XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures.

The combination of X-ray free-electron lasers (XFELs) with serial femtosecond crystallography represents cutting-edge technology in structural biology, allowing the study of enzyme reactions and dynamics in real time through the generation of `molecular movies'. This technology combines short and precise high-energy X-ray exposure to a stream of protein microcrystals. Here, the XFEL structure of carbonic anhydrase II, a ubiquitous enzyme responsible for the interconversion of CO2 and bicarbonate, is reported, and is compared with previously reported NMR and synchrotron X-ray and neutron single-crystal structures.

Development of combined hypersonic test facility for aerothermodynamic testing.

In this study, a combined test facility was developed using a combination of an arc-jet tunnel and a shock tunnel for aerothermodynamic testing. The performance validation of individual parts was performed, and results were obtained from the combined test. A small-scale Huels-type arc-jet tunnel was used to preheat the test model by aerodynamic heating before conducting the experiments in the shock tunnel to duplicate the hot surfaces of flight objects encountered during hypersonic flight. The high-enthalpy flow in the arc-jet tunnel provided a heat flux of 1.99±0.03 MW/m2 for a flat-faced model of 10 mm diameters, and the flow condition of the shock tunnel used in this study simulated a Mach 5 flight at a pressure altitude of about 24 km. The two combined experiments employing different shape and material models were carried out to examine the effect of aerothermodynamic phenomena. In the first experiment, the effect of ablation-induced shape change on the fluid-structure was investigated using a cone model manufactured of AL6061 material. The effect of surface roughness on the fluid-structure was examined in the second experiment, which used a hemisphere model constructed of STS303 material. Although substantial findings could not be validated due to the limits of qualitative evaluations utilizing visualization methods, however preheating-related changes in surface roughness were found. As a follow-up study, a force measuring experiment based on the test procedures is being carried out at this facility utilizing a preheated model with an accelerometer. The performance and experimental results obtained using this integrated setup are discussed in detail, highlighting the potential of this combined hypersonic test facility.

Optical control of ultrafast structural dynamics in a fluorescent protein.

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors.

The bioactive lysophospholipid sphingosine-1-phosphate (S1P) acts via five different subtypes of S1P receptors (S1PRs) - S1P1-5. S1P5 is predominantly expressed in nervous and immune systems, regulating the egress of natural killer cells from lymph nodes and playing a role in immune and neurodegenerative disorders, as well as carcinogenesis. Several S1PR therapeutic drugs have been developed to treat these diseases; however, they lack receptor subtype selectivity, which leads to side effects. In this article, we describe a 2.2 Å resolution room temperature crystal structure of the human S1P5 receptor in complex with a selective inverse agonist determined by serial femtosecond crystallography (SFX) at the Pohang Accelerator Laboratory X-Ray Free Electron Laser (PAL-XFEL) and analyze its structure-activity relationship data. The structure demonstrates a unique ligand-binding mode, involving an allosteric sub-pocket, which clarifies the receptor subtype selectivity and provides a template for structure-based drug design. Together with previously published S1PR structures in complex with antagonists and agonists, our structure with S1P5-inverse agonist sheds light on the activation mechanism and reveals structural determinants of the inverse agonism in the S1PR family.

Assessment of drag measurement techniques in a shock tunnel.

Three force measurement techniques in a shock tunnel, the free-flight, movable-support force balance, and stress-wave force balance techniques were employed, and each technique's characteristics were assessed. For each force measurement technique, the system setup, data processing method, measurement uncertainties, and applied range of the test model size-flow establishment time were described in detail and compared. For a comparison and discussion, the drag coefficients of a circular pointed cone model with a semi-angle of 18.4° at a nominal freestream Mach number of 6 were measured. As a result, three force measurement techniques yield similar drag coefficients. However, the measurement uncertainties were increased in the order of the free-flight, the stress-wave force balance, and the movable-support force balance techniques. The main causes of the measurement uncertainties were the corner detection uncertainties for the free-flight techniques, and the propagation of the internal or external vibrations for the movable-support and stress-wave force balance techniques. To estimate the appropriate range of the test model size and flow establishment time for each technique's application, the force measurement systems of the present work and the available literature were compared. As a result of comparative discussion, force measurement environments that can be advantageous for each technique are suggested.

Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I.

Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A1A and A1B. The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A1A. These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.

Thermochemical nonequilibrium flow analysis in low enthalpy shock-tunnel facility.

