Simon Chung, Vedran Vonk, David Pennicard, Heinz Graafsma, Andreas Stierle
Pulsed laser heating of an ensemble of Pd nanoparticles, supported by a MgO substrate, is studied by x-ray diffraction. By time-resolved Bragg peak shift measurements due to thermal lattice expansion, the transient temperature of the Pd nanoparticles is determined, which quickly rises by at least 100 K upon laser excitation and then decays within 90 ns. The diffraction experiments were carried out using a Cu x-ray tube, giving continuous radiation, and the hybrid pixel detector Timepix3 operating with single photon counting in a time-of-arrival mode. This type of detection scheme does not require time-consuming scanning of the pump-probe delay. The experimental time resolution is estimated at 15 ± 5 ns, which is very close to the detector's limit and matches with the 7 ns laser pulse duration. Compared to bulk metal single crystals, it is discussed that the maximum temperature reached by the Pd nanoparticles is higher and their cooling rate is lower. These effects are explained by the oxide support having a lower heat conductivity.
通过 X 射线衍射研究了由氧化镁基底支撑的钯纳米粒子群的脉冲激光加热。通过热晶格膨胀引起的时间分辨布拉格峰移测量，确定了钯纳米粒子的瞬态温度，该温度在激光激发后迅速上升至少 100 K，然后在 90 ns 内衰减。衍射实验使用连续辐射的铜 x 射线管和混合像素检测器 Timepix3 进行，Timepix3 在到达时间模式下进行单光子计数。这种检测方案不需要对泵-探针延迟进行耗时的扫描。实验时间分辨率估计为 15 ± 5 ns，非常接近探测器的极限，与 7 ns 的激光脉冲持续时间相匹配。与块状金属单晶相比，钯纳米粒子达到的最高温度更高，冷却速度更低。这些影响的原因是氧化物支架具有较低的热传导率。
{"title":"Transient heating of Pd nanoparticles studied by x-ray diffraction with time of arrival photon detection","authors":"Simon Chung, Vedran Vonk, David Pennicard, Heinz Graafsma, Andreas Stierle","doi":"10.1063/5.0189052","DOIUrl":"https://doi.org/10.1063/5.0189052","url":null,"abstract":"Pulsed laser heating of an ensemble of Pd nanoparticles, supported by a MgO substrate, is studied by x-ray diffraction. By time-resolved Bragg peak shift measurements due to thermal lattice expansion, the transient temperature of the Pd nanoparticles is determined, which quickly rises by at least 100 K upon laser excitation and then decays within 90 ns. The diffraction experiments were carried out using a Cu x-ray tube, giving continuous radiation, and the hybrid pixel detector Timepix3 operating with single photon counting in a time-of-arrival mode. This type of detection scheme does not require time-consuming scanning of the pump-probe delay. The experimental time resolution is estimated at 15 ± 5 ns, which is very close to the detector's limit and matches with the 7 ns laser pulse duration. Compared to bulk metal single crystals, it is discussed that the maximum temperature reached by the Pd nanoparticles is higher and their cooling rate is lower. These effects are explained by the oxide support having a lower heat conductivity.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141547269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Joseph I. J. Ellaway, Stephen Anyango, S. Nair, Hossam A. Zaki, Nurul Nadzirin, Harold R. Powell, Aleksandras Gutmanas, Mihaly Varadi, Sameer Velankar
Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems and treating disease. Despite the deposition of over 215 000 macromolecular structures in the Protein Data Bank and the advent of AI-based structure prediction tools such as AlphaFold2, RoseTTAFold, and ESMFold, static representations are typically produced, which fail to fully capture macromolecular motion. Here, we discuss the importance of integrating experimental structures with computational clustering to explore the conformational landscapes that manifest protein function. We describe the method developed by the Protein Data Bank in Europe – Knowledge Base to identify distinct conformational states, demonstrate the resource's primary use cases, through examples, and discuss the need for further efforts to annotate protein conformations with functional information. Such initiatives will be crucial in unlocking the potential of protein dynamics data, expediting drug discovery research, and deepening our understanding of macromolecular mechanisms.
