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Appraising protein conformational changes by resampling time-resolved serial x-ray crystallography data. 通过重采样时间分辨序列 X 射线晶体学数据评估蛋白质构象变化
IF 2.3 2区 物理与天体物理 Q3 CHEMISTRY, PHYSICAL Pub Date : 2024-07-24 eCollection Date: 2024-07-01 DOI: 10.1063/4.0000258
Adams Vallejos, Gergely Katona, Richard Neutze

With the development of serial crystallography at both x-ray free electron laser and synchrotron radiation sources, time-resolved x-ray crystallography is increasingly being applied to study conformational changes in macromolecules. A successful time-resolved serial crystallography study requires the growth of microcrystals, a mechanism for synchronized and homogeneous excitation of the reaction of interest within microcrystals, and tools for structural interpretation. Here, we utilize time-resolved serial femtosecond crystallography data collected from microcrystals of bacteriorhodopsin to compare results from partial occupancy structural refinement and refinement against extrapolated data. We illustrate the domain wherein the amplitude of refined conformational changes is inversely proportional to the activated state occupancy. We illustrate how resampling strategies allow coordinate uncertainty to be estimated and demonstrate that these two approaches to structural refinement agree within coordinate errors. We illustrate how singular value decomposition of a set of difference Fourier electron density maps calculated from resampled data can minimize phase bias in these maps, and we quantify residual densities for transient water molecules by analyzing difference Fourier and Polder omit maps from resampled data. We suggest that these tools may assist others in judging the confidence with which observed electron density differences may be interpreted as functionally important conformational changes.

随着 X 射线自由电子激光和同步辐射源系列晶体学的发展,时间分辨 X 射线晶体学正越来越多地应用于研究大分子的构象变化。成功的时间分辨序列晶体学研究需要微晶体的生长、微晶体内相关反应的同步和均匀激发机制以及结构解释工具。在这里,我们利用从细菌眼色素微晶体中收集到的时间分辨串行飞秒晶体学数据,比较了部分占位结构细化和根据外推数据细化的结果。我们说明了细化构象变化的幅度与激活状态占位成反比的领域。我们说明了重采样策略如何允许估计坐标不确定性,并证明这两种结构细化方法在坐标误差范围内是一致的。我们说明了通过重采样数据计算出的一组差分傅立叶电子密度图的奇异值分解如何最大限度地减少这些图中的相位偏差,我们还通过分析重采样数据中的差分傅立叶图和波德省略图量化了瞬态水分子的残余密度。我们认为这些工具可以帮助他人判断观察到的电子密度差异是否可以解释为具有重要功能的构象变化。
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引用次数: 0
Preface to Special Topic: The Advent of Ultrafast X-Ray Absorption Spectroscopy. 专题序言:超快 X 射线吸收光谱学的到来。
IF 2.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-06-21 eCollection Date: 2024-05-01 DOI: 10.1063/4.0000259
Emiliano Principi
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引用次数: 0
A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics. 时间分辨 X 射线和电子散射探测结构动态的比较综述。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-05-01 DOI: 10.1063/4.0000249
Yunbeom Lee, Key Young Oang, Doyeong Kim, Hyotcherl Ihee

The structure of molecules, particularly the dynamic changes in structure, plays an essential role in understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through scattering signals. Over the past decade, the advent of x-ray free-electron lasers (XFELs) and mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR scattering experiments into a new era, garnering significant attention. In this review, we delve into the basic principles of TR scattering experiments, especially focusing on those that employ x-rays and electrons. We highlight the variations in experimental conditions when employing x-rays vs electrons and discuss their complementarity. Additionally, cutting-edge XFELs and MeV-UED facilities for TR x-ray and electron scattering experiments and the experiments performed at those facilities are reviewed. As new facilities are constructed and existing ones undergo upgrades, the landscape for TR x-ray and electron scattering experiments is poised for further expansion. Through this review, we aim to facilitate the effective utilization of these emerging opportunities, assisting researchers in delving deeper into the intricate dynamics of molecular structures.

