Biomedical subjects

Jiyong Zhao

Publications and source records attributed to Jiyong Zhao.

12 recordsLinked to original sources

PubMed2006

Anti-HER2 antibody trastuzumab inhibits CDK2-mediated NPAT and histone H4 expression via the PI3K pathway.

The anti-HER2 antibody trastuzumab (Herceptin) has been used to treat patients with breast cancers that overexpress HER2. We have demonstrated that p27(Kip1) upregulation is one of the key events that cause G(1) arrest upon trastuzumab treatment. Here, we have examined the effect of trastuzumab on expression of CDK2, Rb, E2F, NPAT and histone H4 in breast cancer cells that overexpress HER2. Trastuzumab treatment dramatically inhibited the kinase activity and expression of CDK2, whereas the kinase activity and expression of CDK4 were not affected. Unlike the p27(Kip1) upregulation that occurs primarily through post-translational mechanisms, CDK2 was downregulated primarily at a transcriptional level as shown by Northern blotting and real-time RT-PCR analyses. With a decrease in CDK2 activity, trastuzumab decreased the kinase activity of cyclin E but had little effect on cyclin E protein level. Overexpression of wild-type cyclin E or its lower molecular weight forms did not influence the response to trastuzumab. Levels and activities of CDK6, cyclin A, and cyclin D1 were all suppressed by trastuzumab. As a result, trastuzumab inhibited Rb phosphorylation that associates with CDK2, cyclin E, CDK6, cyclin A, or cyclin D1. As predicted from these changes, trastuzumab decreased the DNA-binding activity of E2F, decreased the level of NPAT protein, and decreased the level of histone H4 mRNA. Blockade of the PI3K pathway with LY294002 produced similar effects to trastuzumab treatment on expression of each of these genes. Taken together, treatment of breast cancer cells that overexpress HER2 with the anti-HER2 antibody trastuzumab inhibits CDK2, Rb phosphorylation, E2F activity, NPAT, and histone H4 via PI3K signaling that are needed for both DNA and histone synthesis during progression from G(1) phase to S phase of the cell cycle.

Antibodies, Monoclonal↗

PubMed2006

How nitrogenase shakes--initial information about P-cluster and FeMo-cofactor normal modes from nuclear resonance vibrational spectroscopy (NRVS).

Nitrogenase catalyzes a reaction critical for life, the reduction of N(2) to 2NH(3), yet we still know relatively little about its catalytic mechanism. We have used the synchrotron technique of (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the dynamics of the Fe-S clusters in this enzyme. The catalytic site FeMo-cofactor exhibits a strong signal near 190 cm(-)(1), where conventional Fe-S clusters have weak NRVS. This intensity is ascribed to cluster breathing modes whose frequency is raised by an interstitial atom. A variety of Fe-S stretching modes are also observed between 250 and 400 cm(-)(1). This work is the first spectroscopic information about the vibrational modes of the intact nitrogenase FeMo-cofactor and P-cluster.

Algorithms↗

PubMed2006

Iron-rich post-perovskite and the origin of ultralow-velocity zones.

The boundary layer between the crystalline silicate lower mantle and the liquid iron core contains regions with ultralow seismic velocities. Such low compressional and shear wave velocities and high Poisson's ratio are also observed experimentally in post-perovskite silicate phase containing up to 40 mol% FeSiO3 endmember. The iron-rich post-perovskite silicate is stable at the pressure-temperature and chemical environment of the core-mantle boundary and can be formed by core-mantle reaction. Mantle dynamics may lead to further accumulation of this material into the ultralow-velocity patches that are observable by seismology.

Journal Article↗

PubMed2005

Normal mode analysis of Pyrococcus furiosus rubredoxin via nuclear resonance vibrational spectroscopy (NRVS) and resonance raman spectroscopy.