研究蛋白质动力学和构象异质性对于了解生物分子系统和治疗疾病至关重要。尽管蛋白质数据库（Protein Data Bank）中储存了 215,000 多种大分子结构，而且出现了 AlphaFold2、RoseTTAFold 和 ESMFold 等基于人工智能的结构预测工具，但这些工具通常生成的是静态表征，无法完全捕捉大分子的运动。在此，我们讨论了将实验结构与计算聚类相结合以探索体现蛋白质功能的构象景观的重要性。我们介绍了欧洲蛋白质数据库--知识库（Protein Data Bank in Europe - Knowledge Base）开发的识别不同构象状态的方法，通过实例展示了该资源的主要用例，并讨论了进一步努力为蛋白质构象注释功能信息的必要性。这些举措对于释放蛋白质动力学数据的潜力、加快药物发现研究以及加深我们对大分子机理的理解至关重要。
{"title":"Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies","authors":"Joseph I. J. Ellaway, Stephen Anyango, S. Nair, Hossam A. Zaki, Nurul Nadzirin, Harold R. Powell, Aleksandras Gutmanas, Mihaly Varadi, Sameer Velankar","doi":"10.1063/4.0000251","DOIUrl":"https://doi.org/10.1063/4.0000251","url":null,"abstract":"Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems and treating disease. Despite the deposition of over 215 000 macromolecular structures in the Protein Data Bank and the advent of AI-based structure prediction tools such as AlphaFold2, RoseTTAFold, and ESMFold, static representations are typically produced, which fail to fully capture macromolecular motion. Here, we discuss the importance of integrating experimental structures with computational clustering to explore the conformational landscapes that manifest protein function. We describe the method developed by the Protein Data Bank in Europe – Knowledge Base to identify distinct conformational states, demonstrate the resource's primary use cases, through examples, and discuss the need for further efforts to annotate protein conformations with functional information. Such initiatives will be crucial in unlocking the potential of protein dynamics data, expediting drug discovery research, and deepening our understanding of macromolecular mechanisms.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"14 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141047881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohamed A. K. Othman, Annika E. Gabriel, Emma C. Snively, Michael E. Kozina, Xiaozhe Shen, Fuhao Ji, Samantha Lewis, Stephen Weathersby, Praful Vasireddy, Duan Luo, Xijie Wang, Matthias C. Hoffmann, Emilio A. Nanni
We present an experimental demonstration of ultrafast electron diffraction (UED) with THz-driven electron bunch compression and time-stamping that enables UED probes with improved temporal resolution. Through THz-driven longitudinal bunch compression, a compression factor of approximately four is achieved. Moreover, the time-of-arrival jitter between the compressed electron bunch and a pump laser pulse is suppressed by a factor of three. Simultaneously, the THz interaction imparts a transverse spatiotemporal correlation on the electron distribution, which we utilize to further enhance the precision of time-resolved UED measurements. We use this technique to probe single-crystal gold nanofilms and reveal transient oscillations in the THz near fields with a temporal resolution down to 50 fs. These oscillations were previously beyond reach in the absence of THz compression and time-stamping.
