Structure and mobility of electron gain and loss centres in proteins

Radiation damage to proteins is a topic of intense interest to those involved in radiation effects in biology, and also to those involved in radiotherapy. Although it has been widely studied, fundamental processes in protein damage are very hard to specify because of the complexity of the final damage products. But the non-invasive technique of electron-spin resonance is ideally suited to the task of detecting and identifying the primary and secondary products as these are expected to contains unpaired electrons (that is, free-radicals) and such species are uniquely detected by this sensitive form of spectroscopy. Our present study shows that a major radical species formed by electron loss in a range of proteins is the backbone amido radical, -N.(CO)-, characterized by hyperfine coupling to one 14N nucleus. These centres are efficiently trapped in proteins at low temperatures. In contrast, the expected backbone electron-capture centres, -NH(CO.-)-, are not readily trapped and electron transfer occurs until the ejected electron is trapped by some electrophilic centre. Such electron mobility was in fact established in our previous work on oxyhaemoglobin (FeO2----FeO2-), superoxide dismutase (Cu(II)----Cu(I] haemocyanin (Cu(II)O2Cu(I)----Cu(I)O2Cu(II] and various proteins containing S-S bonds (-S-S-)----(-S.-S-) (refs 1-4 respectively). This is strongly supported by our observation that such electrons are captured by DNA molecules, giving T.- centres, when nucleohistones are irradiated, and that Fe(CN)3-(6) ions readily scavenge such electrons from proteins which are devoid of highly electrophilic centres.     

Real-space imaging of an orbital Kondo resonance on the Cr(001) surface

The Kondo effect is usually connected with the interaction between a localized spin moment and itinerant electrons. This interaction leads to the formation of a narrow resonance at the Fermi level, which is called the Abrikosov-Suhl or Kondo resonance. Scanning tunnelling microscopy is an ideal technique for real-space investigations of complicated electronic structures and many-body phenomena, such as the formation of the Kondo resonance or d-wave pairing in high-T(c) superconductors. Theory has predicted that similar, Kondo-like many-electron resonances are possible for scattering centres with orbital instead of spin degrees of freedom--the quadruple momenta in uranium-based compounds or two-level systems in metallic glasses are examples of such 'pseudo-Kondo' scattering centres. Here we present evidence for the orbital Kondo resonance on a transition-metal surface. Investigations of an atomically clean Cr(001) surface at low temperature using scanning tunnelling microscopy reveal a very narrow resonance at 26 meV above the Fermi level, and enable us to visualize the orbital character of the corresponding state. The experimental data, together with many-body calculations, demonstrate that the observed resonance is an orbital Kondo resonance formed by two degenerate d(xz), d(yz) surface states.     

Short alanine-based peptides may form 3(10)-helices and not alpha-helices in aqueous solution.

Short alanine peptides, containing 16 or 17 residues, appear to form alpha-helices in aqueous solution. But the main spectroscopic analyses used on helical peptides (circular dichroism and nuclear magnetic resonance) cannot distinguish between an alpha-helix (in which the ith residue is hydrogen-bonded to residue i + 4; ref. 9) and the next most common peptide helix, the 3(10)-helix10 (i-->i + 3 hydrogen-bonding). To address this problem we have designed single and doubly spin-labelled analogues of alanine-based peptides in which the nitroxide spin label forms an unbranched side chain extending from the sulphur atom of a cysteine residue. Here we report the circular dichroism, Fourier-transform infrared and electron-spin resonance spectra of these peptides under helix-forming conditions. The infrared absorbance gives an amide I' band with a frequency that is substantially different from that observed for alpha-helices. The electron-spin resonance spectra of doubly labelled helices show that the ranking of distances between side chains, around a single turn (residues 4-8), is inconsistent with an alpha-helical structure. Our experiments suggest that the more likely peptide geometry is a 3(10)-helix.     