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(S(cys))(4) site in reduced and oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). The oxidized form has also been investigated by resonance Raman spectroscopy. In the oxidized Rd NRVS, strong asymmetric Fe-S stretching modes are observed between 355 and 375 cm(-1); upon reduction these modes shift to 300-320 cm(-1). This is the first observation of Fe-S stretching modes in a reduced Rd. The peak in S-Fe-S bend mode intensity is at approximately 150 cm(-1) for the oxidized protein and only slightly lower in the reduced case. A third band occurs near 70 cm(-1) for both samples; this is assigned primarily as a collective motion of entire cysteine residues with respect to the central Fe. The (57)Fe partial vibrational density of states (PVDOS) were interpreted by normal mode analysis with optimization of Urey-Bradley force fields. The three main bands were qualitatively reproduced using a D(2)(d) Fe(SC)(4) model. A C(1) Fe(SCC)(4) model based on crystallographic coordinates was then used to simulate the splitting of the asymmetric stretching band into at least 3 components. Finally, a model employing complete cysteines and 2 additional neighboring atoms was used to reproduce the detailed structure of the PVDOS in the Fe-S stretch region. These results confirm the delocalization of the dynamic properties of the redox-active Fe site. Depending on the molecular model employed, the force constant K(Fe-S) for Fe-S stretching modes ranged from 1.24 to 1.32 mdyn/A. K(Fe-S) is clearly diminished in reduced Rd; values from approximately 0.89 to 1.00 mdyn/A were derived from different models. In contrast, in the final models the force constants for S-Fe-S bending motion, H(S-Fe-S), were 0.18 mdyn/A for oxidized Rd and 0.15 mdyn/A for reduced Rd. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.

Iron Isotopes↗

PubMed2005

Direct probe of iron vibrations elucidates NO activation of heme proteins.

We use nuclear resonance vibrational spectroscopy (NRVS) to identify the Fe-NO stretching frequency in the NO adduct of myoglobin (MbNO) and in the related six-coordinate porphyrin Fe(TPP)(1-MeIm)(NO). Frequency shifts observed in MbNO Raman spectra upon isotopic substitution of Fe or the nitrosyl nitrogen confirm and extend the NRVS results. In contrast with previous assignments, the Fe-NO frequency of these six-coordinate complexes lies 70-100 cm-1 lower than in the analogous five-coordinate nitrosyl complexes, indicating a significant weakening of the Fe-NO bond in the presence of a trans imidazole ligand. This result supports proposed mechanisms for NO activation of heme proteins and underscores the value of NRVS as a direct probe of metal reactivity in complex biomolecules.

Hemeproteins↗

PubMed2005

Normal-mode analysis of FeCl4- and Fe2S2Cl42- via vibrational mössbauer, resonance Raman, and FT-IR spectroscopies.

[NEt(4)][FeCl(4)], [P(C(6)H(5))(4)][FeCl(4)], and [NEt(4)](2)[Fe(2)S(2)Cl(4)] have been examined using (57)Fe nuclear resonance vibrational spectroscopy (NRVS). These complexes serve as simple models for Fe-S clusters in metalloproteins. The (57)Fe partial vibrational density of states (PVDOS) spectra were interpreted by computation of the normal modes assuming Urey-Bradley force fields, using additional information from infrared and Raman spectra. Previously published force constants were used as initial values; the new constraints from NRVS frequencies and amplitudes were then used to refine the force field parameters in a nonlinear least-squares analysis. The normal-mode calculations were able to quantitatively reproduce both the frequencies and the amplitudes of the intramolecular-mode (57)Fe PVDOS. The optimized force constants for bending, stretching, and nonbonded interactions agree well with previously reported values. In addition, the NRVS technique also allowed clear observation of anion-cation lattice modes below 100 cm(-1) that are nontrivial to observe by conventional spectroscopies. These features were successfully reproduced, either by assuming whole-body motions of point-mass anions and cations or by simulations using all of the atoms in the unit cell. The advantages of a combined NRVS, Raman, and IR approach to characterization of Fe-S complexes are discussed.

Algorithms↗

PubMed2005

Sound velocities of hot dense iron: Birch's law revisited.

Sound velocities of hexagonal close-packed iron (hcp-Fe) were measured at pressures up to 73 gigapascals and at temperatures up to 1700 kelvin with nuclear inelastic x-ray scattering in a laser-heated diamond anvil cell. The compressional-wave velocities (VP) and shear-wave velocities (VS) of hcp-Fe decreased significantly with increasing temperature under moderately high pressures. VP and VS under high pressures and temperatures thus cannot be fitted to a linear relation, Birch's law, which has been used to extrapolate measured sound velocities to densities of iron in Earth's interior. This result means that there are more light elements in Earth's core than have been inferred from linear extrapolation at room temperature.

Journal Article↗

PubMed2004

Phonon density of states and compression behavior in iron sulfide under pressure.

We report the partial phonon densities of states (DOS) of iron sulfide, a possible component of the rocky planet's core, measured by the 57Fe nuclear resonant inelastic x-ray scattering and calculate the total phonon DOS under pressure. From the phonon DOS, we drive thermodynamic parameters. A comparison of the observed and estimated compressibilities makes it clear that there is a large pure electronic contribution in the observed compressibility in the metallic state. Our results present the observation of thermodynamic parameters of iron sulfide with the low-spin state of an Fe2+ ion at the high density, which is similar to the condition of the Martian core.

