Cryo-EM reveals the conformational epitope of human monoclonal antibody PAM1.4 broadly reacting with polymorphic malarial protein VAR2CSA.

Malaria during pregnancy is a major global health problem caused by infection with Plasmodium falciparum parasites. Severe effects arise from the accumulation of infected erythrocytes in the placenta. Here, erythrocytes infected by late blood-stage parasites adhere to placental chondroitin sulphate A (CS) via VAR2CSA-type P. falciparum erythrocyte membrane protein 1 (PfEMP1) adhesion proteins. Immunity to placental malaria is acquired through exposure and mediated through antibodies to VAR2CSA. Through evolution, the VAR2CSA proteins have diversified in sequence to escape immune recognition but retained their overall macromolecular structure to maintain CS binding affinity. This structural conservation may also have allowed development of broadly reactive antibodies to VAR2CSA in immune women. Here we show the negative stain and cryo-EM structure of the only known broadly reactive human monoclonal antibody, PAM1.4, in complex with VAR2CSA. The data shows how PAM1.4's broad VAR2CSA reactivity is achieved through interactions with multiple conserved residues of different sub-domains forming conformational epitope distant from the CS binding site on the VAR2CSA core structure. Thus, while PAM1.4 may represent a class of antibodies mediating placental malaria immunity by inducing phagocytosis or NK cell-mediated cytotoxicity, it is likely that broadly CS binding-inhibitory antibodies target other epitopes at the CS binding site. Insights on both types of broadly reactive monoclonal antibodies may aid the development of a vaccine against placental malaria.

Accurate charge densities from powder X-ray diffraction - a new version of the Aarhus vacuum imaging-plate diffractometer.

In recent years powder X-ray diffraction has proven to be a valuable alternative to single-crystal X-ray diffraction for determining electron-density distributions in high-symmetry inorganic materials, including subtle deformation in the core electron density. This was made possible by performing diffraction measurements in vacuum using high-energy X-rays at a synchrotron-radiation facility. Here we present a new version of our custom-built in-vacuum powder diffractometer with the sample-to-detector distance increased by a factor of four. In practice this is found to give a reduction in instrumental peak broadening by approximately a factor of three and a large improvement in signal-to-background ratio compared to the previous instrument. Structure factors of silicon at room temperature are extracted using a combined multipole-Rietveld procedure and compared with ab initio calculations and the results from the previous diffractometer. Despite some remaining issues regarding peak asymmetry, the new diffractometer yields structure factors of comparable accuracy to the previous diffractometer at low angles and improved accuracy at high angles. The high quality of the structure factors is further assessed by modelling of core electron deformation with results in good agreement with previous investigations.

Structural disorder, anisotropic micro-strain and cation vacancies in thermo-electric lead chalcogenides.

Thermoelectric materials can interconvert heat and electricity, and the extraordinary thermoelectric properties of lead chalcogenides (PbX, X = S, Se, Te) attract immense scientific interest. A key topic is the role of the cation in reaching a very low thermal conductivity necessary for efficient energy conversion. Here we present new structural insights about the deceptively simple rock-salt lead chalcogenides through a comparative multi-temperature synchrotron powder X-ray diffraction study. For the first time, the presence of anisotropic microstrain broadening as well as lead vacancies are quantified for all three compounds. The microstrain implies extended breakage of cubic symmetry as a sign of the incipient ferroelectric nature of PbX. The degree of microstrain is correlated to the transition pressure of a symmetry reducing phase transition, and this trend can be explained by anion mediated s-p hybridization on lead. The observed number of vacancies is greatest for PbS (4-8%), but two samples of PbS show different cation occupancy, and thus sample-dependent vacancies might be the property that unifies conflicting results reported for PbX. Gram-Charlier analysis identifies a local non-spherical distribution of Pb; however, model unbiased maximum entropy analysis indicates that any static displacement of Pb, if present, is less than 0.2 Å at 100 K.

Carrier concentration dependence of structural disorder in thermoelectric Sn1-x Te.

