The H-NOX protein structure adapts to different mechanisms in sensors interacting with nitric oxide.

Some classes of bacteria within phyla possess protein sensors identified as homologous to the heme domain of soluble guanylate cyclase, the mammalian NO-receptor. Named H-NOX domain (Heme-Nitric Oxide or OXygen-binding), their heme binds nitric oxide (NO) and O for some of them. The signaling pathways where these proteins act as NO or O sensors appear various and are fully established for only some species.

Computational identification of a systemic antibiotic for gram-negative bacteria.

Discovery of antibiotics acting against Gram-negative species is uniquely challenging due to their restrictive penetration barrier. BamA, which inserts proteins into the outer membrane, is an attractive target due to its surface location. Darobactins produced by Photorhabdus, a nematode gut microbiome symbiont, target BamA.

Nanoscale-Femtosecond Imaging of Evanescent Surface Plasmons on Silver Film by Photon-Induced Near-Field Electron Microscopy.

Surface plasmons on silver nanostructures have a broad range of tunable resonance properties in visible and near-infrared regimes, which possess wide applications in nanophotonics and optoelectronics. Here we use a femtosecond laser to excite surface plasmons on a silver film and trace the subsequent transient dynamics via photon-induced near-field electron microscopy (PINEM). A polarization experiment of PINEM demonstrates a conspicuous polarization dependence of the transient surface plasmon field on the silver film; however, unlike silver nanowires and nanorods, there is no polarization dependence for the PINEM intensity.

CaMn O Cubane Models of the Oxygen-Evolving Complex: Spin Ground States S<9/2 and the Effect of Oxo Protonation.

We report the single crystal XRD and MicroED structure, magnetic susceptibility, and EPR data of a series of CaMn O and YMn O complexes as structural and spectroscopic models of the cuboidal subunit of the oxygen-evolving complex (OEC). The effect of changes in heterometal identity, cluster geometry, and bridging oxo protonation on the spin-state structure was investigated. In contrast to previous computational models, we show that the spin ground state of CaMn O complexes and variants with protonated oxo moieties need not be S=9/2.

Ultrafast dynamics of heme distortion in the O-sensor of a thermophilic anaerobe bacterium.

Heme-Nitric oxide and Oxygen binding protein domains (H-NOX) are found in signaling pathways of both prokaryotes and eukaryotes and share sequence homology with soluble guanylate cyclase, the mammalian NO receptor. In bacteria, H-NOX is associated with kinase or methyl accepting chemotaxis domains. In the O-sensor of the strict anaerobe Caldanaerobacter tengcongensis (Ct H-NOX) the heme appears highly distorted after O binding, but the role of heme distortion in allosteric transitions was not yet evidenced.

Microcrystal Electron Diffraction Elucidates Water-Specific Polymorphism-Induced Emission Enhancement of Bis-arylacylhydrazone.

Aggregation-induced emission (AIE) phenomena have gained intense interest over the last decades because of its importance in solid-state emission. However, the elucidation of a working mechanism is difficult owing to the limited characterization methods on solid-state molecules, further complicated if dynamic structural changes occur. Here, a series of bis-arylacylhydrazones () were synthesized, for which their AIE properties are only turned on by the reversible adsorption of water molecules.

4D electron microscopy of T cell activation.

T cells can be controllably stimulated through antigen-specific or nonspecific protocols. Accompanying functional hallmarks of T cell activation can include cytoskeletal reorganization, cell size increase, and cytokine secretion. Photon-induced near-field electron microscopy (PINEM) is used to image and quantify evanescent electric fields at the surface of T cells as a function of various stimulation conditions.

Optical manipulation of magnetic vortices visualized in situ by Lorentz electron microscopy.

Understanding the fundamental dynamics of topological vortex and antivortex naturally formed in microscale/nanoscale ferromagnetic building blocks under external perturbations is crucial to magnetic vortex-based information processing and spintronic devices. All previous studies have focused on magnetic vortex-core switching via external magnetic fields, spin-polarized currents, or spin waves, which have largely prohibited the investigation of novel spin configurations that could emerge from the ground states in ferromagnetic disks and their underlying dynamics. We report in situ visualization of femtosecond laser quenching-induced magnetic vortex changes in various symmetric ferromagnetic Permalloy disks by using Lorentz phase imaging of four-dimensional electron microscopy that enables in situ laser excitation.

