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Abstract: Here we describe an x-ray structure of wild-type lactose permease (LacY) from Escherichia coli determined by manipulating phospholipid content during crystallization. The structure exhibits the same global fold as the previous x-ray structures of a mutant that binds sugar but cannot catalyze translocation across the membrane. LacY is organized into two six-helix bundles with twofold pseudosymmetry separated by a large interior hydrophilic cavity open only to the cytoplasmic side and containing the side chains important for sugar and H+ binding. To initiate transport, binding of sugar and/or an H+ electrochemical gradient increases the probability of opening on the periplasmic side. Because the inward-facing conformation represents the lowest free-energy state, the rate-limiting step for transport may be the conformational change leading to the outward-facing conformation.

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Abstract: The biological role of manganese (Mn2+) has been a long-standing puzzle, since at low concentrations it activates several polymerases whilst at higher concentrations it inhibits. Viral RNA polymerases possess a common architecture, reminiscent of a closed right hand. The RNA-dependent RNA polymerase (RdRp) of bacteriophage {phi}6 is one of the best understood examples of this important class of polymerases. We have probed the role of Mn2+ by biochemical, biophysical and structural analyses of the wild-type enzyme and of a mutant form with an altered Mn2+-binding site (E491 to Q). The E491Q mutant has much reduced affinity for Mn2+, reduced RNA binding and a compromised elongation rate. Loss of Mn2+ binding structurally stabilizes the enzyme. These data and a re-examination of the structures of other viral RNA polymerases clarify the role of manganese in the activation of polymerization: Mn2+ coordination of a catalytic aspartate is necessary to allow the active site to properly engage with the triphosphates of the incoming NTPs. The structural flexibility caused by Mn2+ is also important for the enzyme dynamics, explaining the requirement for manganese throughout RNA polymerization.

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Abstract: Context. Silicate dust grains exist in a wide range of astronomical environments and understanding the effect of these on grain structure is of great interest, particularly the effect of thermal annealing on amorphous silicates as a possible route to the formation of crystalline grains. Although laboratory simulations have largely focussed on IR-spectroscopic measurements, since these relate directly to observational data, laboratory synchrotron techniques such as X-ray absorption spectroscopy (XAS) and X-ray scattering are becoming increasingly routine in the analysis of recovered materials. With the increasing prospect of performing astronomical XAS observations, there is much to be gained from applying these techniques to laboratory analogues. Aims. Diagnostic markers for medium-range order and the effect of thermal annealing on these in amorphous silicates of differing Mg content are characterised using synchrotron X-ray methods. Methods. Three synthetic amorphous silicates with high, medium and low Mg:Si ratios were annealed at varying temperatures up to 1300 K. X-ray Absorption Near Edge Structure (XANES) spectra at the Si and Mg K-shell absorption edges and X-ray scattering patterns for low values of the X-ray scattering wavevector were recorded for these along with comparative data for commercially produced amorphous SiO2 and mineral samples of forsterite, enstatite and quartz. Results. XANES features due to short- and medium-range structure are identified at both Mg and Si edges and a new temperature dependent behaviour observed in the medium-range structure surrounding Mg and Si. Based on changes to the morphological details of the XANES spectra, the medium-range structure changes between an enstatite-like and forsterite-like coordination with increasing temperature and appears to correlate directly with Mg content. Low wavevector X-ray scattering features were also found to be diagnostic of the type of medium-range structural ordering. However, these features depend on whether the relative arrangement of clusters of medium-range structure exhibit semi-periodic ordering over the longer-range, which can vary with annealing.

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Abstract: By using absorption and fluorescence spectroscopy, we compared the effects of heat and light treatments on the phycobilisome (PBS) antenna of Synechocystis sp. PCC 6803 cells. Fluorescence emission spectra obtained upon exciting predominantly PBS, recorded at 25 °C and 77 K, revealed characteristic changes upon heat treatment of the cells. A 5-min incubation at 50 °C, which completely inactivated the activity of photosystem II, led to a small but statistically significant decrease in the F680/F655 fluorescence intensity ratio. In contrast, heat treatment at 60 °C resulted in a much larger decrease in the same ratio and was accompanied by a blue-shift of the main PBS emission band at around 655 nm (F655), indicating an energetic decoupling of PBS from chlorophylls and reorganizations in its internal structure. (Upon exciting PBS, F680 originates from photosystem II and from the terminal emitter of PBS.). Very similar changes were obtained upon exposing the cells to high light (600–7500 μmol photons m−2 s−1) for different time periods (10 min to 3 h). In cells with heat-inactivated photosystem II, the variations caused by light treatment could clearly be assigned to a similar energetic decoupling of the PBS from the membrane and internal reorganizations as induced at around 60 °C. These data can be explained within the frameworks of thermo-optic mechanism [Cseh et al. 2000, Biochemistry 39, 15250]: in high light the heat packages originating from dissipation might lead to elementary structural changes in the close vicinity of dissipation in heat-sensitive structural elements, e.g. around the site where PBS is anchored to the membrane. This, in turn, brings about a diminishment in the energy supply from PBS to the photosystems and reorganization in the molecular architecture of PBS.

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Abstract: The development of the capability to engineer the surface properties of materials to match specific requirements demands high quality surface characterization techniques. The ideal tool should provide chemically specific structural characterization as well as surface sensitivity and depth profiling. Ideally the characterization method should also be applicable to systems both with and without long range order. X-ray absorption spectroscopy fine structure, when using the standard transmission detection system, provides all this information with the significant exception of surface sensitivity. In contrast, by detecting the reflected instead of the transmitted beam, it encompasses all these requirements because when the incident beam impinges onto a sample surface at glancing angles, in conditions close to the total reflection, only the outermost regions of the system under study are sampled. Such a technique provides information about the local structure as a function of depth as well as thin layer structure in the case of layered samples. Although it is potentially the ideal tool to study surface modified materials, experimental difficulties have hampered its widespread use in the fields of surface and materials sciences. As a solution to the experimental challenges, we provide a detailed description of an appropriate experimental station, the sample requirements, the measuring protocols, and software routines needed to optimize the collection of the data. To illustrate the capabilities of the technique the results obtained for a model multilayer sample are presented and analyzed under the total external reflection approximation.