{"title":"Improved temporal resolution in ultrafast electron diffraction measurements through THz compression and time-stamping","authors":"Mohamed A. K. Othman, Annika E. Gabriel, Emma C. Snively, Michael E. Kozina, Xiaozhe Shen, Fuhao Ji, Samantha Lewis, Stephen Weathersby, Praful Vasireddy, Duan Luo, Xijie Wang, Matthias C. Hoffmann, Emilio A. Nanni","doi":"10.1063/4.0000230","DOIUrl":"https://doi.org/10.1063/4.0000230","url":null,"abstract":"We present an experimental demonstration of ultrafast electron diffraction (UED) with THz-driven electron bunch compression and time-stamping that enables UED probes with improved temporal resolution. Through THz-driven longitudinal bunch compression, a compression factor of approximately four is achieved. Moreover, the time-of-arrival jitter between the compressed electron bunch and a pump laser pulse is suppressed by a factor of three. Simultaneously, the THz interaction imparts a transverse spatiotemporal correlation on the electron distribution, which we utilize to further enhance the precision of time-resolved UED measurements. We use this technique to probe single-crystal gold nanofilms and reveal transient oscillations in the THz near fields with a temporal resolution down to 50 fs. These oscillations were previously beyond reach in the absence of THz compression and time-stamping.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140636775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samuel Perrett, Alisia Fadini, Christopher D. M. Hutchison, Sayantan Bhattacharya, Cade Morrison, Oleksii Turkot, Mads Bregenholt Jakobsen, Michael Größler, José Licón-Saláiz, Florian Griese, Samuel Flewett, Joana Valerio, Joachim Schulz, Mykola Biednov, Yifeng Jiang, Huijong Han, Hazem Yousef, Dmitry Khakhulin, Christopher Milne, Anton Barty, Jasper J. van Thor
X-ray Free Electron Lasers (XFELs) allow the collection of high-quality serial femtosecond crystallography data. The next generation of megahertz superconducting FELs promises to drastically reduce data collection times, enabling the capture of more structures with higher signal-to-noise ratios and facilitating more complex experiments. Currently, gas dynamic virtual nozzles (GDVNs) stand as the sole delivery method capable of best utilizing the repetition rate of megahertz sources for crystallography. However, their substantial sample consumption renders their use impractical for many protein targets in serial crystallography experiments. Here, we present a novel application of a droplet-on-demand injection method, which allowed operation at 47 kHz at the European XFEL (EuXFEL) by tailoring a multi-droplet injection scheme for each macro-pulse. We demonstrate a collection rate of 150 000 indexed patterns per hour. We show that the performance and effective data collection rate are comparable to GDVN, with a sample consumption reduction of two orders of magnitude. We present lysozyme crystallographic data using the Large Pixel Detector at the femtosecond x-ray experiment endstation. Significant improvement of the crystallographic statistics was made by correcting for a systematic drift of the photon energy in the EuXFEL macro-pulse train, which was characterized from indexing the individual frames in the pulse train. This is the highest resolution protein structure collected and reported at the EuXFEL at 1.38 Å resolution.
X 射线自由电子激光器（XFEL）可以收集高质量的串行飞秒晶体学数据。下一代百万赫兹超导自由电子激光器有望大幅缩短数据采集时间，以更高的信噪比捕捉更多的结构，促进更复杂的实验。目前，气体动态虚拟喷嘴（GDVN）是唯一一种能够充分利用百万赫兹源重复率进行晶体学研究的传输方式。然而，在连续晶体学实验中，大量的样品消耗使其无法用于许多蛋白质靶标。在这里，我们介绍了一种按需注入液滴方法的新应用，通过为每个宏脉冲定制多液滴注入方案，该方法可在欧洲 XFEL（EuXFEL）上以 47 kHz 的频率运行。我们展示了每小时 150 000 个索引图案的收集率。我们表明，其性能和有效数据收集率与 GDVN 不相上下，而样品消耗量则减少了两个数量级。我们利用飞秒 X 射线实验终端站的大像素探测器展示了溶菌酶晶体学数据。通过校正 EuXFEL 宏脉冲序列中光子能量的系统漂移，晶体学统计数据得到了显著改善。这是 EuXFEL 以 1.38 Å 分辨率收集和报告的最高分辨率蛋白质结构。
{"title":"Kilohertz droplet-on-demand serial femtosecond crystallography at the European XFEL station FXE","authors":"Samuel Perrett, Alisia Fadini, Christopher D. M. Hutchison, Sayantan Bhattacharya, Cade Morrison, Oleksii Turkot, Mads Bregenholt Jakobsen, Michael Größler, José Licón-Saláiz, Florian Griese, Samuel Flewett, Joana Valerio, Joachim Schulz, Mykola Biednov, Yifeng Jiang, Huijong Han, Hazem Yousef, Dmitry Khakhulin, Christopher Milne, Anton Barty, Jasper J. van Thor","doi":"10.1063/4.0000248","DOIUrl":"https://doi.org/10.1063/4.0000248","url":null,"abstract":"X-ray Free Electron Lasers (XFELs) allow the collection of high-quality serial femtosecond crystallography data. The next generation of megahertz superconducting FELs promises to drastically reduce data collection times, enabling the capture of more structures with higher signal-to-noise ratios and facilitating more complex experiments. Currently, gas dynamic virtual nozzles (GDVNs) stand as the sole delivery method capable of best utilizing the repetition