Structural Dynamics-Us最新文献_第5页

Progress in the development of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography. 低温电子断层扫描用超快脉冲有源相板的研制进展。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-08-26 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000770

Daniel X Du, Adam C Bartnik, Cameron J R Duncan, Usama Choudhry, Tanya Tabachnik, Chaim Sallah, Ebrahim Najafi, Ding-Shyue Yang, Jared M Maxson, Anthony W P Fitzpatrick

{"title":"Progress in the development of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography.","authors":"Daniel X Du, Adam C Bartnik, Cameron J R Duncan, Usama Choudhry, Tanya Tabachnik, Chaim Sallah, Ebrahim Najafi, Ding-Shyue Yang, Jared M Maxson, Anthony W P Fitzpatrick","doi":"10.1063/4.0000770","DOIUrl":"10.1063/4.0000770","url":null,"abstract":"Cryo-electron tomography (cryo-ET) is a powerful modality for resolving cellular structures in their native state. While single-particle cryo-electron microscopy excels in determining protein structures purified from recombinant or endogenous sources due to an abundance of particles, weak contrast issues are accentuated in cryo-ET by low copy numbers in crowded cellular milieux. Continuous laser phase plates offer improved contrast in cryo-ET; however, their implementation demands exceptionally high-peak optical intensities. Instead, a novel experimental approach to enhance contrast in cryo-ET is to manipulate the phase of scattered pulsed electrons using ultrafast pulsed photons. Here, we outline the experimental design of a proof-of-concept electron microscope and demonstrate synchronization between electron packets and laser pulses. Furthermore, we show ultrabright photoemission of electrons from an alloy field emission tip using femtosecond ultraviolet pulses. These experiments pave the way toward exploring the utility of the ponderomotive effect using pulsed radiation to increase phase contrast in cryo-ET of subcellular protein complexes in situ, thus advancing the field of cell biology.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"044302"},"PeriodicalIF":2.3,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12396848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975048","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

Molecular chameleons adaptability in target binding. 分子变色龙在靶结合中的适应性。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-08-13 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000757

Guanhong Bu, Måns Eriksson, Emma Rova Danelius

{"title":"Molecular chameleons adaptability in target binding.","authors":"Guanhong Bu, Måns Eriksson, Emma Rova Danelius","doi":"10.1063/4.0000757","DOIUrl":"10.1063/4.0000757","url":null,"abstract":"Estimates show that up to 85% of the human therapeutic proteomes are undruggable by traditional small molecules. Macrocycles, a class of molecular leads, often extend beyond the traditional drug space and offer the potential to modulate challenging targets within this 85%. These modalities exhibit significant conformational flexibility and often function as molecular chameleons, enabling them to adapt to environments with varying polarities while ensuring good oral bioavailability. In this study, we explore the conformational adaptability in target binding of the three known molecular chameleons, paritaprevir, grazoprevir, and simeprevir, by docking their experimental crystal structures, solution conformations, and target-bound structures into multiple protein targets, including human drug transporters associated with drug-drug interactions and COVID-19 related proteins. Our findings reveal that the macrocyclic core conformational class, or \"chameleonic group,\" determines the overall pharmacophore conformations and influences the conformational changes required for binding to various proteins. These insights provide a pathway toward rationalizing drug optimizations for molecular chameleons as well as offering specific guidance for improving Hepatitis C virus nonstructural protein 3/4A inhibitors, including providing a starting point for their COVID-19 repurposing and cancer therapy.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"044701"},"PeriodicalIF":2.9,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12352931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876126","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

Modeling electron dynamics in silicon driven by high-intensity femtosecond x-rays. 由高强度飞秒x射线驱动的硅中的电子动力学建模。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-08-01 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000299

Sebastian Cardoch, Nicusor Timneanu

{"title":"Modeling electron dynamics in silicon driven by high-intensity femtosecond x-rays.","authors":"Sebastian Cardoch, Nicusor Timneanu","doi":"10.1063/4.0000299","DOIUrl":"10.1063/4.0000299","url":null,"abstract":"High-intensity femtosecond-duration x-rays from free electron lasers have enabled innovative imaging techniques that employ smaller crystal sizes than conventional crystallography. Developments aimed at increasing x-ray pulse intensities bring opportunities and constraints due to ultra-fast changes to atomic scattering form factors from electron dynamics. Experiments on silicon by Inoue et al. [Inoue et al., Phys. Rev. Lett. 131, 163201 (2023)] illustrate this by measuring diffraction efficiencies with increasing x-ray pulse intensities. Results at the highest experimental x-ray pulse intensity have been theoretically studied [Inoue et al., Phys. Rev. Lett. 131, 163201 (2023); Ziaja et al., Atoms 11, 154 (2023)] but not fully reproduced, which raises questions about the mechanisms behind these changes. Using collisional radiative simulations and relativistic configuration-averaged atomic data, we compute the ionization dynamics and diffraction efficiency of silicon and find good agreement within the experimental uncertainty. We incorporate the effects of ionization potential depression by removing energy levels close to the ionization threshold over selected charge states. We identify the main electron impact mechanisms present in our simulations. We bridge the gap between high and low intensity and find regimes where electronic damage affects the efficiency of high- and low-momentum transfer. We computationally examine the effects of free electron degeneracy and find that it does not influence ionization dynamics. Finally, we consider how a non-thermal electron distribution may modify our results. This investigation gives insight into the mechanisms and helps guide future experiments that utilize intense x-ray pulses to achieve high-resolution structural determination.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"044101"},"PeriodicalIF":2.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12317780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144776676","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

