Structure and reactivity of a mononuclear non-haem iron(III)-peroxo complex

Oxygen-containing mononuclear iron species--iron(III)-peroxo, iron(III)-hydroperoxo and iron(IV)-oxo--are key intermediates in the catalytic activation of dioxygen by iron-containing metalloenzymes. It has been difficult to generate synthetic analogues of these three active iron-oxygen species in identical host complexes, which is necessary to elucidate changes to the structure of the iron centre during catalysis and the factors that control their chemical reactivities with substrates. Here we report the high-resolution crystal structure of a mononuclear non-haem side-on iron(III)-peroxo complex, [Fe(III)(TMC)(OO)](+). We also report a series of chemical reactions in which this iron(III)-peroxo complex is cleanly converted to the iron(III)-hydroperoxo complex, [Fe(III)(TMC)(OOH)](2+), via a short-lived intermediate on protonation. This iron(III)-hydroperoxo complex then cleanly converts to the ferryl complex, [Fe(IV)(TMC)(O)](2+), via homolytic O-O bond cleavage of the iron(III)-hydroperoxo species. All three of these iron species--the three most biologically relevant iron-oxygen intermediates--have been spectroscopically characterized; we note that they have been obtained using a simple macrocyclic ligand. We have performed relative reactivity studies on these three iron species which reveal that the iron(III)-hydroperoxo complex is the most reactive of the three in the deformylation of aldehydes and that it has a similar reactivity to the iron(IV)-oxo complex in C-H bond activation of alkylaromatics. These reactivity results demonstrate that iron(III)-hydroperoxo species are viable oxidants in both nucleophilic and electrophilic reactions by iron-containing enzymes.     

Coupled quantized mechanical oscillators

The harmonic oscillator is one of the simplest physical systems but also one of the most fundamental. It is ubiquitous in nature, often serving as an approximation for a more complicated system or as a building block in larger models. Realizations of harmonic oscillators in the quantum regime include electromagnetic fields in a cavity and the mechanical modes of a trapped atom or macroscopic solid. Quantized interaction between two motional modes of an individual trapped ion has been achieved by coupling through optical fields, and entangled motion of two ions in separate locations has been accomplished indirectly through their internal states. However, direct controllable coupling between quantized mechanical oscillators held in separate locations has not been realized previously. Here we implement such coupling through the mutual Coulomb interaction of two ions held in trapping potentials separated by 40?μm (similar work is reported in a related paper). By tuning the confining wells into resonance, energy is exchanged between the ions at the quantum level, establishing that direct coherent motional coupling is possible for separately trapped ions. The system demonstrates a building block for quantum information processing and quantum simulation. More broadly, this work is a natural precursor to experiments in hybrid quantum systems, such as coupling a trapped ion to a quantized macroscopic mechanical or electrical oscillator.     

Eocene global warming events driven by ventilation of oceanic dissolved organic carbon

'Hyperthermals' are intervals of rapid, pronounced global warming known from six episodes within the Palaeocene and Eocene epochs (～65-34 million years (Myr) ago). The most extreme hyperthermal was the ～170 thousand year (kyr) interval of 5-7 °C global warming during the Palaeocene-Eocene Thermal Maximum (PETM, 56?Myr ago). The PETM is widely attributed to massive release of greenhouse gases from buried sedimentary carbon reservoirs, and other, comparatively modest, hyperthermals have also been linked to the release of sedimentary carbon. Here we show, using new 2.4-Myr-long Eocene deep ocean records, that the comparatively modest hyperthermals are much more numerous than previously documented, paced by the eccentricity of Earth's orbit and have shorter durations (～40?kyr) and more rapid recovery phases than the PETM. These findings point to the operation of fundamentally different forcing and feedback mechanisms than for the PETM, involving redistribution of carbon among Earth's readily exchangeable surface reservoirs rather than carbon exhumation from, and subsequent burial back into, the sedimentary reservoir. Specifically, we interpret our records to indicate repeated, large-scale releases of dissolved organic carbon (at least 1,600 gigatonnes) from the ocean by ventilation (strengthened oxidation) of the ocean interior. The rapid recovery of the carbon cycle following each Eocene hyperthermal strongly suggests that carbon was re-sequestered by the ocean, rather than the much slower process of silicate rock weathering proposed for the PETM. Our findings suggest that these pronounced climate warming events were driven not by repeated releases of carbon from buried sedimentary sources, but, rather, by patterns of surficial carbon redistribution familiar from younger intervals of Earth history.     

Inactivation of the p53 pathway in retinoblastoma

Most human tumours have genetic mutations in their Rb and p53 pathways, but retinoblastoma is thought to be an exception. Studies suggest that retinoblastomas, which initiate with mutations in the gene retinoblastoma 1 (RB1), bypass the p53 pathway because they arise from intrinsically death-resistant cells during retinal development. In contrast to this prevailing theory, here we show that the tumour surveillance pathway mediated by Arf, MDM2, MDMX and p53 is activated after loss of RB1 during retinogenesis. RB1-deficient retinoblasts undergo p53-mediated apoptosis and exit the cell cycle. Subsequently, amplification of the MDMX gene and increased expression of MDMX protein are strongly selected for during tumour progression as a mechanism to suppress the p53 response in RB1-deficient retinal cells. Our data provide evidence that the p53 pathway is inactivated in retinoblastoma and that this cancer does not originate from intrinsically death-resistant cells as previously thought. In addition, they support the idea that MDMX is a specific chemotherapeutic target for treating retinoblastoma.     

