Energetic landscape of alpha-lytic protease optimizes longevity through kinetic stability.

During the evolution of proteins the pressure to optimize biological activity is moderated by a need for efficient folding. For most proteins, this is accomplished through spontaneous folding to a thermodynamically stable and active native state. However, in the extracellular bacterial alpha-lytic protease (alphaLP) these two processes have become decoupled. The native state of alphaLP is thermodynamically unstable, and when denatured, requires millennia (t1/2 approximately 1,800 years) to refold. Folding is made possible by an attached folding catalyst, the pro-region, which is degraded on completion of folding, leaving alphaLP trapped in its native state by a large kinetic unfolding barrier (t1/2 approximately 1.2 years). alphaLP faces two very different folding landscapes: one in the presence of the pro-region controlling folding, and one in its absence restricting unfolding. Here we demonstrate that this separation of folding and unfolding pathways has removed constraints placed on the folding of thermodynamically stable proteins, and allowed the evolution of a native state having markedly reduced dynamic fluctuations. This, in turn, has led to a significant extension of the functional lifetime of alphaLP by the optimal suppression of proteolytic sensitivity.     

HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus

Early treatment of acute HIV-1 infection followed by treatment interruptions has shown promise for enhancing immune control of infection. A subsequent loss of control, however, allows the correlates of protective immunity to be assessed. Here we show that sudden breakthrough of plasma viraemia occurred after prolonged immune containment in an individual infected with HIV-1 at a time when 25 distinct CD8+ T-cell epitopes in the viral proteins Gag, RT, Integrase, Env, Nef, Vpr, Vif and Rev were being targeted. Sequencing of the virus in plasma and cells showed that superinfection with a second clade-B virus was coincident with the loss of immune control. This sudden increase in viraemia was associated with a decline in half of the CD8+ T-cell responses. The declining CD8+ T-cell responses were coupled with sequence changes relative to the initial virus that resulted in impaired recognition. Our data show that HIV-1 superinfection can occur in the setting of a strong and broadly directed virus-specific CD8+ T-cell response. The lack of cross-protective immunity for closely related HIV-1 strains, despite persistent recognition of multiple CD8 epitopes, has important implications for public health and vaccine development.     

Molecular imprinting of bulk, microporous silica

Molecular imprinting aims to create solid materials containing chemical functionalities that are spatially organized by covalent or non-covalent interactions with imprint (or template) molecules during the synthesis process. Subsequent removal of the imprint molecules leaves behind designed sites for the recognition of small molecules, making the material ideally suited for applications such as separations, chemical sensing and catalysis. Until now, the molecular imprinting of bulk polymers and polymer and silica surfaces has been reported, but the extension of these methods to a wider range of materials remains problematic. For example, the formation of substrate-specific cavities within bulk silica, while conceptually straightforward, has been difficult to accomplish experimentally. Here we describe the imprinting of bulk amorphous silicas with single aromatic rings carrying up to three 3-aminopropyltriethoxysilane side groups; this generates and occupies microporosity and attaches functional organic groups to the pore walls in a controlled fashion. The triethoxysilane part of the molecules' side groups is incorporated into the silica framework during sol-gel synthesis, and subsequent removal of the aromatic core creates a cavity with spatially organized aminopropyl groups covalently anchored to the pore walls. We find that the imprinted silicas act as shape-selective base catalysts. Our strategy can be extended to imprint other functional groups, which should give access to a wide range of functionalized materials.     

Imaging the effects of individual zinc impurity atoms on superconductivity in Bi2Sr2CaCu2O8+delta

Although the crystal structures of the copper oxide high-temperature superconductors are complex and diverse, they all contain some crystal planes consisting of only copper and oxygen atoms in a square lattice: superconductivity is believed to originate from strongly interacting electrons in these CuO2 planes. Substituting a single impurity atom for a copper atom strongly perturbs the surrounding electronic environment and can therefore be used to probe high-temperature superconductivity at the atomic scale. This has provided the motivation for several experimental and theoretical studies. Scanning tunnelling microscopy (STM) is an ideal technique for the study of such effects at the atomic scale, as it has been used very successfully to probe individual impurity atoms in several other systems. Here we use STM to investigate the effects of individual zinc impurity atoms in the high-temperature superconductor Bi2Sr2CaCu2O8+delta. We find intense quasiparticle scattering resonances at the Zn sites, coincident with strong suppression of superconductivity within approximately 15 A of the scattering sites. Imaging of the spatial dependence of the quasiparticle density of states in the vicinity of the impurity atoms reveals the long-sought four-fold symmetric quasiparticle 'cloud' aligned with the nodes of the d-wave superconducting gap which is believed to characterize superconductivity in these materials.     