Accelerating structural dynamics through integrated research informatics. 通过综合研究信息学加速结构动力学。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-30 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000759

Ben Eisenbraun, Alex Ho, Peter A Meyer, Piotr Sliz

{"title":"Accelerating structural dynamics through integrated research informatics.","authors":"Ben Eisenbraun, Alex Ho, Peter A Meyer, Piotr Sliz","doi":"10.1063/4.0000759","DOIUrl":"10.1063/4.0000759","url":null,"abstract":"Structural dynamics research requires robust computational methods, reliable software, accessible data, and scalable infrastructure. Managing these components is complex and directly affects reproducibility and efficiency. The SBGrid Consortium addresses these challenges through a three-pillar approach that encompasses Software, Data, and Infrastructure, designed to foster a consistent and rigorous computational environment. At the core is the SBGrid software collection (>620 curated applications), supported by the Capsules Software Execution Environment, which ensures conflict-free, version-controlled execution. The SBGrid Data Bank supports open science by enabling the publication of primary experimental data. SBCloud, a fully managed cloud computing platform, provides scalable, on-demand infrastructure optimized for structural biology workloads. Together, they reduce computational friction, enabling researchers to focus on interpreting time-resolved data, modeling structural transitions, and managing large simulation datasets for advancing structural dynamics. This integrated platform delivers a reliable and accessible foundation for computationally intensive research across diverse scientific fields sharing common computational methods.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"041101"},"PeriodicalIF":2.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12313326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144761828","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

The 2024 challenges in structural biology summit. 2024结构生物学峰会的挑战。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-22 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000752

Brent L Nannenga, Tamir Gonen

引用次数: 0

Helical spin dynamics in Cu₂OSeO₃ as measured with small-angle neutron scattering. 用小角中子散射测量Cu2OSeO3的螺旋自旋动力学。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-18 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000305

Victor Ukleev, Priya R Baral, Robert Cubitt, Nina-Juliane Steinke, Arnaud Magrez, Oleg I Utesov

引用次数: 0

Structure and ultrafast dynamics of tri-nuclear Ag-/Tl-Pt₂POP₄ complexes in solution. 溶液中三核Ag-/Tl-Pt2POP4配合物的结构和超快动力学。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-10 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000293

Philipp Lenzen, Kristoffer Haldrup, Asmus O Dohn, Frederik Beyer, Elisa Biasin, Morten Christensen, Bianca L Hansen, Tobias Harlang, Kasper Skov Kjær, Mads Goldschmidt Laursen, Peter Vester, Tim B van Driel, Matthieu Chollet, James M Glownia, Robert J Hartsock, Henrik T Lemke, Silke Nelson, Sanghoon Song, Kasper Steen Pedersen, Kelly J Gaffney, Klaus B Møller, Martin M Nielsen