分子结构,尤其是结构的动态变化,对理解物理和化学现象起着至关重要的作用。时间分辨(TR)散射技术是研究结构动态的重要实验工具,通过散射信号提供对分子结构的直接敏感性。在过去十年中,X 射线自由电子激光器(XFEL)和兆电子伏特超快电子衍射(MeV-UED)设备的出现将 TR 散射实验带入了一个新时代,引起了广泛关注。在这篇综述中,我们将深入探讨 TR 散射实验的基本原理,尤其是那些采用 X 射线和电子的实验。我们强调了采用 X 射线和电子时实验条件的不同,并讨论了它们之间的互补性。此外,我们还回顾了用于 TR x 射线和电子散射实验的 XFEL 和 MeV-UED 尖端设备以及在这些设备上进行的实验。随着新设施的建设和现有设施的升级,TR x射线和电子散射实验的范围将进一步扩大。通过本综述,我们旨在促进有效利用这些新兴机会,帮助研究人员深入研究分子结构的复杂动力学。
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引用次数: 0
High-energy-resolution off-resonant spectroscopy with self-seeded x-ray free-electron laser pulses. 利用自种子 X 射线自由电子激光脉冲进行高能分辨率非共振光谱分析。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-03-26 eCollection Date: 2024-03-01 DOI: 10.1063/4.0000243
Jang Hyeob Sohn, Gyeongbo Kang, Tae-Kyu Choi, Gyusang Lee, Changhoo Lee, Sae Hwan Chun, Jaeku Park, Dongbin Shin, Byoung-Ick Cho

This paper presents the implementation of high-energy-resolution off-resonant spectroscopy (HEROS) measurements using self-seeded x-ray free-electron laser (XFEL) pulses. This study systematically investigated XFEL conditions, including photon energy and accumulated shot numbers, to optimize the measurement efficiency for copper foil samples near the K-edge. The x-ray absorption spectra reconstructed using HEROS were compared with those derived from fluorescence-yield measurements. The HEROS-based spectra exhibited consistent line shapes independent of the sample thickness. The potential application of HEROS to high-temperature copper was also explored. HEROS offers distinct advantages including scan-free measurement of x-ray absorption spectra with reduced core-hole lifetime broadening and self-absorption effects. Using self-seeded XFEL pulses, HEROS facilitates single-shot-based pump-probe measurements to investigate the ultrafast dynamics in various materials and diverse conditions.

本文介绍了利用自播散 X 射线自由电子激光(XFEL)脉冲实施高能分辨率非共振光谱(HEROS)测量的情况。这项研究系统地研究了 XFEL 的条件,包括光子能量和累积发射数,以优化 K 边附近铜箔样品的测量效率。使用 HEROS 重建的 X 射线吸收光谱与荧光产率测量得出的光谱进行了比较。基于 HEROS 的光谱显示出一致的线形,与样品厚度无关。此外,还探讨了 HEROS 在高温铜方面的潜在应用。HEROS 具有明显的优势,包括免扫描测量 X 射线吸收光谱,减少了芯孔寿命展宽和自吸收效应。利用自seed XFEL 脉冲,HEROS 可进行基于泵探头的单次测量,以研究各种材料和各种条件下的超快动力学。
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引用次数: 0
Vector-based feedback of continuous wave radiofrequency compression cavity for ultrafast electron diffraction. 基于矢量反馈的连续波射频压缩腔用于超快电子衍射。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-03-25 eCollection Date: 2024-03-01 DOI: 10.1063/4.0000231
Thomas M Sutter, Joshua S H Lee, Atharva V Kulkarni, Pietro Musumeci, Anshul Kogar

The temporal resolution of ultrafast electron diffraction at weakly relativistic beam energies (100 keV) suffers from space-charge induced electron pulse broadening. We describe the implementation of a radio frequency (RF) cavity operating in the continuous wave regime to compress high repetition rate electron bunches from a 40.4 kV DC photoinjector for ultrafast electron diffraction applications. Active stabilization of the RF amplitude and phase through a feedback loop based on the demodulated in-phase and quadrature components of the RF signal is demonstrated. This scheme yields 144 ± 19 fs RMS temporal resolution in pump-probe studies.

弱相对论光束能量(≲100 keV)下的超快电子衍射的时间分辨率受到空间电荷引起的电子脉冲展宽的影响。我们介绍了如何利用在连续波条件下工作的射频(RF)腔来压缩来自 40.4 千伏直流光注入器的高重复率电子束,从而实现超快电子衍射应用。通过基于射频信号的解调同相和正交分量的反馈回路,对射频振幅和相位进行主动稳定。在泵探研究中,该方案可获得 144 ± 19 fs RMS 时间分辨率。
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引用次数: 0
High energy electron diffraction instrument with tunable camera length. 相机长度可调的高能电子衍射仪。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-03-25 eCollection Date: 2024-03-01 DOI: 10.1063/4.0000240
P Denham, Y Yang, V Guo, A Fisher, X Shen, T Xu, R J England, R K Li, P Musumeci

Ultrafast electron diffraction (UED) stands as a powerful technique for real-time observation of structural dynamics at the atomic level. In recent years, the use of MeV electrons from radio frequency guns has been widely adopted to take advantage of the relativistic suppression of the space charge effects that otherwise limit the temporal resolution of the technique. Nevertheless, there is not a clear choice for the optimal energy for a UED instrument. Scaling to beam energies higher than a few MeV does pose significant technical challenges, mainly related to the inherent increase in diffraction camera length associated with the smaller Bragg angles. In this study, we report a solution by using a compact post-sample magnetic optical system to magnify the diffraction pattern from a crystal Au sample illuminated by an 8.2 MeV electron beam. Our method employs, as one of the lenses of the optical system, a triplet of compact, high field gradients (>500 T/m), small-gap (3.5 mm) Halbach permanent magnet quadrupoles. Shifting the relative position of the quadrupoles, we demonstrate tuning the magnification by more than a factor of two, a 6× improvement in camera length, and reciprocal space resolution better than 0.1 Å-1 in agreement with beam transport simulations.