Virus-mediated killing of cells that lack p53 activity

A major goal of molecular oncology is to identify means to kill cells lacking p53 function. Most current cancer therapy is based on damaging cellular DNA by irradiation or chemicals. Recent reports support the notion that, in the event of DNA damage, the p53 tumour-suppressor protein is able to prevent cell death by sustaining an arrest of the cell cycle at the G2 phase. We report here that adeno-associated virus (AAV) selectively induces apoptosis in cells that lack active p53. Cells with intact p53 activity are not killed but undergo arrest in the G2 phase of the cell cycle. This arrest is characterized by an increase in p53 activity and p21 levels and by the targeted destruction of CDC25C. Neither cell killing nor arrest depends upon AAV-encoded proteins. Rather, AAV DNA, which is single-stranded with hairpin structures at both ends, elicits in cells a DNA damage response that, in the absence of active p53, leads to cell death. AAV inhibits tumour growth in mice. Thus viruses can be used to deliver DNA of unusual structure into cells to trigger a DNA damage response without damaging cellular DNA and to selectively eliminate those cells lacking p53 activity.     

Resonance in the electron-doped high-transition-temperature superconductor Pr0.88LaCe0.12CuO4-delta

In conventional superconductors, the interaction that pairs the electrons to form the superconducting state is mediated by lattice vibrations (phonons). In high-transition-temperature (high-T(c)) copper oxides, it is generally believed that magnetic excitations might play a fundamental role in the superconducting mechanism because superconductivity occurs when mobile 'electrons' or 'holes' are doped into the antiferromagnetic parent compounds. Indeed, a sharp magnetic excitation termed 'resonance' has been observed by neutron scattering in a number of hole-doped materials. The resonance is intimately related to superconductivity, and its interaction with charged quasi-particles observed by photoemission, optical conductivity, and tunnelling suggests that it might play a part similar to that of phonons in conventional superconductors. The relevance of the resonance to high-T(c) superconductivity, however, has been in doubt because so far it has been found only in hole-doped materials. Here we report the discovery of the resonance in electron-doped superconducting Pr0.88LaCe0.12CuO4-delta (T(c) = 24 K). We find that the resonance energy (E(r)) is proportional to T(c) via E(r) approximately 5.8k(B)T(c) for all high-T(c) superconductors irrespective of electron- or hole-doping. Our results demonstrate that the resonance is a fundamental property of the superconducting copper oxides and therefore must be essential in the mechanism of superconductivity.     

Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA

Spontaneous oxidation of guanine residues in DNA generates 8-oxoguanine (oxoG). By mispairing with adenine during replication, oxoG gives rise to a G x C --> T x A transversion, a frequent somatic mutation in human cancers. The dedicated repair pathway for oxoG centres on 8-oxoguanine DNA glycosylase (hOGG1), an enzyme that recognizes oxoG x C base pairs, catalysing expulsion of the oxoG and cleavage of the DNA backbone. Here we report the X-ray structure of the catalytic core of hOGG1 bound to oxoG x C-containing DNA at 2.1 A resolution. The structure reveals the mechanistic basis for the recognition and catalytic excision of DNA damage by hOGG1 and by other members of the enzyme superfamily to which it belongs. The structure also provides a rationale for the biochemical effects of inactivating mutations and polymorphisms in hOGG1. One known mutation, R154H, converts hOGG1 to a promutator by relaxing the specificity of the enzyme for the base opposite oxoG.     

Progress in dynamic study on the triplet excited states and radical ions of DNA and its components

Progress in dynamic study on the triplet excited states and radical ions of DNA and its components is reviewed. It has been found that acetone is the only effective sensitizer for the study of the triplet excited states of DNA components. The transient absorption spectrum of guanyl radical cation resulting from the interaction of triplet acetone and DNA was observed directly, and the original evidence for selective damage of DNA by excited photosensitizer was obtained for the first time, which offered a new pathway for obtaining the main transient species of selective damage of DNA by photonucleases and illustrating initial oxidation mechanism of DNA via electron transfer.     

Progress in dynamic study on the triplet excited states and radical ions of DNA and its components

Progress in dynamic study on the triplet excited states and radical ions of DNA and its components is reviewed. It has been found that acetone is the only effective sensitizer for the study of the triplet excited states of DNA components. The transient absorption spectrum of guanyl radical cation resulting from the interaction of triplet acetone and DNA was observed directly, and the original evidence for selective damage of DNA by excited photosensitizer was obtained for -the first time, which offered a new pathway for obtaining the main transient species of selective damage of DNA by photonucleases and illustrating initial oxidation mechanism of DNA via electron transfer.     