Time-resolved spectroscopy of the ensembled photoluminescence of nitrogen- and boron/nitrogen-doped carbon dots.

Carbon dots (CDs) have potential applications in various fields such as energy, catalysis, and bioimaging due to their strong and tuneable photoluminescence (PL), low toxicity, and robust chemical inertness. Although several PL mechanisms have been proposed, the origin of PL in CDs is still in debate because of the ensembled nature of the heterogeneous luminophores present in the CDs. To unravel the origin of PL in CDs, we performed time-resolved spectroscopy on two types of CDs: nitrogen-doped (N-CD) and boron-nitrogen co-doped (BN-CD).

Photon-Induced Near-Field Electron Microscopy of Eukaryotic Cells.

Photon-induced near-field electron microscopy (PINEM) is a technique to produce and then image evanescent electromagnetic fields on the surfaces of nanostructures. Most previous applications of PINEM have imaged surface plasmon-polariton waves on conducting nanomaterials. Here, the application of PINEM on whole human cancer cells and membrane vesicles isolated from them is reported.

On the dynamical nature of the active center in a single-site photocatalyst visualized by 4D ultrafast electron microscopy.

Understanding the dynamical nature of the catalytic active site embedded in complex systems at the atomic level is critical to developing efficient photocatalytic materials. Here, we report, using 4D ultrafast electron microscopy, the spatiotemporal behaviors of titanium and oxygen in a titanosilicate catalytic material. The observed changes in Bragg diffraction intensity with time at the specific lattice planes, and with a tilted geometry, provide the relaxation pathway: the Ti(4+)=O(2-) double bond transformation to a Ti(3+)-O(1-) single bond via the individual atomic displacements of the titanium and the apical oxygen.

Observing in space and time the ephemeral nucleation of liquid-to-crystal phase transitions.

The phase transition of crystalline ordering is a general phenomenon, but its evolution in space and time requires microscopic probes for visualization. Here we report direct imaging of the transformation of amorphous titanium dioxide nanofilm, from the liquid state, passing through the nucleation step and finally to the ordered crystal phase. Single-pulse transient diffraction profiles at different times provide the structural transformation and the specific degree of crystallinity (η) in the evolution process.

Biochemical perturbations of the mitotic spindle in Xenopus extracts using a diffusion-based microfluidic assay.

A microfluidic device is a powerful tool to manipulate in a controlled manner at spatiotemporal scales for biological systems. Here, we describe a simple diffusion-based assay to generate and measure the effect of biochemical perturbations within the cytoplasm of cell-free extracts from Xenopus eggs. Our approach comprises a microliter reservoir and a model cytoplasm that are separated by a synthetic membrane containing sub-micrometric pores through which small molecules and recombinant proteins can diffuse.

Motion of proximal histidine and structural allosteric transition in soluble guanylate cyclase.

We investigated the changes of heme coordination in purified soluble guanylate cyclase (sGC) by time-resolved spectroscopy in a time range encompassing 11 orders of magnitude (from 1 ps to 0.2 s). After dissociation, NO either recombines geminately to the 4-coordinate (4c) heme (τG1 = 7.

Reactivity and dynamics of H2S, NO, and O2 interacting with hemoglobins from Lucina pectinata.

Hemoglobin HbI from the clam Lucina pectinata is involved in H2S transport, whereas homologous heme protein HbII/III is involved in O2 metabolism. Despite similar tertiary structures, HbI and HbII/III exhibit very different reactivity toward heme ligands H2S, O2, and NO. To investigate this reactivity at the heme level, we measured the dynamics of ligand interaction by time-resolved absorption spectroscopy in the picosecond to nanosecond time range.

Picosecond binding of the His ligand to four-coordinate heme in cytochrome c': a one-way gate for releasing proximal NO.