rate of megahertz sources for crystallography. However, their substantial sample consumption renders their use impractical for many protein targets in serial crystallography experiments. Here, we present a novel application of a droplet-on-demand injection method, which allowed operation at 47 kHz at the European XFEL (EuXFEL) by tailoring a multi-droplet injection scheme for each macro-pulse. We demonstrate a collection rate of 150 000 indexed patterns per hour. We show that the performance and effective data collection rate are comparable to GDVN, with a sample consumption reduction of two orders of magnitude. We present lysozyme crystallographic data using the Large Pixel Detector at the femtosecond x-ray experiment endstation. Significant improvement of the crystallographic statistics was made by correcting for a systematic drift of the photon energy in the EuXFEL macro-pulse train, which was characterized from indexing the individual frames in the pulse train. This is the highest resolution protein structure collected and reported at the EuXFEL at 1.38 Å resolution.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"302 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140611397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This paper introduces spectral incoherent diffractive imaging (SIDI) as a novel method for achieving dark-field imaging of nanostructures with heterogeneous oxidation states. With SIDI, shifts in photoemission profiles can be spatially resolved, enabling the independent imaging of the underlying emitter distributions contributing to each spectral line. In the x-ray domain, this approach offers unique insights beyond the conventional combination of diffraction and x-ray emission spectroscopy. When applied at x-ray free-electron lasers, SIDI promises to be a versatile tool for investigating a broad range of systems, offering unprecedented opportunities for detailed characterization of heterogeneous nanostructures for catalysis and energy storage, including of their ultrafast dynamics.
本文介绍了光谱非相干衍射成像（SIDI），这是一种对具有异质氧化态的纳米结构进行暗场成像的新方法。利用 SIDI，可以在空间上分辨光发射轮廓的变化，从而对每条光谱线的潜在发射体分布进行独立成像。在 X 射线领域，这种方法提供了超越传统衍射和 X 射线发射光谱组合的独特见解。当应用于 X 射线自由电子激光器时，SIDI有望成为研究各种系统的多功能工具，为详细描述催化和储能用的异质纳米结构（包括其超快动力学）提供前所未有的机会。
{"title":"Nanoscale x-ray imaging with high spectral sensitivity using fluorescence intensity correlations","authors":"Tamme Wollweber, Kartik Ayyer","doi":"10.1063/4.0000245","DOIUrl":"https://doi.org/10.1063/4.0000245","url":null,"abstract":"This paper introduces spectral incoherent diffractive imaging (SIDI) as a novel method for achieving dark-field imaging of nanostructures with heterogeneous oxidation states. With SIDI, shifts in photoemission profiles can be spatially resolved, enabling the independent imaging of the underlying emitter distributions contributing to each spectral line. In the x-ray domain, this approach offers unique insights beyond the conventional combination of diffraction and x-ray emission spectroscopy. When applied at x-ray free-electron lasers, SIDI promises to be a versatile tool for investigating a broad range of systems, offering unprecedented opportunities for detailed characterization of heterogeneous nanostructures for catalysis and energy storage, including of their ultrafast dynamics.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140613281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Georgii Khusainov, Joerg Standfuss, Tobias Weinert
Macromolecular crystallography has historically provided the atomic structures of proteins fundamental to cellular functions. However, the advent of cryo-electron microscopy for structure determination of large and increasingly smaller and flexible proteins signaled a paradigm shift in structural biology. The extensive structural and sequence data from crystallography and advanced sequencing techniques have been pivotal for training computational models for accurate structure prediction, unveiling the general fold of most proteins. Here, we present a perspective on the rise of time-resolved crystallography as the new frontier of macromolecular structure determination. We trace the evolution from the pioneering time-resolved crystallography methods to modern serial crystallography, highlighting the synergy between rapid detection technologies and state-of-the-art x-ray sources. These innovations are redefining our exploration of protein dynamics, with high-resolution crystallography uniquely positioned to elucidate rapid dynamic processes at ambient temperatures, thus deepening our understanding of protein functionality. We propose that the integration of dynamic structural data with machine learning advancements will unlock predictive capabilities for protein kinetics, revolutionizing dynamics like macromolecular crystallography revolutionized structural biology.