Magnetic order close to superconductivity in the iron-based layered LaO1-xFxFeAs systems

Following the discovery of long-range antiferromagnetic order in the parent compounds of high-transition-temperature (high-T(c)) copper oxides, there have been efforts to understand the role of magnetism in the superconductivity that occurs when mobile 'electrons' or 'holes' are doped into the antiferromagnetic parent compounds. Superconductivity in the newly discovered rare-earth iron-based oxide systems ROFeAs (R, rare-earth metal) also arises from either electron or hole doping of their non-superconducting parent compounds. The parent material LaOFeAs is metallic but shows anomalies near 150 K in both resistivity and d.c. magnetic susceptibility. Although optical conductivity and theoretical calculations suggest that LaOFeAs exhibits a spin-density-wave (SDW) instability that is suppressed by doping with electrons to induce superconductivity, there has been no direct evidence of SDW order. Here we report neutron-scattering experiments that demonstrate that LaOFeAs undergoes an abrupt structural distortion below 155 K, changing the symmetry from tetragonal (space group P4/nmm) to monoclinic (space group P112/n) at low temperatures, and then, at approximately 137 K, develops long-range SDW-type antiferromagnetic order with a small moment but simple magnetic structure. Doping the system with fluorine suppresses both the magnetic order and the structural distortion in favour of superconductivity. Therefore, like high-T(c) copper oxides, the superconducting regime in these iron-based materials occurs in close proximity to a long-range-ordered antiferromagnetic ground state.     

电子顺磁共振成像的微波局域场方法

报导了电子顺磁共振成像的微波局域场方法．在改进的自制小型顺磁共振谱仪上，给出了测试样品ＤＰＰＨ的二维电子自旋密度分布图像．使用退卷积算法和反向滤波图像处理技术，提高了分辨率．     

基于核磁共振的不同含水状态砂岩动态损伤规律

为研究不同含水状态岩石的动态损伤特性,制备干燥、半饱和、饱和3种不同含水状态的砂岩试样.采用分离式霍普金森压杆(SHPB),以4种不同的低入射能对岩石进行损伤冲击试验.通过核磁共振测试实验对岩石试样进行孔隙扫描,获取岩石孔隙的T2谱曲线、孔隙度以及孔隙成像等数据.通过试验发现:(1)冲击能量的增加导致岩石的平均应变率和强度的增大;(2)不同含水状态的岩石受到冲击后,孔隙度与孔隙度变化率均有不同程度的增加;(3)与冲击前相比,岩石的T2谱曲线有明显右移趋势,同时出现谱峰增加的现象,而且冲击能量越大,孔隙谱峰增加越明显;(4)核磁共振成像显示岩石孔隙数量和尺寸有明显的增加,展现出岩石内部孔隙扩展和演化的过程.     

Clustered DNA damage induced by protons radiation in plasmid DNA

Clustered DNA damage is considered as a critical type of lesions induced by ionizing radiation, which can be converted into the fatal or strong mutagenic complex double strand breaks (DSBs) during damage processing in the cells. The new data show that high energy protons produce more potentially lethal DSBs than low LET radiation. In this study, plasmid DNA were used to in-vestigate and re-evaluate the biological effects induced by the protons with the LET of ～3.6 keV/μm at the molecular level in vitro, including single strand breaks (SSBs), DSBs, isolated and clustered base damages. The results of complex DNA damage detections indicated that protons at the given LET value induce about 1.6 fold more non-DSB clustered DNA damages than the prompt DSB. The DNA damage yields by protons were greater than that by γ-rays, specifically by 6 fold for the isolated type of DNA damage and 14 fold for the clustered damage. Furthermore, the spectrum of damages was also demonstrated to be depended on the radiation quality, with protons producing more DSBs relative to clusters than do γ-rays.     

复合磁电垒纳米结构中的电子自旋过滤器

采用转移矩阵法,我们研究了在偏压存在的情况下,由沉积在InAs半导体异质结上的两条铁磁条带和一条肖特基金属条带构建的电子自旋过滤器中电子的自旋过滤特性.研究发现,该电子自旋过滤器中,电子自旋极化的大小和幅度与偏压密切相关,这些有趣的性质对如何制造一个偏压可调的电子自旋过滤器十分有益.     

