Structural Dynamics-Us最新文献

Polyamines are polycations involved in both differentiation and proliferation of cells. Highly conserved polyamine biosynthetic enzymes are involved in the synthesis of polyamines. Spermidine synthase (SPDS) is an important enzyme in the polyamine biosynthetic pathway, and it is an aminopropyl-transferase that catalyzes the synthesis of the polyamine, spermidine, from putrescine and decarboxylated S-adenosine methionine. Spermidine has a variety of biological roles, including the formation of eIF5A, regulating autophagy, and stabilizing DNA and RNA. While there are numerous structures of human SPDS in complex with its substrates, products, or inhibitors, and numerous apo structures from various species, there is no structure of the apo form of human SPDS reported to date. In this study, the crystal structure of apo human SPDS was determined at 1.95 Å resolution. Comparison of the inherently flexible gatekeeping loop in the apo human structure with apo homologues revealed species-specific differences in loop conformation, indicating dynamics. Significant conformational change was observed in active site residues that are involved in catalysis when the apo human structure was compared to human ligand-bound complexes. These findings provide structural insights into the conformational dynamics and ligand-binding properties of spermidine synthase.

We demonstrate a novel shot-to-shot acquisition method for optical pump-keV electron energy probe in ultrafast scattering experiments. We integrate a phase-locked acquisition scheme at a repetition rate of 20 kHz in a conventional ultrafast electron diffraction setup. We proceed to a full characterization of the noise level in different configurations and for realistic scenarios. The shot-to-shot acquisition improves the signal-to-noise ratio by one order of magnitude and can be readily implemented in other high-repetition-rate electron diffraction and spectroscopy setups.

The arms race between bacteria and bacteriophages has driven the evolution of both CRISPR-Cas systems and anti-CRISPR (Acr) proteins. AcrIE9, a type I-E Acr protein identified in Pseudomonas aeruginosa, inhibits Cascade-mediated DNA binding by interacting with the Cas7e subunit. However, its structural basis and precise inhibitory mechanism have remained unclear. Here, we report the crystal structure of AcrIE9 at 1.73 Å resolution, along with additional structural and biochemical analyses. AcrIE9 exists as both monomer and dimer in solution, while the crystal structure reveals a homodimeric assembly. Each protomer adopts a unique α/β architecture, and structural similarity searches indicate that AcrIE9 represents a previously uncharacterized protein fold. In vitro binding assays using individually purified type I-E Cas subunits from P. aeruginosa did not detect direct interaction with AcrIE9, including with Cas7e. These findings suggest that AcrIE9 may recognize a composite interface formed only within the intact Cascade complex, consistent with the AlphaFold3 prediction of multivalent interactions with Cas7e subunits. Taken together, this study provides the structural characterization of AcrIE9 and supports an inhibitory mechanism involving a multi-subunit binding surface on Cascade.

Transmission electron microscopy (TEM) has significantly advanced fields such as materials science, nanotechnology, and structural biology by providing detailed structural and analytical information at picometer resolutions. To further enhance TEM's capabilities, time-resolved electron microscopy introduces the temporal domain, using ultrafast electron pulses to capture dynamic processes. Traditional methods generate these pulses via photocathode illumination by femtosecond lasers and face challenges like complex alignment and limited repetition rates. An alternative approach employing electronic devices as beam choppers, specifically resonant RF cavities in combination with electrostatic beam blankers, simplifies alignment and increases repetition rates, achieving picosecond and sub-picosecond pulses. Additionally, these devices do not compromise the performance of the microscope in any other imaging mode. The microscope can be rapidly toggled between continuous and pulsed imaging, providing flexibility of operation in modern research labs. This study integrates these beam choppers into high-end TEMs and demonstrates their effectiveness in achieving high temporal resolution for pump-probe experiments. Results show that these methods maintain high spatial resolution and coherence, making them a promising solution for ultrafast electron microscopy.

Time-resolved (TR) Raman spectroscopy is a unique tool for studying the dynamic properties of quantum matter and can become a key element of the multi-messenger research in the time domain. We present here the features and results of a novel setup for TR Raman, designed to expand the NFFA-SPRINT facility by integrating it with TR optical, transient grating and electron spectroscopy and spin polarization techniques. The TR Raman setup is characterized by a wide energy tunability of the pump and probe pulses, owing to the presence of a laser system providing ultrashort (50 fs to 2 ps) light pulses from the near ultraviolet to the infrared spectral regions. The ultra-high vacuum sample environment allows for the measurement of air-sensitive samples and ensures the full compatibility with photoelectron spectroscopies, as well as a wide sample temperature range. The functionalities of the setup and the multi-messenger research approach are here demonstrated by presenting studies of the relaxation dynamics in photoexcited semiconductor systems, namely, Si and MoS₂. In addition, the pump-probe response of magnetite across the Verwey transition is presented, highlighting the capability of TR spontaneous Raman spectroscopy to be a valuable tool for probing photoinduced phase transitions in the time domain.

Interfacial thermal and acoustic phenomena have an important role in quantum science and technology, including in spintronic and spincaloritronic materials and devices. Simultaneous measurements of the low-temperature thermal and acoustic properties of a metal/insulator heterostructure reveal distinct dynamics in the characteristic phonon frequency ranges of acoustic and thermal transport. The measurements probed a heterostructure consisting of a thin film of Pt on the ferrimagnetic insulator gadolinium iron garnet (Gd₃Fe₅O₁₂, GdIG) grown epitaxially on a gadolinium gallium garnet substrate. Ultrafast structural dynamics within the Pt layer were tracked using time-resolved ultrafast x-ray diffraction and analyzed to probe interfacial acoustic and thermal properties. The rapid heating of the Pt layer by a 400 nm wavelength femtosecond-duration optical pulse produced transient structural changes that provided the stimulus for these measurements. Rapid heating produced a broadband acoustic pulse that was partially reflected by the Pt/GdIG interface. Temporal frequencies up to 740 GHz, corresponding to angular frequencies of several THz, were detected in a wavelet analysis of the acoustic oscillations of the strain in the Pt layer. The structural results were analyzed to determine (i) the acoustic damping coefficient and phonon mean free path in Pt at frequencies of hundreds of GHz and (ii) the Grüneisen anharmonicity parameter. The thermal conductance of the Pt/GdIG interface was tracked using the slower, tens-of-picosecond-scale, dynamics of the initial cooling of the heated Pt layer. Analysis using a model based on the Boltzmann transport equation shows that the phonon transmission is lower at the phonon frequencies relevant to thermal transport than for subterahertz regime acoustics.

Given proteins' fundamental importance in human health and catalysis, the relationships between protein sequence, structure, dynamics, and function have become a topic of great interest. One way to extract information from proteins is to compute the local energetic frustration of their native state. Traditionally, energetic frustration calculations require protein structures as a starting point. However, using a single protein structure to evaluate the energetic frustration for a given amino acid sequence does not always fully represent the protein's structural ensemble. Therefore, we have developed a sequence-based method to evaluate energetic frustration in proteins using direct coupling analysis and statistical potentials. Our approach exhibits significant agreement with established structure-based frustration methods in terms of their mutual agreement with crystallographic B-factor. Moreover, our sequence-based method shows elevated precision in classifying high B-factor residues, suggesting that it has some robustness to unstructured regions of proteins.

About 100 years ago, the field of structural biology was born, led by James B. Sumner who recognized that enzymes were molecules with specific functions. In its contemporary form structural biology is used to interpret and understand molecular and cellular function, to design drugs, and to advance biotechnology in general.