Structural Dynamics-Us最新文献_第2页

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

Structural Dynamics-Us Pub Date : 2024-07-24 eCollection Date: 2024-07-01 DOI: 10.1063/4.0000258

Adams Vallejos, Gergely Katona, Richard Neutze

{"title":"Appraising protein conformational changes by resampling time-resolved serial x-ray crystallography data.","authors":"Adams Vallejos, Gergely Katona, Richard Neutze","doi":"10.1063/4.0000258","DOIUrl":"10.1063/4.0000258","url":null,"abstract":"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.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 4","pages":"044302"},"PeriodicalIF":2.3,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11272219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141761869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Structural Dynamics-Us Pub Date : 2024-06-21 eCollection Date: 2024-05-01 DOI: 10.1063/4.0000259

Emiliano Principi

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

Structural Dynamics-Us Pub Date : 2024-05-01 DOI: 10.1063/4.0000249

Yunbeom Lee, Key Young Oang, Doyeong Kim, Hyotcherl Ihee

{"title":"A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics.","authors":"Yunbeom Lee, Key Young Oang, Doyeong Kim, Hyotcherl Ihee","doi":"10.1063/4.0000249","DOIUrl":"https://doi.org/10.1063/4.0000249","url":null,"abstract":"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.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 3","pages":"031301"},"PeriodicalIF":2.8,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11065455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140872246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Structural Dynamics-Us 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

{"title":"High-energy-resolution off-resonant spectroscopy with self-seeded x-ray free-electron laser pulses.","authors":"Jang Hyeob Sohn, Gyeongbo Kang, Tae-Kyu Choi, Gyusang Lee, Changhoo Lee, Sae Hwan Chun, Jaeku Park, Dongbin Shin, Byoung-Ick Cho","doi":"10.1063/4.0000243","DOIUrl":"10.1063/4.0000243","url":null,"abstract":"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.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 2","pages":"024304"},"PeriodicalIF":2.8,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10972604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140307505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Structural Dynamics-Us 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

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

Structural Dynamics-Us 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

{"title":"High energy electron diffraction instrument with tunable camera length.","authors":"P Denham, Y Yang, V Guo, A Fisher, X Shen, T Xu, R J England, R K Li, P Musumeci","doi":"10.1063/4.0000240","DOIUrl":"10.1063/4.0000240","url":null,"abstract":"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.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 2","pages":"024302"},"PeriodicalIF":2.8,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10965247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140295048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Structural Dynamics-Us 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

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

Structural Dynamics-Us 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

{"title":"Advanced manufacturing provides tailor-made solutions for crystallography with x-ray free-electron lasers.","authors":"Lars Paulson, Sankar Raju Narayanasamy, Megan L Shelby, Matthias Frank, Martin Trebbin","doi":"10.1063/4.0000229","DOIUrl":"10.1063/4.0000229","url":null,"abstract":"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.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 1","pages":"011101"},"PeriodicalIF":2.8,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10883715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139933675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Structural Dynamics-Us 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

{"title":"Raw diffraction data and reproducibility.","authors":"Loes M J Kroon-Batenburg, Matthew P Lightfoot, Natalie T Johnson, John R Helliwell","doi":"10.1063/4.0000232","DOIUrl":"10.1063/4.0000232","url":null,"abstract":"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.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"11 1","pages":"011301"},"PeriodicalIF":2.8,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10869167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139742324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Structural Dynamics-Us 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

引用次数: 0