{"title":"Structure and ultrafast dynamics of tri-nuclear Ag-/Tl-Pt2POP4 complexes in solution.","authors":"Philipp Lenzen, Kristoffer Haldrup, Asmus O Dohn, Frederik Beyer, Elisa Biasin, Morten Christensen, Bianca L Hansen, Tobias Harlang, Kasper Skov Kjær, Mads Goldschmidt Laursen, Peter Vester, Tim B van Driel, Matthieu Chollet, James M Glownia, Robert J Hartsock, Henrik T Lemke, Silke Nelson, Sanghoon Song, Kasper Steen Pedersen, Kelly J Gaffney, Klaus B Møller, Martin M Nielsen","doi":"10.1063/4.0000293","DOIUrl":"10.1063/4.0000293","url":null,"abstract":"The energetics and dynamics of ion assembly in solution has broad influence in nanomaterials and inorganic synthesis. To investigate the fundamental processes involved, we present a time-resolved x-ray solution scattering (TR-XSS) study of the trinuclear silver and thallium complexes of the diplatinum ion PtPOP [Pt2(H2P2O5) <math> <mrow> <mrow><msubsup><mrow></mrow> <mn>4</mn> <mrow><mn>4</mn> <mo>-</mo></mrow> </msubsup> </mrow> </mrow> </math> ] in aqueous solution. These complexes, their structural properties, and their electronic structure are not well understood and afford a unique opportunity to study the metal-metal bond formation that influences molecular and material assembly in solution. We present model-independent analysis of the observed dynamics as well as an analysis incorporating time-resolved structural refinements of key bond lengths with <100 fs time resolution. We find that upon photoexcitation, the Pt atoms contract <math><mo>∼</mo></math> 0.25 Å toward the center of both the Ag- and the Tl-PtPOP complexes, as previously observed for the PtPOP anion. For the AgPtPOP system, an ultrafast Ag-Pt bond expansion of <math><mo>∼</mo></math> 0.2 Å is observed, whereas in contrast, the TlPtPOP system exhibits a Tl-Pt bond contraction of <math><mo>∼</mo></math> 0.3 Å upon photoexcitation. For both complexes, the change in electronic state leads to coherent (\"wave-packet\") oscillations along the metal-Pt coordinates. Based on these structural dynamics, we propose an electronic structure model that describes the metal-metal bonding behavior in both the ground and excited state for both complexes.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"044902"},"PeriodicalIF":2.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12263179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144643877","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

Unveiling hidden wavepacket dynamics in time-resolved x-ray scattering data via singular spectrum analysis. 通过奇异谱分析揭示时间分辨x射线散射数据中隐藏的波包动力学。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-09 eCollection Date: 2025-07-01 DOI: 10.1063/4.0000764

Jaeseok Kim, Hyunwoo Jeong, Jae Hyuk Lee, Rory Ma, Daewoong Nam, Minseok Kim, Dogeun Jang, Jong Goo Kim

{"title":"Unveiling hidden wavepacket dynamics in time-resolved x-ray scattering data via singular spectrum analysis.","authors":"Jaeseok Kim, Hyunwoo Jeong, Jae Hyuk Lee, Rory Ma, Daewoong Nam, Minseok Kim, Dogeun Jang, Jong Goo Kim","doi":"10.1063/4.0000764","DOIUrl":"10.1063/4.0000764","url":null,"abstract":"Time-resolved x-ray liquidography (TRXL) is a powerful technique for directly tracking ultrafast structural dynamics in real space. However, resolving the motion of vibrational wavepackets generated by femtosecond laser pulses remains challenging due to the limited temporal resolution and signal-to-noise ratio (SNR) of experimental data. This study addresses these challenges by introducing singular spectrum analysis (SSA) as an efficient method for extracting oscillatory signals associated with vibrational wavepackets from TRXL data. To evaluate its performance, we conducted a comparative study using simulated TRXL data, demonstrating that SSA outperforms conventional analysis methods such as the Fourier transform of temporal profiles and singular value decomposition, particularly under low SNR conditions. We further applied SSA to experimental TRXL data on the photodissociation of triiodide ( <math> <mrow> <mrow> <msubsup><mrow><mi>I</mi></mrow> <mn>3</mn> <mo>-</mo></msubsup> </mrow> </mrow> </math> ) in methanol, successfully isolating oscillatory signals arising from wavepacket dynamics in ground-state <math> <mrow> <mrow> <msubsup><mrow><mi>I</mi></mrow> <mn>3</mn> <mo>-</mo></msubsup> </mrow> </mrow> </math> and excited-state <math> <mrow> <mrow> <msubsup><mrow><mi>I</mi></mrow> <mn>2</mn> <mo>-</mo></msubsup> </mrow> </mrow> </math> , which had been challenging to resolve in previous TRXL studies. These results establish SSA as a highly effective tool for analyzing ultrafast structural dynamics in time-resolved experiments and open new opportunities for studying wavepacket dynamics in a wide range of photoinduced reactions.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 4","pages":"044901"},"PeriodicalIF":2.3,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12245396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610048","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: Celebrating the work and achievements of Keith Moffat. 专题序言：庆祝基思·莫法特的工作和成就。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-07-01 DOI: 10.1063/4.0000771

Richard Neutze

引用次数: 0

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning. 从序列到蛋白质结构和构象动力学与人工智能/机器学习。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2025-06-24 eCollection Date: 2025-05-01 DOI: 10.1063/4.0000765

Alexander M Ille, Emily Anas, Michael B Mathews, Stephen K Burley

{"title":"From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning.","authors":"Alexander M Ille, Emily Anas, Michael B Mathews, Stephen K Burley","doi":"10.1063/4.0000765","DOIUrl":"10.1063/4.0000765","url":null,"abstract":"The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"030902"},"PeriodicalIF":2.3,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12195464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144498778","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