Recognition of haemagglutinins on virus-infected cells by NKp46 activates lysis by human NK cells

Natural killer (NK) cells destroy virus-infected and tumour cells, apparently without the need for previous antigen stimulation. In part, target cells are recognized by their diminished expression of major histocompatibility complex (MHC) class I molecules, which normally interact with inhibitory receptors on the NK cell surface. NK cells also express triggering receptors that are specific for non-MHC ligands; but the nature of the ligands recognized on target cells is undefined. NKp46 is thought to be the main activating receptor for human NK cells. Here we show that a soluble NKp46-immunoglobulin fusion protein binds to both the haemagglutinin of influenza virus and the haemagglutinin-neuraminidase of parainfluenza virus. In a substantial subset of NK cells, recognition by NKp46 is required to lyse cells expressing the corresponding viral glycoproteins. The binding requires the sialylation of NKp46 oligosaccharides, which is consistent with the known sialic binding capacity of the viral glycoproteins. These findings indicate how NKp46-expressing NK cells may recognize target cells infected by influenza or parainfluenza without the decreased expression of target-cell MHC class I protein.     

An inherited limb deformity created by insertional mutagenesis in a transgenic mouse

We have created an insertional mutation that leads to a severe defect in the pattern of limb formation in the developing mouse. The novel recessive mutation is phenotypically identical and non-complementary to two previously encountered limb deformity mutations, and is closely linked to a dominant mutation that gives rise to a related limb dysmorphism. The inserted element thus provides a molecular genetic link with the control of pattern formation in the mammalian embryo.     

No supernovae associated with two long-duration gamma-ray bursts

It is now accepted that long-duration gamma-ray bursts (GRBs) are produced during the collapse of a massive star. The standard 'collapsar' model predicts that a broad-lined and luminous type Ic core-collapse supernova accompanies every long-duration GRB. This association has been confirmed in observations of several nearby GRBs. Here we report that GRB 060505 (ref. 10) and GRB 060614 (ref. 11) were not accompanied by supernova emission down to limits hundreds of times fainter than the archetypal supernova SN 1998bw that accompanied GRB 980425, and fainter than any type Ic supernova ever observed. Multi-band observations of the early afterglows, as well as spectroscopy of the host galaxies, exclude the possibility of significant dust obscuration and show that the bursts originated in actively star-forming regions. The absence of a supernova to such deep limits is qualitatively different from all previous nearby long-duration GRBs and suggests a new phenomenological type of massive stellar death.     

Bacteriophytochromes are photochromic histidine kinases using a biliverdin chromophore.

Phytochromes comprise a principal family of red/far-red light sensors in plants. Although phytochromes were thought originally to be confined to photosynthetic organisms, we have recently detected phytochrome-like proteins in two heterotrophic eubacteria, Deinococcus radiodurans and Pseudomonas aeruginosa. Here we show that these form part of a widespread family of bacteriophytochromes (BphPs) with homology to two-component sensor histidine kinases. Whereas plant phytochromes use phytochromobilin as the chromophore, BphPs assemble with biliverdin, an immediate breakdown product of haem, to generate photochromic kinases that are modulated by red and far-red light. In some cases, a unique haem oxygenase responsible for the synthesis of biliverdin is part of the BphP operon. Co-expression of this oxygenase with a BphP apoprotein and a haem source is sufficient to assemble holo-BphP in vivo. Both their presence in many diverse bacteria and their simplified assembly with biliverdin suggest that BphPs are the progenitors of phytochrome-type photoreceptors.     

New evidence for enhanced cosmogenic isotope production rate in the atmosphere ≈37 kaBP from the Guliya ice core

A³⁶Cl peak was found in the predicted section of Guliya ice core, from the Qinghai-Tibetan Plateau, at about 37 kaBP. This cannot be interpreted by means of changes in the accumulation rate, but by the enhanced cosmogenic isotope production rate in the atmosphere. Compared with the records of¹⁰Be and³⁶Cl in the other regions, the peaks of the cosmogenic isotopes are global and can be considered as time marks. An intriguing fact is that the peaks coincided with cold periods.