A thermochemical nonequilibrium analysis was performed under the low enthalpy shock-tunnel flows. A quasi-one-dimensional flow calculation was employed by dividing the flow calculations into two parts, for the shock-tube and the Mach 6 nozzle. To describe the thermochemical nonequilibrium of the low enthalpy shock-tunnel flows, a three-temperature model is proposed. The three-temperature model treats the vibrational nonequilibrium of O2 and NO separately from the single nonequilibrium energy mode of the previous two-temperature model. In the three-temperature model, electron-electronic energies and vibrational energy of N2 are grouped as one energy mode, and vibrational energies of O2, O2+, and NO are grouped as another energy mode. The results for the shock-tunnel flows calculated using the three-temperature model were then compared with existing experimental data and the results obtained from one- and two-temperature models, for various operating conditions of the K1 shock-tunnel facility. The results of the thermochemical nonequilibrium analysis of the low enthalpy shock-tunnel flows suggest that the nonequilibrium characteristics of N2 and O2 need to be treated separately. The vibrational relaxation of O2 is much faster than that of N2 in low enthalpy condition, and the dissociation rate of O2 is manly influenced by the species vibrational temperature of O2. The proposed three-temperature model is able to describe the thermochemical nonequilibrium characteristics of N2 and O2 behind the incident and reflected shock waves, and the rapid vibrational freezing of N2 in nozzle expanding flows.

Time-resolved resonant elastic soft x-ray scattering at Pohang Accelerator Laboratory X-ray Free Electron Laser.

Resonant elastic x-ray scattering has been widely employed for exploring complex electronic ordering phenomena, such as charge, spin, and orbital order, in particular, in strongly correlated electronic systems. In addition, recent developments in pump-probe x-ray scattering allow us to expand the investigation of the temporal dynamics of such orders. Here, we introduce a new time-resolved Resonant Soft X-ray Scattering (tr-RSXS) endstation developed at the Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL). This endstation has an optical laser (wavelength of 800 nm plus harmonics) as the pump source. Based on the commissioning results, the tr-RSXS at PAL-XFEL can deliver a soft x-ray probe (400 eV-1300 eV) with a time resolution of ∼100 fs without jitter correction. As an example, the temporal dynamics of a charge density wave on a high-temperature cuprate superconductor is demonstrated.

Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography.

Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Šresolution.

Polyacrylamide injection matrix for serial femtosecond crystallography.

Serial femtosecond crystallography (SFX) provides opportunities to observe the dynamics of macromolecules without causing radiation damage at room temperature. Although SFX provides a biologically more reliable crystal structure than provided by the existing synchrotron sources, there are limitations due to the consumption of many crystal samples. A viscous medium as a carrier matrix reduces the flow rate of the crystal sample from the injector, thereby dramatically reducing sample consumption. However, the currently available media cannot be applied to specific crystal samples owing to reactions between the viscous medium and crystal sample. The discovery and characterisation of a new delivery medium for SFX can further expand its use. Herein, we report the preparation of a polyacrylamide (PAM) injection matrix to determine the crystal structure with an X-ray free-electron laser. We obtained 11,936 and 22,213 indexed images using 0.5 mg lysozyme and 1.0 mg thermolysin, respectively. We determined the crystal structures of lysozyme and thermolysin delivered in PAM at 1.7 Å and 1.8 Å resolutions. The maximum background scattering from PAM was lower than monoolein, a commonly used viscous medium. Our results show that PAM can be used as a sample delivery media in SFX studies.

Analysis of latency performance of bluetooth low energy (BLE) networks.

Bluetooth Low Energy (BLE) is a short-range wireless communication technology aiming at low-cost and low-power communication. The performance evaluation of classical Bluetooth device discovery have been intensively studied using analytical modeling and simulative methods, but these techniques are not applicable to BLE, since BLE has a fundamental change in the design of the discovery mechanism, including the usage of three advertising channels. Recently, there several works have analyzed the topic of BLE device discovery, but these studies are still far from thorough. It is thus necessary to develop a new, accurate model for the BLE discovery process. In particular, the wide range settings of the parameters introduce lots of potential for BLE devices to customize their discovery performance. This motivates our study of modeling the BLE discovery process and performing intensive simulation. This paper is focused on building an analytical model to investigate the discovery probability, as well as the expected discovery latency, which are then validated via extensive experiments. Our analysis considers both continuous and discontinuous scanning modes. We analyze the sensitivity of these performance metrics to parameter settings to quantitatively examine to what extent parameters influence the performance metric of the discovery processes.