Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

Proteins are inherently plastic molecules, whose function often critically depends on excursions between different molecular conformations (conformers). However, a rigorous understanding of the relation between a protein's structure, dynamics and function remains elusive. This is because many of the conformers on its energy landscape are only transiently formed and marginally populated (less than a few per cent of the total number of molecules), so that they cannot be individually characterized by most biophysical tools. Here we study a lysozyme mutant from phage T4 that binds hydrophobic molecules and populates an excited state transiently (about 1?ms) to about 3% at 25?°C (ref. 5). We show that such binding occurs only via the ground state, and present the atomic-level model of the 'invisible', excited state obtained using a combined strategy of relaxation-dispersion NMR (ref. 6) and CS-Rosetta model building that rationalizes this observation. The model was tested using structure-based design calculations identifying point mutants predicted to stabilize the excited state relative to the ground state. In this way a pair of mutations were introduced, inverting the relative populations of the ground and excited states and altering function. Our results suggest a mechanism for the evolution of a protein's function by changing the delicate balance between the states on its energy landscape. More generally, they show that our approach can generate and validate models of excited protein states.     

ATM controls meiotic double-strand-break formation

In many organisms, developmentally programmed double-strand breaks (DSBs) formed by the SPO11 transesterase initiate meiotic recombination, which promotes pairing and segregation of homologous chromosomes. Because every chromosome must receive a minimum number of DSBs, attention has focused on factors that support DSB formation. However, improperly repaired DSBs can cause meiotic arrest or mutation; thus, having too many DSBs is probably as deleterious as having too few. Only a small fraction of SPO11 protein ever makes a DSB in yeast or mouse and SPO11 and its accessory factors remain abundant long after most DSB formation ceases, implying the existence of mechanisms that restrain SPO11 activity to limit DSB numbers. Here we report that the number of meiotic DSBs in mouse is controlled by ATM, a kinase activated by DNA damage to trigger checkpoint signalling and promote DSB repair. Levels of SPO11-oligonucleotide complexes, by-products of meiotic DSB formation, are elevated at least tenfold in spermatocytes lacking ATM. Moreover, Atm mutation renders SPO11-oligonucleotide levels sensitive to genetic manipulations that modulate SPO11 protein levels. We propose that ATM restrains SPO11 via a negative feedback loop in which kinase activation by DSBs suppresses further DSB formation. Our findings explain previously puzzling phenotypes of Atm-null mice and provide a molecular basis for the gonadal dysgenesis observed in ataxia telangiectasia, the human syndrome caused by ATM deficiency.     

Surface composition of Hyperion

Hyperion, Saturn's eighth largest icy satellite, is a body of irregular shape in a state of chaotic rotation. The surface is segregated into two distinct units. A spatially dominant high-albedo unit having the strong signature of H2O ice contrasts with a unit that is about a factor of four lower in albedo and is found mostly in the bottoms of cup-like craters. Here we report observations of Hyperion's surface in the ultraviolet and near-infrared spectral regions with two optical remote sensing instruments on the Cassini spacecraft at closest approach during a fly-by on 25-26 September 2005. The close fly-by afforded us the opportunity to obtain separate reflectance spectra of the high- and low-albedo surface components. The low-albedo material has spectral similarities and compositional signatures that link it with the surface of Phoebe and a hemisphere-wide superficial coating on Iapetus.     

复杂软件系统的分散式构造:一个电子商务案例研究

Software development skills are only partially trained with traditional programming languages and software engineering courses. To achieve practical skills needed in software industry, complex examples are necessary which have to be generated in a project-like setting. This includes common solution finding, intensive communication and structured programming tasks. Here, a case study from the domain of eCommerce is presented, showing the complexity needed for these learning processes.     

New grass distribution records for New Mexico and the United States

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Evolution of the Archaean crust by delamination and shallow subduction

The Archaean oceanic crust was probably thicker than present-day oceanic crust owing to higher heat flow and thus higher degrees of melting at mid-ocean ridges. These conditions would also have led to a different bulk composition of oceanic crust in the early Archaean, that would probably have consisted of magnesium-rich picrite (with variably differentiated portions made up of basalt, gabbro, ultramafic cumulates and picrite). It is unclear whether these differences would have influenced crustal subduction and recycling processes, as experiments that have investigated the metamorphic reactions that take place during subduction have to date considered only modern mid-ocean-ridge basalts. Here we present data from high-pressure experiments that show that metamorphism of ultramafic cumulates and picrites produces pyroxenites, which we infer would have delaminated and melted to produce basaltic rocks, rather than continental crust as has previously been thought. Instead, the formation of continental crust requires subduction and melting of garnet-amphibolite--formed only in the upper regions of oceanic crust--which is thought to have first occurred on a large scale during subduction in the late Archaean. We deduce from this that shallow subduction and recycling of oceanic crust took place in the early Archaean, and that this would have resulted in strong depletion of only a thin layer of the uppermost mantle.The misfit between geochemical depletion models and geophysical models for mantle convection (which include deep subduction) might therefore be explained by continuous deepening of this depleted layer through geological time.     

Germline mutations and sequence variants of the macrophage scavenger receptor 1 gene are associated with prostate cancer risk

Deletions on human chromosome 8p22-23 in prostate cancer cells and linkage studies in families affected with hereditary prostate cancer (HPC) have implicated this region in the development of prostate cancer. The macrophage scavenger receptor 1 gene (MSR1, also known as SR-A) is located at 8p22 and functions in several processes proposed to be relevant to prostate carcinogenesis. Here we report the results of genetic analyses that indicate that mutations in MSR1 may be associated with risk of prostate cancer. Among families affected with HPC, we identified six rare missense mutations and one nonsense mutation in MSR1. A family-based linkage and association test indicated that these mutations co-segregate with prostate cancer (P = 0.0007). In addition, among men of European descent, MSR1 mutations were detected in 4.4% of individuals affected with non-HPC as compared with 0.8% of unaffected men (P = 0.009). Among African American men, these values were 12.5% and 1.8%, respectively (P = 0.01). These results show that MSR1 may be important in susceptibility to prostate cancer in men of both African American and European descent.     

Structural identification of a bacterial quorum-sensing signal containing boron

Cell-cell communication in bacteria is accomplished through the exchange of extracellular signalling molecules called autoinducers. This process, termed quorum sensing, allows bacterial populations to coordinate gene expression. Community cooperation probably enhances the effectiveness of processes such as bioluminescence, virulence factor expression, antibiotic production and biofilm development. Unlike other autoinducers, which are specific to a particular species of bacteria, a recently discovered autoinducer (AI-2) is produced by a large number of bacterial species. AI-2 has been proposed to serve as a 'universal' signal for inter-species communication. The chemical identity of AI-2 has, however, proved elusive. Here we present the crystal structure of an AI-2 sensor protein, LuxP, in a complex with autoinducer. The bound ligand is a furanosyl borate diester that bears no resemblance to previously characterized autoinducers. Our findings suggest that addition of naturally occurring borate to an AI-2 precursor generates active AI-2. Furthermore, they indicate a potential biological role for boron, an element required by a number of organisms but for unknown reasons.