Structural Dynamics最新文献

Transient heating of Pd nanoparticles studied by x-ray diffraction with time of arrival photon detection 通过 X 射线衍射和到达时间光子探测研究钯纳米粒子的瞬态加热

Structural Dynamics Pub Date : 2024-07-03 DOI: 10.1063/5.0189052

Simon Chung, Vedran Vonk, David Pennicard, Heinz Graafsma, Andreas Stierle

引用次数: 0

Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies 在蛋白质数据库中识别蛋白质构象状态：挖掘综合动力学研究的潜力

Structural Dynamics Pub Date : 2024-05-01 DOI: 10.1063/4.0000251

Joseph I. J. Ellaway, Stephen Anyango, S. Nair, Hossam A. Zaki, Nurul Nadzirin, Harold R. Powell, Aleksandras Gutmanas, Mihaly Varadi, Sameer Velankar

{"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}

引用次数: 0

Improved temporal resolution in ultrafast electron diffraction measurements through THz compression and time-stamping 通过太赫兹压缩和时间标记提高超快电子衍射测量的时间分辨率

Structural Dynamics Pub Date : 2024-04-22 DOI: 10.1063/4.0000230

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

引用次数: 0

Kilohertz droplet-on-demand serial femtosecond crystallography at the European XFEL station FXE 欧洲 XFEL 站 FXE 的千赫兹按需液滴串行飞秒晶体学技术

Structural Dynamics Pub Date : 2024-04-17 DOI: 10.1063/4.0000248

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

{"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}

引用次数: 0

Nanoscale x-ray imaging with high spectral sensitivity using fluorescence intensity correlations 利用荧光强度相关性实现具有高光谱灵敏度的纳米级 X 射线成像

Structural Dynamics Pub Date : 2024-04-17 DOI: 10.1063/4.0000245

Tamme Wollweber, Kartik Ayyer

引用次数: 0

The time revolution in macromolecular crystallography 大分子晶体学的时间革命

Structural Dynamics Pub Date : 2024-04-12 DOI: 10.1063/4.0000247

Georgii Khusainov, Joerg Standfuss, Tobias Weinert

{"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}

引用次数: 0

Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein 观察信号蛋白的功能：四十年来对光活性黄蛋白进行时间分辨研究的收获

Structural Dynamics Pub Date : 2024-04-08 DOI: 10.1063/4.0000241

Friedrich Schotte, Hyun Sun Cho, Fred Dyda, Philip Anfinrud

{"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}

引用次数: 0

High bunch charge low-energy electron streak diffraction 高串电荷低能电子条纹衍射

Structural Dynamics Pub Date : 2024-04-08 DOI: 10.1063/4.0000246

Chiwon Lee, Günther H. Kassier, R. J. Dwayne Miller

{"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}

引用次数: 0

A setup for hard x-ray time-resolved resonant inelastic x-ray scattering at SwissFEL 在 SwissFEL 进行硬 X 射线时间分辨共振非弹性 X 射线散射的装置

Structural Dynamics Pub Date : 2024-04-05 DOI: 10.1063/4.0000236

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

{"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}

引用次数: 0

Precision-controlled ultrafast electron microscope platforms. A case study: Multiple-order coherent phonon dynamics in 1T-TaSe2 probed at 50 fs–10 fm scales 精确控制的超快电子显微镜平台。案例研究：以 50 fs-10 fm 的尺度探测 1T-TaSe2 中的多阶相干声子动力学

Structural Dynamics Pub Date : 2024-04-01 DOI: 10.1063/4.0000242

Xiaoyi Sun, Joseph Williams, Sachin Sharma, Shriraj Kunjir, Dan Morris, Shen Zhao, Chong-Yu Ruan

引用次数: 0