An integrated environment for biological small-angle X-ray scattering (BioSAXS) at the high-brilliance P12 synchrotron beamline of the EMBL (DESY, Hamburg) allows for a broad range of solution scattering experiments. Automated hardware and software systems have been designed to ensure that data collection and processing are efficient, streamlined and user friendly.

Small-angle X-ray scattering (SAXS) is an established technique that provides low-resolution structural information on macromolecular solutions. Recent decades have witnessed significant progress in both experimental facilities and in novel data-analysis approaches, making SAXS a mainstream method for structural biology. The technique is routinely applied to directly reconstruct lowresolution shapes of proteins and to generate atomistic models of macromolecular assemblies using hybrid approaches. Very importantly, SAXS is capable of yielding structural information on systems with size and conformational polydispersity, including highly flexible objects. In addition, utilizing high-flux synchrotron facilities, time-resolved SAXS allows analysis of kinetic processes over time ranges from microseconds to hours. Dedicated bioSAXS beamlines now offer fully automated data-collection and analysis pipelines, where analysis and modelling is conducted on the fly. This enables SAXS to be employed as a high-throughput method to rapidly screen various sample conditions and additives. The growing SAXS user community is supported by developments in data and model archiving and quality criteria. This review illustrates the latest developments in SAXS, in particular highlighting timeresolved applications aimed at flexible and evolving systems.

Transfer ribonucleic acid (tRNA) modifications, especially at the wobble position, are crucial for proper and efficient protein translation. MnmE and MnmG form a protein complex that is implicated in the carboxymethylaminomethyl modification of wobble uridine (cmnm5U34) of certain tRNAs. MnmE is a G protein activated by dimerization (GAD), and active guanosine-5'-triphosphate (GTP) hydrolysis is required for the tRNA modification to occur. Although crystal structures of MnmE and MnmG are available, the structure of the MnmE/MnmG complex (MnmEG) and the nature of the nucleotide-induced conformational changes and their relevance for the tRNA modification reaction remain unknown. In this study, we mainly used small-angle X-ray scattering to characterize these conformational changes in solution and to unravel the mode of interaction between MnmE, MnmG and tRNA. In the nucleotide-free state MnmE and MnmG form an unanticipated asymmetric α2β2 complex. Unexpectedly, GTP binding promotes further oligomerization of the MnmEG complex leading to an α4β2 complex. The transition from the α2β2 to the α4β2 complex is fast, reversible and coupled to GTP binding and hydrolysis. We propose a model in which the nucleotide-induced changes in conformation and oligomerization of MnmEG form an integral part of the tRNA modification reaction cycle.

Here, for the first time, we demonstrate formation of virus-like nanoparticles (VNPs) utilizing gold-coated iron oxide nanoparticles as cores and capsid protein of brome mosaic virus (BMV) or hepatitis B virus (HBV) as shells. Further, utilizing cryo-electron microscopy and single particle methods, we are able to show that the BMV coat on VNPs assembles into a structure very close to that of a native virion. This is a consequence of an optimal iron oxide NP size (∼11 nm) fitting the virus cavity and an ultrathin gold layer on the maghemite cores, which allows for utilization of SH-(CH 2 ) 11 -(CH 2 -CH 2 -O) 4 -OCH 2 -COOH as capping molecules to provide sufficient stability, charge density, and small form factor. MRI studies show unique relaxivity ratios that diminish only slightly with gold coating. A virus protein coating of a magnetic core mimicking the wild-type virus makes these VNPs a versatile platform for biomedical applications.

We report the formation of multicore iron oxide mesocrystals using the thermal decomposition of iron acetyl acetonate in the presence of the multifunctional and rigid poly(phenylenepyridyl) dendron and dendrimer. We thoroughly analyze the influence of capping molecules of two different architectures and demonstrate for the first time that dendron/dendrimer self-assembly leads to multicore morphologies. Single-crystalline ordering in multicore NPs leads to cooperative magnetic behavior: mesocrystals exhibit ambient blocking temperatures, allowing subtle control over magnetic properties using a minor temperature change.

Here we report control of iron oxide and palladium nanoparticle (NP) formation via stabilization with polyphenylenepyridyl dendrons of the second and third generations with dodecyl periphery. These nanomaterials are developed as magnetically recoverable catalysts. To accurately assess the influence of the dodecyl exterior for the same dendron generation, we also designed a second generation dendron with partial dodecyl periphery. For all dendrons studied, the multicore iron oxide mesocrystals were formed, the sizes and morphology of which were controlled by the dendron generation. Analysis of the static and dynamic magnetic properties, in combination with transmission electron microscopy observations, demonstrate that magnetism is sensitive on the structure-directing capabilities of the type of the dendron which was employed for the mesocrystal stabilization. Close proximity of single cores in such multicore mesocrystals promotes the coupling of the neighboring magnetic moments, thus boosting their magnetization and allowing easy crossover between superparamagnetic and ferrimagnetic behaviors at room temperature. The particularly dramatic role of the dendron structure was also witnessed via the Pd NP formation, which was found to depend on both the dendron generation and its dodecyl periphery. In the case of the catalyst based on the second generation dendron with full dodecyl periphery, no Pd NPs were observed by TEM indicating that these species are of a subnanometer size and are not visible on or near the iron oxide NPs. For the catalyst based on the second generation dendron with partial dodecyl periphery, hydrogen reduction leads to much larger Pd NPs (2.7 nm) due to an unimpeded exchange of Pd species between dendrons and nondense dendron coating with asymmetrical dendrons. The third generation dendron with full dodecyl periphery allows nearly monodisperse 1.2 nm Pd NPs in the shells of iron oxide mesocrystals and the best catalytic properties in selective hydrogenation of dimethylethynylcarbinol. This study suggests a robust approach to control NP formation in magnetically recoverable catalysts for a wide variety of catalytic reactions using dendrons combining rigidity and flexibility in one molecule.