大分子晶体学历来提供对细胞功能至关重要的蛋白质原子结构。然而，冷冻电镜技术的出现标志着结构生物学范式的转变，该技术可用于确定大型蛋白质以及越来越小和越来越灵活的蛋白质的结构。来自晶体学和先进测序技术的大量结构和序列数据对于训练精确结构预测的计算模型至关重要，揭示了大多数蛋白质的一般折叠。在此，我们从时间分辨晶体学作为大分子结构测定新前沿的崛起角度进行了阐述。我们追溯了从开创性的时间分辨晶体学方法到现代序列晶体学的演变过程，强调了快速检测技术与最先进的 X 射线源之间的协同作用。这些创新正在重新定义我们对蛋白质动态的探索，高分辨率晶体学在阐明常温下的快速动态过程方面具有得天独厚的优势，从而加深了我们对蛋白质功能的理解。我们认为，将动态结构数据与机器学习的进步相结合，将开启蛋白质动力学的预测能力，从而彻底改变动力学，就像大分子晶体学彻底改变结构生物学一样。
{"title":"The time revolution in macromolecular crystallography","authors":"Georgii Khusainov, Joerg Standfuss, Tobias Weinert","doi":"10.1063/4.0000247","DOIUrl":"https://doi.org/10.1063/4.0000247","url":null,"abstract":"Macromolecular crystallography has historically provided the atomic structures of proteins fundamental to cellular functions. However, the advent of cryo-electron microscopy for structure determination of large and increasingly smaller and flexible proteins signaled a paradigm shift in structural biology. The extensive structural and sequence data from crystallography and advanced sequencing techniques have been pivotal for training computational models for accurate structure prediction, unveiling the general fold of most proteins. Here, we present a perspective on the rise of time-resolved crystallography as the new frontier of macromolecular structure determination. We trace the evolution from the pioneering time-resolved crystallography methods to modern serial crystallography, highlighting the synergy between rapid detection technologies and state-of-the-art x-ray sources. These innovations are redefining our exploration of protein dynamics, with high-resolution crystallography uniquely positioned to elucidate rapid dynamic processes at ambient temperatures, thus deepening our understanding of protein functionality. We propose that the integration of dynamic structural data with machine learning advancements will unlock predictive capabilities for protein kinetics, revolutionizing dynamics like macromolecular crystallography revolutionized structural biology.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140591740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Friedrich Schotte, Hyun Sun Cho, Fred Dyda, Philip Anfinrud
Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.
{"title":"Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein","authors":"Friedrich Schotte, Hyun Sun Cho, Fred Dyda, Philip Anfinrud","doi":"10.1063/4.0000241","DOIUrl":"https://doi.org/10.1063/4.0000241","url":null,"abstract":"Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140591657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chiwon Lee, Günther H. Kassier, R. J. Dwayne Miller
For time-resolved diffraction studies of irreversible structural dynamics upon photoexcitation, there are constraints on the number of perturbation cycles due to thermal effects and accumulated strain, which impact the degree of crystal order and spatial resolution. This problem is exasperated for surface studies that are more prone to disordering and defect formation. Ultrafast electron diffraction studies of these systems, with the conventional stroboscopic pump–probe protocol, require repetitive measurements on well-prepared diffraction samples to acquire and average signals above background in the dynamic range of interest from few tens to hundreds of picoseconds. Here, we present ultrafast streaked low-energy electron diffraction (LEED) that demands, in principle, only a single excitation per nominal data acquisition timeframe. By exploiting the space–time correlation characteristics of the streaking method and high-charge 2 keV electron bunches in the transmission geometry, we demonstrate about one order of magnitude reduction in the accumulated number of the excitation cycles and total electron dose, and 48% decrease in the root mean square error of the model fit residual compared to the conventional time-scanning measurement. We believe that our results demonstrate a viable alternative method with higher sensitivity to that of nanotip-based ultrafast LEED studies relying on a few electrons per a single excitation, to access to all classes of structural dynamics to provide an atomic level view of surface processes.
