Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme

The Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis

MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics

We describe a method to compute photon-matter interaction and atomic dynamics with X-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically computed based on changes to their electronic occupations and the free electron cloud created due to the irradiation of photons in the X-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, which reduces the number of non-bonded interactions required to compute. In combination with parallelisation through domain decomposition, large-scale molecular dynamics and ionisation induced by X-ray lasers can be followed. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters and crystals) that when exposed to an X-ray laser pulse turn into a plasma in the first few femtoseconds of the interaction. We show several examples of the applicability of the method and we quantify the sizes that the method is suitable for. For large systems, we investigate non-thermal heating and scattering of bulk water, which we compare to previous experiments. We simulate molecular dynamics of a protein crystal induced by an X-ray pump, X-ray probe scheme, and find good agreement of the damage dynamics with experiments. For single particle imaging, we simulate ultrafast dynamics of a methane cluster exposed to a femtosecond X-ray laser. In the context of coherent diffractive imaging we study the fragmentation as given by an X-ray pump X-ray probe setup to understand the evolution of radiation damage.Comment: 12 pages, 11 figures, 50 reference

Distinct transient structural rearrangement of ionized water revealed by XFEL X-ray pump X-ray probe experiment

Using X-ray free electron laser (XFEL) radiation to conduct an X-ray pump X-ray probe experiment, we studied strongly ionized water as part of our ongoing work on radiation damage. After irradiance with a pump pulse with a nominal fluence of ~$5 \times 10^5$ J/cm$^2$, we observed for pump-probe delays of 75 fs and longer an unexpected structural rearrangement, exhibiting a characteristic length scale of ~9 \r{A}. Simulations suggest that the experiment probes a superposition of ionized water in two distinct regimes. In the first, fluences expected at the X-ray focus create nearly completely ionized water, which as a result becomes effectively transparent to the probe. In the second regime, out of focus pump radiation produces O$^{1+}$ and O$^{2+}$ ions, which rearrange due to Coulombic repulsion over 10s of fs. Importantly, structural changes in the low fluence regime have implications for the design of two-pulse X-ray experiments that aim to study unperturbed liquid samples. Our simulations account for two key observations in the experimental data: the decrease in ambient water signal and an increase in low-angle X-ray scattering. They cannot, however, account for the experimentally observed 9 \r{A} feature. A satisfactory account of this feature presents a new challenge for theory.Comment: 24 main text pages, 6 supplement pages (30 total), 4 main text figures, 3 supplemental figures, 2 supplemental table

Deliverable D4.4 Simulated coherent scattering data from plasma and non–plasma samples

Deliverable D4.4 of work package 4 (SIMEX) in EUCALL

Tomography of a Cryo-immobilized Yeast Cell Using Ptychographic Coherent X-Ray Diffractive Imaging

The structural investigation of noncrystalline, soft biological matter using x-rays is of rapidly increasing interest. Large-scale x-ray sources, such as synchrotrons and x-ray free electron lasers, are becoming ever brighter and make the study of such weakly scattering materials more feasible. Variants of coherent diffractive imaging (CDI) are particularly attractive, as the absence of an objective lens between sample and detector ensures that no x-ray photons scattered by a sample are lost in a limited-efficiency imaging system. Furthermore, the reconstructed complex image contains quantitative density information, most directly accessible through its phase, which is proportional to the projected electron density of the sample. If applied in three dimensions, CDI can thus recover the sample's electron density distribution. As the extension to three dimensions is accompanied by a considerable dose applied to the sample, cryogenic cooling is necessary to optimize the structural preservation of a unique sample in the beam. This, however, imposes considerable technical challenges on the experimental realization. Here, we show a route toward the solution of these challenges using ptychographic CDI (PCDI), a scanning variant of coherent imaging. We present an experimental demonstration of the combination of three-dimensional structure determination through PCDI with a cryogenically cooled biological sample—a budding yeast cell (Saccharomyces cerevisiae)—using hard (7.9 keV) synchrotron x-rays. This proof-of-principle demonstration in particular illustrates the potential of PCDI for highly sensitive, quantitative three-dimensional density determination of cryogenically cooled, hydrated, and unstained biological matter and paves the way to future studies of unique, nonreproducible biological cells at higher resolution

Online dynamic flat-field correction for MHz Microscopy data at European XFEL

The X-ray microscopy technique at the European X-ray free-electron laser (EuXFEL), operating at a MHz repetition rate, provides superior contrast and spatial-temporal resolution compared to typical microscopy techniques at other X-ray sources. In both online visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of XFEL sources hinders the use of existing flat-flied normalization methods during MHz X-ray microscopy experiments. Here, we present an online dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images. The method is used for the normalization of individual X-ray projections and has been implemented as an online analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.Comment: 14 pages, 7 figure

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a wellcharacterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 mu m diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 angstrom ngstrom were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.11Ysciescopu

Ultrasound cavitation and exfoliation dynamics of 2D materials re-vealed in operando by X-ray free electron laser megahertz imaging

Ultrasonic liquid phase exfoliation is a promising method for the production of two-dimensional (2D) layered materials. A large number of studies have been made in investigating the underlying ultrasound exfoliation mechanisms. However, due to the experimental challenges for capturing the highly transient and dynamic phenomena in real-time at sub-microsecond time and micrometer length scales simultaneously, most theories reported to date still remain elusive. Here, using the ultra-short X-ray Free Electron Laser pulses (~25ps) with a unique pulse train structure, we applied MHz X-ray Microscopy and machine-learning technique to reveal unambiguously the full cycles of the ultrasound cavitation and graphite layer exfoliation dynamics with sub-microsecond and micrometer resolution. Cyclic fatigue shock wave impacts produced by ultrasound cloud implosion were identified as the dominant mechanism to deflect and exfoliate graphite layers mechanically. For the graphite flakes, exfoliation rate as high as ~5 angstroms per shock wave impact was observed. For the HOPG graphite, the highest exfoliation rate was ~0.15 angstroms per impact. These new findings are scientifically and technologically important for developing industrial upscaling strategies for ultrasonic exfoliation of 2D materials

Nanoscale subsurface dynamics of solids upon high-intensity laser irradiation observed by femtosecond grazing-incidence x-ray scattering

Observing ultrafast laser-induced structural changes in nanoscale systems is essential for understanding the dynamics of intense light-matter interactions. For laser intensities on the order of $10^{14} \, \rm W/cm^2$, highly-collisional plasmas are generated at and below the surface. Subsequent transport processes such as heat conduction, electron-ion thermalization, surface ablation and resolidification occur at picosecond and nanosecond time scales. Imaging methods, e.g. using x-ray free-electron lasers (XFEL), were hitherto unable to measure the depth-resolved subsurface dynamics of laser-solid interactions with appropriate temporal and spatial resolution. Here we demonstrate picosecond grazing-incidence small-angle x-ray scattering (GISAXS) from laser-produced plasmas using XFEL pulses. Using multi-layer (ML) samples, both the surface ablation and subsurface density dynamics are measured with nanometer depth resolution. Our experimental data challenges the state-of-the-art modeling of matter under extreme conditions and opens new perspectives for laser material processing and high-energy-density science.Comment: 16 pages, 4 figures. This is the version of the article before peer review, as submitted by authors. There is a Supplementary Information file in the Ancillary files director