We provide a direct demonstration of a "kinetic trap" mechanism in the proximal 5-coordinate heme-nitrosyl complex (5c-NO) of cytochrome c' from Alcaligenes xylosoxidans (AXCP) in which picosecond rebinding of the endogenous His ligand following heme-NO dissociation acts as a one-way gate for the release of proximal NO into solution. This demonstration is based upon picosecond transient absorption changes following NO photodissociation of the proximal 5c-NO AXCP complex. We have determined the absolute transient absorption spectrum of 4-coordinate ferrous heme to which NO rebinds with a time constant τ(NO) = 7 ps (k(NO) = 1.

Association of the Neuronal Cell Adhesion Molecule (NrCAM) Gene Variants with Personality Traits and Addictive Symptoms in Methamphetamine Use Disorder.

Objective: 1) To investigate the relationship between NrCAM polymorphisms and methamphetamine abuse in an ethnically homogenous Korean population. 2) To further support our findings by investigating the association among NrCAM gene variants, certain personality traits, and addictive symptoms of methamphetamine abusers.

Methods: Thirty-seven male methamphetamine abusers (age=43.

Direct observation of conformation-dependent pathways in the excited-state proton transfer of 7-hydroxyquinoline in bulk alcohols.

The excited-state proton transfer (ESPT) of 7-hydroxyquinoline (7HQ) in bulk alcoholic solvents has been explored with variation of protic hydrogen atoms as well as alcohols. By measuring time-resolved kinetic profiles at two different excitation wavelengths, we have observed conformation-specific pathways in the ESPT of 7HQ. There are two possible rotamers of 7HQ according to the configuration of its hydroxyl group, which are trans and cis.

Picosecond to second dynamics reveals a structural transition in Clostridium botulinum NO-sensor triggered by the activator BAY-41-2272.

Soluble guanylate cyclase (sGC) is the mammalian endogenous nitric oxide (NO) receptor that synthesizes cGMP upon NO activation. In synergy with the artificial allosteric effector BAY 41-2272 (a lead compound for drug design in cardiovascular treatment), sGC can also be activated by carbon monoxide (CO), but the structural basis for this synergistic effect are unknown. We recorded in the unusually broad time range from 1 ps to 1 s the dynamics of the interaction of CO binding to full length sGC, to the isolated sGC heme domain β(1)(200) and to the homologous bacterial NO-sensor from Clostridium botulinum.

Confinement induces actin flow in a meiotic cytoplasm.

In vivo, F-actin flows are observed at different cell life stages and participate in various developmental processes during asymmetric divisions in vertebrate oocytes, cell migration, or wound healing. Here, we show that confinement has a dramatic effect on F-actin spatiotemporal organization. We reconstitute in vitro the spontaneous generation of F-actin flow using Xenopus meiotic extracts artificially confined within a geometry mimicking the cell boundary.

Absorption band III kinetics probe the picosecond heme iron motion triggered by nitric oxide binding to hemoglobin and myoglobin.

To study the ultrafast movement of the heme iron induced by nitric oxide (NO) binding to hemoglobin (Hb) and myoglobin (Mb), we probed the picosecond spectral evolution of absorption band III (∼760 nm) and vibrational modes (iron-histidine stretching, ν(4) and ν(7) in-plane modes) in time-resolved resonance Raman spectra. The time constants of band III intensity kinetics induced by NO rebinding (25 ps for hemoglobin and 40 ps for myoglobin) are larger than in Soret bands and Q-bands. Band III intensity kinetics is retarded with respect to NO rebinding to Hb and to Mb.

Quaternary structure controls ligand dynamics in soluble guanylate cyclase.

Soluble guanylate cyclase (sGC) is the mammalian endogenous nitric oxide (NO) receptor. The mechanisms of activation and deactivation of this heterodimeric enzyme are unknown. For deciphering them, functional domains can be overexpressed.

Picosecond primary structural transition of the heme is retarded after nitric oxide binding to heme proteins.

We investigated the ultrafast structural transitions of the heme induced by nitric oxide (NO) binding for several heme proteins by subpicosecond time-resolved resonance Raman and femtosecond transient absorption spectroscopy. We probed the heme iron motion by the evolution of the iron-histidine Raman band intensity after NO photolysis. Unexpectedly, we found that the heme response and iron motion do not follow the kinetics of NO rebinding.