Journal Article↗

PubMed2004

Coordination of DNA synthesis and histone gene expression during normal cell cycle progression and after DNA damage.

Chromosomal DNA replication and histone synthesis are tightly coupled during S phase of the eukaryotic cell division cycle. Recently we reported that mRNA levels of mammalian replication-dependent histones, both linker histone H1 and four core histones (H2A, H2B, H3 and H4), are coordinately downregulated in parallel with the inhibition of DNA synthesis upon DNA damage. Moreover, we showed that ionizing radiation induces inhibition of histone gene transcription through the G(1) checkpoint pathway. These results demonstrate that histone synthesis is coordinated with DNA synthesis not only under normal growth conditions but also under conditions where DNA damage may occur. Regulation of the cyclin E-Cdk2 substrate NPAT, which is essential for both histone gene expression and S phase entry, provides a mechanism coordinating histone and DNA synthesis in mammalian cells.

Animals↗

PubMed2004

DNA damage induces downregulation of histone gene expression through the G1 checkpoint pathway.

Activation of the G(1) checkpoint following DNA damage leads to inhibition of cyclin E-Cdk2 and subsequent G(1) arrest in higher eucaryotes. Little, however, is known about the molecular events downstream of cyclin E-Cdk2 inhibition. Here we show that, in addition to the inhibition of DNA synthesis, ionizing radiation induces downregulation of histone mRNA levels in mammalian cells. This downregulation occurs at the level of transcription and requires functional p53 and p21(CIP1/WAF1) proteins. We demonstrate that DNA damage induced by ionizing radiation results in the suppression of phosphorylation of NPAT, an in vivo substrate of cyclin E-Cdk2 kinase and an essential regulator of histone gene transcription, and its dissociation from histone gene clusters in a p53/p21-dependent manner. Inhibition of Cdk2 activity by specific inhibitors in the absence of DNA damage similarly disperses NPAT from histone gene clusters and represses histone gene expression. Our results thus suggest that inhibition of Cdk2 activity following DNA damage results in the downregulation of histone gene transcription through dissociation of NPAT from histone gene clusters.

CDC2-CDC28 Kinases↗

PubMed2004

Nuclear reorganization of mammalian DNA synthesis prior to cell cycle exit.

In primary mammalian cells, DNA replication initiates in a small number of perinucleolar, lamin A/C-associated foci. During S-phase progression in proliferating cells, replication foci distribute to hundreds of sites throughout the nucleus. In contrast, we find that the limited perinucleolar replication sites persist throughout S phase as cells prepare to exit the cell cycle in response to contact inhibition, serum starvation, or replicative senescence. Proteins known to be involved in DNA synthesis, such as PCNA and DNA polymerase delta, are concentrated in perinucleolar foci throughout S phase under these conditions. Moreover, chromosomal loci are redirected toward the nucleolus and overlap with the perinucleolar replication foci in cells poised to undergo cell cycle exit. These same loci remain in the periphery of the nucleus during replication under highly proliferative conditions. These results suggest that mammalian cells undergo a large-scale reorganization of chromatin during the rounds of DNA replication that precede cell cycle exit.

Cell Count↗

PubMed2003

NPAT expression is regulated by E2F and is essential for cell cycle progression.

NPAT is an in vivo substrate of cyclin E-Cdk2 kinase and is thought to play a critical role in coordinated transcriptional activation of histone genes during the G(1)/S-phase transition and in S-phase entry in mammalian cells. Here we show that NPAT transcription is up-regulated at the G(1)/S-phase boundary in growth-stimulated cells and that the NPAT promoter responds to activation by E2F proteins. We demonstrate that endogenous E2F proteins interact with the promoter of the NPAT gene in vivo and that induced expression of E2F1 stimulates NPAT mRNA expression, supporting the idea that the expression of NPAT is regulated by E2F. Consistently, we find that the E2F sites in the NPAT promoter are required for its activation during the G(1)/S-phase transition. Moreover, we show that the expression of NPAT accelerates S-phase entry in cells released from quiescence. The inhibition of NPAT expression by small interfering RNA duplexes impedes cell cycle progression and histone gene expression in tissue culture cells. Thus, NPAT is an important E2F target that is required for cell cycle progression in mammalian cells. As NPAT is involved in the regulation of S-phase-specific histone gene transcription, our findings indicate that NPAT links E2F to the activation of S-phase-specific histone gene transcription.

3T3 Cells↗