A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response

DNA breaks are extremely harmful lesions that need to be repaired efficiently throughout the genome. However, the packaging of DNA into nucleosomes is a significant barrier to DNA repair, and the mechanisms of repair in the context of chromatin are poorly understood. Here we show that lysine 56 (K56) acetylation is an abundant modification of newly synthesized histone H3 molecules that are incorporated into chromosomes during S phase. Defects in the acetylation of K56 in histone H3 result in sensitivity to genotoxic agents that cause DNA strand breaks during replication. In the absence of DNA damage, the acetylation of histone H3 K56 largely disappears in G2. In contrast, cells with DNA breaks maintain high levels of acetylation, and the persistence of the modification is dependent on DNA damage checkpoint proteins. We suggest that the acetylation of histone H3 K56 creates a favourable chromatin environment for DNA repair and that a key component of the DNA damage response is to preserve this acetylation.     

偏压可调的铁磁-肖特基金属和半导体纳米电子自旋过滤器

在半导体异质结上沉积一条纳米级的铁磁条带和一条肖特基金属条带可获得一个电子自旋过滤器.采用转移矩阵法,我们研究了偏压对该电子自旋过滤器中电子自旋过滤性质的影响.通过数值计算,我们发现,该电子自旋过滤器中,电子自旋极化的幅度和符号与偏压密切相关,这可用来制造一个偏压可调的电子自旋过滤器.     

Quantum magnetic excitations from stripes in copper oxide superconductors

In the copper oxide parent compounds of the high-transition-temperature superconductors the valence electrons are localized--one per copper site--by strong intra-atomic Coulomb repulsion. A symptom of this localization is antiferromagnetism, where the spins of localized electrons alternate between up and down. Superconductivity appears when mobile 'holes' are doped into this insulating state, and it coexists with antiferromagnetic fluctuations. In one approach to describing the coexistence, the holes are believed to self-organize into 'stripes' that alternate with antiferromagnetic (insulating) regions within copper oxide planes, which would necessitate an unconventional mechanism of superconductivity. There is an apparent problem with this picture, however: measurements of magnetic excitations in superconducting YBa2Cu3O6+x near optimum doping are incompatible with the naive expectations for a material with stripes. Here we report neutron scattering measurements on stripe-ordered La1.875Ba0.125CuO4. We show that the measured excitations are, surprisingly, quite similar to those in YBa2Cu3O6+x (refs 9, 10) (that is, the predicted spectrum of magnetic excitations is wrong). We find instead that the observed spectrum can be understood within a stripe model by taking account of quantum excitations. Our results support the concept that stripe correlations are essential to high-transition-temperature superconductivity.     

Role of Ppt1 in multiple stress responses in Candida albicans

To study the function of CaPptl, we deleted PPT1 gene from the Candida albicans genome by sequentially replacing the entire coding region with the selectable markers ARG4 and HIS1. The results showed that the deletion of Pptl did not affect the hyphal formation of C. albicans under serum induction and caused enhanced sensitivity to DNA damage, Calcofluor white and salt- induced stress. We also found that Pptl was not required for the phenotypic response of cells treated with the genotoxins, methylmethane sulfonate and hydroxyurea. Flow cytometric analyses indicated that pptlA cells and wild-type cells showed similar G2/M arrest profiles when exposed to DNA damage stress. Pptl was not required for the activation of the DNA damage response pathway, as indicated by normal phosphorylation of Rad53 and Rfa2 in pptlA cells under DNA damage stress. We suggest that Pptl plays important roles in response to various stress conditions in C. albicans.     

A pyrimidine dimer-DNA glycosylase activity associated with the v gene product of bacterophage T4

Mutations in the v gene of bacteriophage T4 are associated with a marked increase in sensitivity to killing by UV radiation at 254 nm, but not to a variety of other forms of base damage to DNA. Early studies from this laboratory provided evidence for a role of the v gene in the excision of pyrimidine dimers (PD) from DNA. Specifically, it was shown that extracts of T4v+-infected Escherichia coli catalyse the formation of single-strand breaks (nicks) and/or alkali-labile sites in UIV-irradiated duplex DNA. Comparable hydrolysis of phosphodiester bonds is not observed with extracts of E. coli infected with the mutant T4v1 (ref. 5). The product of the v gene has been extensively purified in a number of laboratories; however, convincing evidence of purification to physical homogeneity has not yet been presented.