Small molecule inhibitors of DNA repair nuclease activities of APE1

APE1 is a multifunctional protein that possesses several nuclease activities, including the ability to incise at apurinic/apyrimidinic (AP) sites in DNA or RNA, to excise 3′-blocking termini from DNA ends, and to cleave at certain oxidized base lesions in DNA. Pre-clinical and clinical data indicate a role for APE1 in the pathogenesis of cancer and in resistance to DNA-interactive drugs, particularly monofunctional alkylators and antimetabolites. In an effort to improve the efficacy of therapeutic compounds, such as temozolomide, groups have begun to develop high-throughput screening assays and to identify small molecule inhibitors against APE1 repair nuclease activities. It is envisioned that such inhibitors will be used in combinatorial treatment paradigms to enhance the efficacy of DNA-interactive drugs that introduce relevant cytotoxic DNA lesions. In this review, we summarize the current state of the efforts to design potent and selective inhibitors against APE1 AP site incision activity.     

四川龙门山中段变形和变质历史(英文)

在龙门山的中段,四川盆地西缘的逆冲断层起源于紧靠汶川-茂汶断裂西侧的变质“根带”。汶川-茂汶断裂代表一条20～25km宽的剪切带的晚期脆性变形阶段。该剪切带活动于大约200Ma前的印支期。在汶川-茂汶剪切带北西侧的松潘-甘孜褶皱带中,印支期的NE-SW向挤压形成D_1逆冲断层,并被NW向F_2直立褶皱所叠加。当松潘-甘孜褶皱带受到D_1-D_2期缩短时,相邻的四川盆地并没有发生变形。两个地区的差异应变被发育于D_3的汶川-茂汶左行剪切带所容纳。松潘-甘孜褶皱带中持续的NE-SW向缩短导致了龙门山地区的SE向挤压。这种SE向挤压引起沿汶川-茂汶剪切带发生局部地壳加厚和巴罗型(Barrovian-type)变质作用。汶川-茂汶剪切带的运动学特点由D_3的左行剪切逐渐转变为D_4的SE向逆冲。这种逆冲作用引起了变质地区的初步隆起,以及龙门山地区第一期推覆体的就位。在印支期变形的后期(D_5),岩石发生褶皱并被花岗岩体侵入。现在的汶川-茂汶断裂位置是在更晚的变形阶段确立的。这个阶段的变形可能导致了彭灌基底杂岩沿着映秀-北川断裂发生隆起。在这一事件中,汶川-茂汶断裂是作为一条具有显著左行走滑分量的脆性正断层活动的。这一事件可能对应于龙门山地区的第二期推覆体运动,并且可能发生于侏罗纪—第三纪之间,或者是在喜马拉雅期。     

The immunodominant site of a synthetic immunogen has a conformational preference in water for a type-II reverse turn

Many short synthetic peptides have now been shown to induce antibodies reactive with their cognate sequences in the intact folded protein. Aside from the usefulness of such antibodies as site-specific reagents, the frequency with which this recognition occurs has raised several theoretical issues, the central one being that of how an antibody to a short synthetic peptide, which represents one of the most disordered states of a site in a protein, can react with the more ordered version of the same sequence in the folded protein. This apparent paradox can be resolved if the target site on the protein approaches disorder or if the peptide in solution or on a carrier adopts, with significant frequency, a conformation compatible with that of the cognate site in the protein. Various studies already suggest that antigenic sites in proteins correspond to regions of high atomic mobility. We now show, using high-field nuclear magnetic resonance (NMR) spectroscopy, that a nonapeptide selected by several monoclonal antibodies as the immunodominant site of a 36-amino-acid immunogen (residues 75-110 of influenza virus haemagglutinin) adopts a highly populated type-II reverse-turn conformation in water. This suggests that in this case the antibodies have selected a sequence possessing a conformational preference. Apart from helping us to understand immunological recognition, anti-peptide antibodies may provide reagents of sufficient precision for an immunological approach to the problem of protein folding.     

3-A resolution structure of a protein with histone-like properties in prokaryotes

The 3-A structure of DNA-binding protein II, which exhibits histone-like properties in bacteria, has been determined. The molecule is dimeric and appears to bind to the phosphate backbone of DNA through two symmetry-related arms. A mechanism by which the protein induces DNA supercoiling is proposed.     

Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing

The controversy surrounding the idea that neutral mutations dominate protein evolution is attributable in part to the inadequacy of the tools available to evolutionary investigators. With a few exceptions, most investigations into the force driving protein evolution have relied on indirect criteria for distinguishing neutral and non-neutral variants. To investigate a particular pathway of molecular evolution, we have reconstructed by site-directed mutagenesis likely ancestral variants of the lysozymes of modern game birds (order Galliformes), tested their activity and thermostability and determined their three-dimensional structure. We focused on amino acids at three positions that are occupied in all known game birds either by the triplet Thr 40, Ile 55, Ser 91, or by the triplet Ser 40, Val 55, Thr 91. We have synthesized proteins representing intermediates along the possible three-step evolutionary pathways between these triplets. Although all of these are active and stable, none of these intermediates is found in known lysozymes. A comparison of the structures and thermostabilities of the variants reveals a linear correlation between the side-chain volume of the triplet and the thermostability of the protein. Each pathway connecting the two extant triplet sequences includes a variant with a thermostability outside the range of the extant proteins. This observation is consistent with a non-neutral evolutionary pathway. The existence of variants that are more stable than the extant proteins suggests that selection for maximum thermostability may not have been an important factor in the evolution of this enzyme.