{"title":"High bunch charge low-energy electron streak diffraction","authors":"Chiwon Lee, Günther H. Kassier, R. J. Dwayne Miller","doi":"10.1063/4.0000246","DOIUrl":"https://doi.org/10.1063/4.0000246","url":null,"abstract":"For time-resolved diffraction studies of irreversible structural dynamics upon photoexcitation, there are constraints on the number of perturbation cycles due to thermal effects and accumulated strain, which impact the degree of crystal order and spatial resolution. This problem is exasperated for surface studies that are more prone to disordering and defect formation. Ultrafast electron diffraction studies of these systems, with the conventional stroboscopic pump–probe protocol, require repetitive measurements on well-prepared diffraction samples to acquire and average signals above background in the dynamic range of interest from few tens to hundreds of picoseconds. Here, we present ultrafast streaked low-energy electron diffraction (LEED) that demands, in principle, only a single excitation per nominal data acquisition timeframe. By exploiting the space–time correlation characteristics of the streaking method and high-charge 2 keV electron bunches in the transmission geometry, we demonstrate about one order of magnitude reduction in the accumulated number of the excitation cycles and total electron dose, and 48% decrease in the root mean square error of the model fit residual compared to the conventional time-scanning measurement. We believe that our results demonstrate a viable alternative method with higher sensitivity to that of nanotip-based ultrafast LEED studies relying on a few electrons per a single excitation, to access to all classes of structural dynamics to provide an atomic level view of surface processes.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140591661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hui-Yuan Chen, Rolf B. Versteeg, Roman Mankowsky, Michele Puppin, Ludmila Leroy, Mathias Sander, Yunpei Deng, Roland Alexander Oggenfuss, Thierry Zamofing, Pirmin Böhler, Claude Pradervand, Aldo Mozzanica, Seraphin Vetter, Grigory Smolentsev, Linda Kerkhoff, Henrik T. Lemke, Majed Chergui, Giulia F. Mancini
We present a new setup for resonant inelastic hard x-ray scattering at the Bernina beamline of SwissFEL with energy, momentum, and temporal resolution. The compact R = 0.5 m Johann-type spectrometer can be equipped with up to three crystal analyzers and allows efficient collection of RIXS spectra. Optical pumping for time-resolved studies can be realized with a broad span of optical wavelengths. We demonstrate the performance of the setup at an overall ∼180 meV resolution in a study of ground-state and photoexcited (at 400 nm) honeycomb 5d iridate α-Li2IrO3. Steady-state RIXS spectra at the iridium L3-edge (11.214 keV) have been collected and are in very good agreement with data collected at synchrotrons. The time-resolved RIXS transients exhibit changes in the energy loss region <2 eV, whose features mostly result from the hopping nature of 5d electrons in the honeycomb lattice. These changes are ascribed to modulations of the Ir-to-Ir inter-site transition scattering efficiency, which we associate to a transient screening of the on-site Coulomb interaction.
