level of wild-type repair was achieved by adding purified Rad23 together with small amounts of Rad4 protein to rad23 mutant cell extracts. Purified Rad23 protein was unable to bind to DNA, but stimulated the binding activity of purified Rad4 protein to N-acetyl-2-aminofluorene-damaged DNA. These results support two roles of Rad23 protein in NER: (i) its direct participation in the repair biochemistry, possibly due to its stimulatory activity on Rad4-mediated damage binding/recognition; and (ii) its stabilization of cellular Rad4 protein.

DNA Repair↗

PubMed2004

Green tea and tea polyphenols in cancer prevention.

The cancer-preventive effects of green tea and its main constituent (-)-epigallocatechin gallate [(-)-EGCG] are widely supported by results from epidemiological, cell culture, animal and clinical studies in the recent decade. In vitro cell culture studies show that tea polyphenols potently induce apoptotic cell death and cell cycle arrest in tumor cells but not in their normal cell counterparts. Green tea polyphenols affect several signal transduction pathways, including growth factor-mediated, the mitogen-activated protein kinase (MAPK)-dependent, and ubiquitin/proteasome degradation pathways. Epidemiological studies have suggested that the consumption of green tea lowers the risk of cancer. Various animal studies have revealed that treatment by green tea inhibits tumor incidence and multiplicity in different organ sites such as skin, lung, liver, stomach, mammary gland and colon. Phase I and II clinical trials were carried out recently to explore the anticancer effects of green tea in patients with cancer. At this time, more mechanistic research, animal studies, and clinical trials are necessary to further evaluate the role of green tea in cancer prevention.

Anticarcinogenic Agents↗

PubMed2004

Role of DNA polymerase eta in the bypass of abasic sites in yeast cells.

Abasic (AP) sites are major DNA lesions and are highly mutagenic. AP site-induced mutagenesis largely depends on translesion synthesis. We have examined the role of DNA polymerase eta (Poleta) in translesion synthesis of AP sites by replicating a plasmid containing a site-specific AP site in yeast cells. In wild-type cells, AP site bypass resulted in preferred C insertion (62%) over A insertion (21%), as well as -1 deletion (3%), and complex event (14%) containing multiple mutations. In cells lacking Poleta (rad30), Rev1, Polzeta (rev3), and both Poleta and Polzeta, translesion synthesis was reduced to 30%, 30%, 15% and 3% of the wild-type level, respectively. C insertion opposite the AP site was reduced in rad30 mutant cells and was abolished in cells lacking Rev1 or Polzeta, but significant A insertion was still detected in these mutant cells. While purified yeast Polalpha effectively inserted an A opposite the AP site in vitro, purified yeast Poldelta was much less effective in A insertion opposite the lesion due to its 3'-->5' proofreading exonuclease activity. Purified yeast Poleta performed extension synthesis from the primer 3' A opposite the lesion. These results show that Poleta is involved in translesion synthesis of AP sites in yeast cells, and suggest that an important role of Poleta is to catalyze extension following A insertion opposite the lesion. Consistent with these conclusions, rad30 mutant cells were sensitive to methyl methanesulfonate (MMS), and rev1 rad30 or rev3 rad30 double mutant cells were synergistically more sensitive to MMS than the respective single mutant strains.

Base Sequence↗