SnTe is a promising thermoelectric and topological insulator material. Here, the presumably simple rock salt crystal structure of SnTe is studied comprehensively by means of high-resolution synchrotron single-crystal and powder X-ray diffraction from 20 to 800 K. Two samples with different carrier concentrations (sample A = high, sample B = low) have remarkably different atomic displacement parameters, especially at low temperatures. Both samples contain significant numbers of cation vacancies (1-2%) and ordering of Sn vacancies possibly occurs on warming, as corroborated by the appearance of multiple phases and strain above 400 K. The possible presence of disorder and anharmonicity is investigated in view of the low thermal conductivity of SnTe. Refinement of anharmonic Gram-Charlier parameters reveals marginal anharmonicity for sample A, whereas sample B exhibits anharmonic effects even at low temperature. For both samples, no indications are found of a low-temperature rhombohedral phase. Maximum entropy method (MEM) calculations are carried out, including nuclear-weighted X-ray MEM calculations (NXMEM). The atomic electron densities are spherical for sample A, whereas for sample B the Te electron density is elongated along the 〈100〉 direction, with the maximum being displaced from the lattice position at higher temperatures. Overall, the crystal structure of SnTe is found to be defective and sample-dependent, and therefore theoretical calculations of perfect rock salt structures are not expected to predict the properties of real materials.

Nuclear-weighted X-ray maximum entropy method - NXMEM.

Subtle structural features such as disorder and anharmonic motion may be accurately characterized from nuclear density distributions (NDDs). As a viable alternative to neutron diffraction, this paper introduces a new approach named the nuclear-weighted X-ray maximum entropy method (NXMEM) for reconstructing pseudo NDDs. It calculates an electron-weighted nuclear density distribution (eNDD), exploiting that X-ray diffraction delivers data of superior quality, requires smaller sample volumes and has higher availability. NXMEM is tested on two widely different systems: PbTe and Ba(8)Ga(16)Sn(30). The first compound, PbTe, possesses a deceptively simple crystal structure on the macroscopic level that is unable to account for its excellent thermoelectric properties. The key mechanism involves local distortions, and the capability of NXMEM to probe this intriguing feature is established with simulated powder diffraction data. In the second compound, Ba(8)Ga(16)Sn(30), disorder among the Ba guest atoms is analysed with both experimental and simulated single-crystal diffraction data. In all cases, NXMEM outperforms the maximum entropy method by substantially enhancing the nuclear resolution. The induced improvements correlate with the amount of available data, rendering NXMEM especially powerful for powder and low-resolution single-crystal diffraction. The NXMEM procedure can be implemented in existing software and facilitates widespread characterization of disorder in functional materials.

Combined X-ray and neutron diffraction study of vacancies and disorder in the dimorphic clathrate Ba8Ga16Sn30 of type I and VIII.

We report detailed structural investigations of the dimorphic clathrate Ba8Ga16Sn30 that crystallizes in both type I and VIII clathrate structures. Single crystals of type I and VIII have been examined using single crystal X-ray and Laue neutron diffraction in the temperature range T = 10 K-500 K. The utilization of both X-ray and neutron diffraction gives a unique ability to reveal the occurrence of minute vacancy occupancies in the host structure. The vacancies are shown to be located on the 6c (type I) and 24g (type VIII) framework sites. Largest vacancy densities are observed for type I p-Ba8Ga16Sn30, 1.3(4)%, and type VIII n-Ba8Ga16Sn30, 0.7(2)%. The relation between guest atom disorder and occurrence of glasslike thermal conductivity in intermetallic clathrates was also investigated. In type VIII Ba8Ga16Sn30 neither n-type (crystalline thermal conductivity) nor p-type (glasslike thermal conductivity) showed any significant disorder of the guest atoms; they do however show anharmonic motion. The glasslike thermal conductivity of p-type Ba8Ga16Sn30 is interpretable as a result of higher effective mass of p-type charge-carriers affecting phonon scattering. In type I Ba8Ga16Sn30 guest atoms are highly disordered for both carrier types and samples of both charge carrier types have glasslike thermal conductivity.