我们在 SwissFEL 的 Bernina 光束线展示了一种用于共振非弹性硬 X 射线散射的新装置，具有能量、动量和时间分辨率。紧凑型 R = 0.5 m 约翰型光谱仪最多可配备三个晶体分析仪，可高效地收集 RIXS 光谱。时间分辨研究的光学泵浦可通过广泛的光学波长实现。我们在对基态和光激发（400 纳米波长）蜂窝状 5d iridate α-Li2IrO3 的研究中展示了该装置的性能，总体分辨率达到 180 meV。在铱 L3 边沿（11.214 千伏）收集到的稳态 RIXS 光谱与同步加速器收集到的数据非常吻合。时间分辨 RIXS 瞬变在能量损失区 <2 eV 显示出变化，其特征主要来自蜂窝晶格中 5d 电子的跳跃特性。这些变化归因于 "Ir-Ir "位间转变散射效率的调节，我们将其与 "Ir-Ir "位间库仑相互作用的瞬时屏蔽联系起来。
{"title":"A setup for hard x-ray time-resolved resonant inelastic x-ray scattering at SwissFEL","authors":"Hui-Yuan Chen, Rolf B. Versteeg, Roman Mankowsky, Michele Puppin, Ludmila Leroy, Mathias Sander, Yunpei Deng, Roland Alexander Oggenfuss, Thierry Zamofing, Pirmin Böhler, Claude Pradervand, Aldo Mozzanica, Seraphin Vetter, Grigory Smolentsev, Linda Kerkhoff, Henrik T. Lemke, Majed Chergui, Giulia F. Mancini","doi":"10.1063/4.0000236","DOIUrl":"https://doi.org/10.1063/4.0000236","url":null,"abstract":"We present a new setup for resonant inelastic hard x-ray scattering at the Bernina beamline of SwissFEL with energy, momentum, and temporal resolution. The compact R = 0.5 m Johann-type spectrometer can be equipped with up to three crystal analyzers and allows efficient collection of RIXS spectra. Optical pumping for time-resolved studies can be realized with a broad span of optical wavelengths. We demonstrate the performance of the setup at an overall ∼180 meV resolution in a study of ground-state and photoexcited (at 400 nm) honeycomb 5d iridate α-Li2IrO3. Steady-state RIXS spectra at the iridium L3-edge (11.214 keV) have been collected and are in very good agreement with data collected at synchrotrons. The time-resolved RIXS transients exhibit changes in the energy loss region &lt;2 eV, whose features mostly result from the hopping nature of 5d electrons in the honeycomb lattice. These changes are ascribed to modulations of the Ir-to-Ir inter-site transition scattering efficiency, which we associate to a transient screening of the on-site Coulomb interaction.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140591668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaoyi Sun, Joseph Williams, Sachin Sharma, Shriraj Kunjir, Dan Morris, Shen Zhao, Chong-Yu Ruan
We report on the first detailed beam tests attesting the fundamental principle behind the development of high-current-efficiency ultrafast electron microscope systems where a radio frequency (RF) cavity is incorporated as a condenser lens in the beam delivery system. To allow for the experiment to be carried out with a sufficient resolution to probe the performance at the emittance floor, a new cascade loop RF controller system is developed to reduce the RF noise floor. Temporal resolution at 50 fs in full-width-at-half-maximum and detection sensitivity better than 1% are demonstrated on exfoliated 1T-TaSe2 system under a moderate repetition rate. To benchmark the performance, multi-terahertz edge-mode coherent phonon excitation is employed as the standard candle. The high temporal resolution and the significant visibility to very low dynamical contrast in diffraction signals via high-precision phase-space manipulation give strong support to the working principle for the new high-brightness femtosecond electron microscope systems.
{"title":"Precision-controlled ultrafast electron microscope platforms. A case study: Multiple-order coherent phonon dynamics in 1T-TaSe2 probed at 50 fs–10 fm scales","authors":"Xiaoyi Sun, Joseph Williams, Sachin Sharma, Shriraj Kunjir, Dan Morris, Shen Zhao, Chong-Yu Ruan","doi":"10.1063/4.0000242","DOIUrl":"https://doi.org/10.1063/4.0000242","url":null,"abstract":"We report on the first detailed beam tests attesting the fundamental principle behind the development of high-current-efficiency ultrafast electron microscope systems where a radio frequency (RF) cavity is incorporated as a condenser lens in the beam delivery system. To allow for the experiment to be carried out with a sufficient resolution to probe the performance at the emittance floor, a new cascade loop RF controller system is developed to reduce the RF noise floor. Temporal resolution at 50 fs in full-width-at-half-maximum and detection sensitivity better than 1% are demonstrated on exfoliated 1T-TaSe2 system under a moderate repetition rate. To benchmark the performance, multi-terahertz edge-mode coherent phonon excitation is employed as the standard candle. The high temporal resolution and the significant visibility to very low dynamical contrast in diffraction signals via high-precision phase-space manipulation give strong support to the working principle for the new high-brightness femtosecond electron microscope systems.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140591513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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