超快电子衍射(UED)是一种实时观测原子级结构动态的强大技术。近年来,人们广泛采用射频枪发射的兆电子伏(MeV)电子,以利用相对论抑制空间电荷效应的优势,否则空间电荷效应将限制该技术的时间分辨率。然而,UED 仪器的最佳能量并没有明确的选择。放大到高于几 MeV 的光束能量确实会带来巨大的技术挑战,这主要与布拉格角变小导致衍射相机长度增加有关。在本研究中,我们报告了一种解决方案,即使用紧凑型后样品磁性光学系统来放大由 8.2 MeV 电子束照射的晶体金样品的衍射图样。作为光学系统的透镜之一,我们的方法采用了紧凑型、高场梯度(>500 T/m)、小间隙(3.5 mm)哈尔巴赫永磁四极杆。通过移动四极杆的相对位置,我们展示了将放大倍率调整了两倍多,相机长度提高了 6 倍,倒数空间分辨率优于 0.1 Å-1,与光束传输模拟一致。
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引用次数: 0
Conformational dynamics of adenylate kinase in crystals. 晶体中腺苷酸激酶的构象动力学。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-02-21 eCollection Date: 2024-01-01 DOI: 10.1063/4.0000205
Junhyung Kim, Sojin Moon, Tod D Romo, Yifei Yang, Euiyoung Bae, George N Phillips

Adenylate kinase is a ubiquitous enzyme in living systems and undergoes dramatic conformational changes during its catalytic cycle. For these reasons, it is widely studied by genetic, biochemical, and biophysical methods, both experimental and theoretical. We have determined the basic crystal structures of three differently liganded states of adenylate kinase from Methanotorrus igneus, a hyperthermophilic organism whose adenylate kinase is a homotrimeric oligomer. The multiple copies of each protomer in the asymmetric unit of the crystal provide a unique opportunity to study the variation in the structure and were further analyzed using advanced crystallographic refinement methods and analysis tools to reveal conformational heterogeneity and, thus, implied dynamic behaviors in the catalytic cycle.

腺苷酸激酶是生命系统中一种无处不在的酶,在其催化周期中会发生巨大的构象变化。因此,人们通过遗传学、生物化学和生物物理学等实验和理论方法对其进行了广泛的研究。我们测定了来自嗜热微生物 Methanotorrus igneus 的腺苷酸激酶的三种不同配位状态的基本晶体结构。在晶体的不对称单元中,每个原体都有多个拷贝,这为研究结构的变化提供了一个独特的机会,利用先进的晶体学细化方法和分析工具对其进行了进一步分析,以揭示构象的异质性,从而揭示催化循环中的动态行为。
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引用次数: 0
Advanced manufacturing provides tailor-made solutions for crystallography with x-ray free-electron lasers. 先进的制造技术为使用 X 射线自由电子激光器进行晶体学研究提供量身定制的解决方案。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-02-21 eCollection Date: 2024-01-01 DOI: 10.1063/4.0000229
Lars Paulson, Sankar Raju Narayanasamy, Megan L Shelby, Matthias Frank, Martin Trebbin

Serial crystallography at large facilities, such as x-ray free-electron lasers and synchrotrons, evolved as a powerful method for the high-resolution structural investigation of proteins that are critical for human health, thus advancing drug discovery and novel therapies. However, a critical barrier to successful serial crystallography experiments lies in the efficient handling of the protein microcrystals and solutions at microscales. Microfluidics are the obvious approach for any high-throughput, nano-to-microliter sample handling, that also requires design flexibility and rapid prototyping to deal with the variable shapes, sizes, and density of crystals. Here, we discuss recent advances in polymer 3D printing for microfluidics-based serial crystallography research and present a demonstration of emerging, large-scale, nano-3D printing approaches leading into the future of 3D sample environment and delivery device fabrication from liquid jet gas-dynamic virtual nozzles devices to fixed-target sample environment technology.