We present a centrifugal microfluidic LabDisk for protein structure analysis via small-angle X-ray scattering (SAXS) on synchrotron beamlines. One LabDisk prepares 120 different measurement conditions, grouped into six dilution matrices. Each dilution matrix: (1) features automatic generation of 20 different measurement conditions from three input liquids and (2) requires only 2.5 μl of protein solution, which corresponds to a tenfold reduction in sample volume in comparison to the state of the art. Total hands on time for preparation of 120 different measurement conditions is less than 5 min. Read-out is performed on disk within the synchrotron beamline P12 at EMBL Hamburg (PETRA III, DESY). We demonstrate: (1) aliquoting of 40 nl aliquots for five different liquids typically used in SAXS and (2) confirm fluidic performance of aliquoting, merging, mixing and read-out from SAXS experiments (2.7-4.4% CV of protein concentration).We apply the LabDisk for SAXS for basic analysis methods, such as measurement of the radius of gyration, and advanced analysis methods, such as the ab initio calculation of 3D models. The suitability of the LabDisk for SAXS for protein structure analysis under different environmental conditions is demonstrated for glucose isomerase under varying protein and NaCl concentrations. We show that the apparent radius of gyration of the negatively charged glucose isomerase decreases with increasing protein concentration at low salt concentration. At high salt concentration the radius of gyration (R g ) does not change with protein concentrations. Such experiments can be performed by a non-expert, since the LabDisk for SAXS does not require attachment of tubings or pumps and can be filled with regular pipettes. The new platform has the potential to introduce routine high-throughput SAXS screening of protein structures with minimal input volumes to the regular operation of synchrotron beamlines.

The acknowledged success of the Monod-Wyman-Changeux (MWC) allosteric model stems from its efficacy in accounting for the functional behavior of many complex proteins starting with hemoglobin (the paradigmatic case) and extending to channels and receptors. The kinetic aspects of the allosteric model, however, have been often neglected, with the exception of hemoglobin and a few other proteins where conformational relaxations can be triggered by a short and intense laser pulse, and monitored by time-resolved optical spectroscopy. Only recently the application of time-resolved wide-angle X-ray scattering (TR-WAXS), a direct structurally sensitive technique, unveiled the time scale of hemoglobin quaternary structural transition. In order to test the generality of the MWC kinetic model, we carried out a TR-WAXS investigation in parallel on adult human hemoglobin and on a recombinant protein (HbYQ) carrying two mutations at the active site [Leu(B10)Tyr and His(E7) Gln]. HbYQ seemed an ideal test because, although exhibiting allosteric properties, its kinetic and structural properties are different from adult human hemoglobin. The structural dynamics of HbYQ unveiled by TR-WAXS can be quantitatively accounted for by the MWC kinetic model. Interestingly, the main structural change associated with the R-T allosteric transition (i.e., the relative rotation and translation of the dimers) is approximately 10-fold slower in HbYQ, and the drop in the allosteric transition rate with ligand saturation is steeper. Our results extend the general validity of the MWC kinetic model and reveal peculiar thermodynamic properties of HbYQ. A possible structural interpretation of the characteristic kinetic behavior of HbYQ is also discussed.time-resolved X-ray scattering | protein conformational changes | cooperativity | flash photolysis E ver since the publication of the Monod-Wyman-Changeux paper on allostery (1), hemoglobin (Hb) has been considered the prototype of an allosteric protein; the molecular basis of positive cooperativity in O 2 binding involving a ligand-linked shift between two different quaternary states. The dynamics of ligand rebinding and of the tertiary and quaternary allosteric changes of tetrameric human Hb have been investigated, by-and-large, using transient spectroscopy in the picosecond to millisecond time range, following laser-induced photolysis of the ligand-heme iron bond. Starting with the carbon monoxide adduct HbCO in the allosteric quaternary state called R 4 , complete photolysis yields the unliganded R 0 state; the destiny of this photoproduct is a complex time-dependent process involving competing events such as ligand rebinding and (tertiary and quaternary) conformational decays. Changes in the optical and resonance Raman spectra of the different states have provided, over the last four decades, a quantitative estimate of the rates of the competing events (2-5). For a review on time-resolved optical absorption (TR-OA) data describing conformational decays as well as rebinding in the dark of a ligand...