在大型设备(如 X 射线自由电子激光器和同步加速器)上进行序列晶体学研究,是对人类健康至关重要的蛋白质进行高分辨率结构研究的有力方法,从而推动了药物发现和新型疗法的发展。然而,序列晶体学实验成功的一个关键障碍在于如何在微观尺度上有效处理蛋白质微晶体和溶液。微流控技术是处理纳米到微升级高通量样品的不二法门,但这也需要设计的灵活性和快速原型,以处理晶体的不同形状、大小和密度。在此,我们将讨论聚合物三维打印在基于微流控技术的串行晶体学研究中的最新进展,并展示新兴的大规模纳米三维打印方法,这些方法将引领未来的三维样品环境和输送装置制造,从液体喷射气体动态虚拟喷嘴装置到固定目标样品环境技术。
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引用次数: 0
Raw diffraction data and reproducibility. 原始衍射数据和重现性。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-02-14 eCollection Date: 2024-01-01 DOI: 10.1063/4.0000232
Loes M J Kroon-Batenburg, Matthew P Lightfoot, Natalie T Johnson, John R Helliwell

In recent years, there has been a major expansion in digital storage capability for hosting raw diffraction datasets. Naturally, the question has now arisen as to the benefits and costs for the preservation of such raw, i.e., experimental diffraction datasets. We describe the consultations made of the global structural chemistry, i.e., chemical crystallography community from the points of view of the International Union of Crystallography (IUCr) Committee on Data, of which JRH was the Chair until very recently, and the IUCrData Raw Data Letters initiative, for which LKB is the Main Editor. The monitoring by the CCDC of CSD depositions which cite the digital object identifiers of raw diffraction datasets provides interesting statistics by probe (x-ray, neutron, or electron) and by home lab vs central facility. Clearly, a better understanding of the reproducibility of current analysis procedures is at hand. Policies for publication requiring raw data have been updated in IUCr Journals for macromolecular crystallography, namely, that raw data should be made available for a new crystal structure or a new method as well as the wwPDB deposition. For chemical crystallography, such a step requiring raw data archiving has not yet been recommended by the IUCr Commission on Structural Chemistry.

近年来,用于保存原始衍射数据集的数字存储能力大幅提高。自然而然,现在就出现了保存这些原始衍射数据集(即实验衍射数据集)的好处和成本问题。我们介绍了从国际晶体学联盟(IUCr)数据委员会(JRH 直到最近一直担任该委员会主席)和 IUCrData 原始数据信函(LKB 是该信函的主编)的角度对全球结构化学(即化学晶体学)界进行的咨询。CCDC对引用原始衍射数据集的数字对象标识符的CSD存放情况进行了监测,提供了按探针(X射线、中子或电子)和按家庭实验室与中央设施划分的有趣统计数据。显然,我们可以更好地了解当前分析程序的可重复性。IUCr 期刊已更新了大分子晶体学需要原始数据的出版政策,即新晶体结构或新方法以及 wwPDB 沉积均应提供原始数据。在化学晶体学方面,IUCr 结构化学委员会尚未建议采取这种要求原始数据存档的步骤。
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引用次数: 0
Coherent acoustic phonons in a coupled hexagonal boron nitride-graphite heterostructure. 耦合六方氮化硼-石墨异质结构中的相干声子。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-02-14 eCollection Date: 2024-01-01 DOI: 10.1063/4.0000228
Arne Ungeheuer, Nora Bach, Mashood T Mir, Ahmed S Hassanien, Lukas Nöding, Thomas Baumert, Sascha Schäfer, Arne Senftleben

Femtosecond optically excited coherent acoustic phonon modes (CAPs) are investigated in a free-standing van der Waals heterostructure composed of a 20-nm transparent hexagonal boron nitride (hBN) and a 42-nm opaque graphite layer. Employing ultrafast electron diffraction, which allows for the independent evaluation of strain dynamics in the constituent material layers, three different CAP modes are identified within the bilayer stack after the optical excitation of the graphite layer. An analytical model is used to discuss the creation of individual CAP modes. Furthermore, their excitation mechanisms in the heterostructure are inferred from the relative phases of these modes by comparison with a numerical linear-chain model. The results support an ultrafast heat transfer mechanism from graphite to the hBN lattice system, which is important to consider when using this material combination in devices.

在由 20 纳米透明六方氮化硼(hBN)和 42 纳米不透明石墨层组成的独立范德华异质结构中研究了飞秒光激发相干声子模式(CAP)。利用超快电子衍射(可独立评估组成材料层中的应变动态),在对石墨层进行光激发后,在双层堆栈中确定了三种不同的 CAP 模式。分析模型用于讨论单个 CAP 模式的产生。此外,通过与数值线性链模型进行比较,从这些模式的相对相位推断出它们在异质结构中的激发机制。研究结果支持从石墨到 hBN 晶格系统的超快热传导机制,这对于在设备中使用这种材料组合非常重要。
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引用次数: 0
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