Structural Dynamics-Us最新文献_第2页

Directional sensitivity of the A 1 g phonon in biaxially strained bismuth heterofilms studied by transient white light reflectivity. 用瞬态白光反射率研究双轴应变铋异质膜中a1g声子的方向灵敏度。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-06-11 eCollection Date: 2026-05-01 DOI: 10.1063/4.0001200

Fabian Thiemann, Maja Penkl, Michael Horn-von Hoegen

{"title":"<ArticleTitle xmlns:ns0=\"http://www.w3.org/1998/Math/MathML\">Directional sensitivity of the <ns0:math> <ns0:mrow> <ns0:mrow> <ns0:msub><ns0:mrow><ns0:mi>A</ns0:mi></ns0:mrow> <ns0:mrow><ns0:mn>1</ns0:mn> <ns0:mi>g</ns0:mi></ns0:mrow> </ns0:msub> </ns0:mrow> </ns0:mrow> </ns0:math> phonon in biaxially strained bismuth heterofilms studied by transient white light reflectivity.","authors":"Fabian Thiemann, Maja Penkl, Michael Horn-von Hoegen","doi":"10.1063/4.0001200","DOIUrl":"10.1063/4.0001200","url":null,"abstract":"Strain engineering in epitaxial Bi(111) films on Si(111) enables temperature-tunable phonon frequencies through thermal expansion mismatch. Using in situ low-energy electron diffraction combined with broadband femtosecond transient reflectivity on the same samples, we directly correlate anisotropic lattice parameters with the redshift of the coherent <math> <mrow> <mrow> <msub><mrow><mi>A</mi></mrow> <mrow><mn>1</mn> <mi>g</mi></mrow> </msub> </mrow> </mrow> </math> phonon mode. The in-plane lattice parameter remains locked to the Si substrate and is therefore nearly temperature-independent, imposing strong biaxial compressive strain, causing an additional expansion of the Bi lattice along the c-axis. By applying an extended phonon-shift model, we disentangle the contributions of intrinsic thermal expansion, thermal-mismatch strain, and anharmonicity to the phonon softening. The enhanced redshift observed in strained films cannot be accounted for by expansion or mismatch alone; instead, it arises from a strengthened anharmonic term that additionally scales with strain along the c-axis, being insensitive to the in-plane lattice parameter and thereby enabling targeted control of phonon frequencies.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 3","pages":"034501"},"PeriodicalIF":2.9,"publicationDate":"2026-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148333841","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

Report of high data rate macromolecular crystallography (HDRMX) meeting, 23 July 2025. 高数据速率高分子晶体学（HDRMX）会议报告，2025年7月23日。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-06-04 eCollection Date: 2026-05-01 DOI: 10.1063/4.0001196

Christine Beavers, Herbert J Bernstein, Aaron S Brewster, Max Burian, Nicholas Devenish, Jiaxin Dawn Duan, Daniel Eriksson, Diego Gämperle, Yang Ha, David R Hall, James Holton, Peter Keller, Loes Kroon-Batenburg, David W Mittan-Moreau, Yasukazu Nakaye, Daniel W Paley, Ezra Peisach, Nicholas K Sauter, Sofia Trampari, Clemens Vonrhein, David G Waterman, Thomas A White, Graeme Winter

引用次数: 0

Bromodomain dimers: A case study of BRD4 and family-wide AlphaFold predictions. 溴域二聚体：BRD4和全家族AlphaFold预测的案例研究。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-05-22 eCollection Date: 2026-05-01 DOI: 10.1063/4.0001211

Alisa S Dengler, Lara Lunglmeir, Matthias J Brandl, T Reid Alderson

{"title":"Bromodomain dimers: A case study of BRD4 and family-wide AlphaFold predictions.","authors":"Alisa S Dengler, Lara Lunglmeir, Matthias J Brandl, T Reid Alderson","doi":"10.1063/4.0001211","DOIUrl":"10.1063/4.0001211","url":null,"abstract":"Bromodomains are conserved acetyl-lysine reader domains that play a central role in the assembly of transcriptional regulatory complexes. While generally presumed to function as monomers, bromodomain homo-dimers have been identified, and several bromodomain-containing proteins have been linked to biomolecular condensates, where locally elevated concentrations may promote dimerization. Here, we investigated bromodomain dimerization with an integrated approach that combines structural and biophysical measurements with AlphaFold-based predictions across the bromodomain family. Using the second bromodomain (BD2) of BRD4 as a model system, we characterized the thermodynamics and kinetics of its monomer-dimer equilibrium by two-dimensional nuclear magnetic resonance (NMR) lineshape analysis and CPMG relaxation dispersion. We found that the BRD4BD2 dimer forms transiently with a dissociation constant near 400 μM and a lifetime near 1 ms. Using our NMR-derived restraints, we performed data-driven docking to generate models of the BRD4BD2 dimer. To assess dimerization propensity across the wider bromodomain family, we leveraged AlphaFold-Multimer and AlphaFold3 to systematically predict homo-dimeric models for all human bromodomains. We identified several predicted dimer architectures, with 15 bromodomain dimers that have higher interface-confidence scores than BRD4BD2. Overall, our results suggest that weak and reversible dimerization may be more widespread among bromodomains, where it could contribute to function in dynamic transcriptional assemblies.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 3","pages":"034702"},"PeriodicalIF":2.9,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148333804","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

Erratum: "First experiments with ultrashort, circularly polarized soft x-ray pulses at FLASH2" [Struct. Dyn. 12, 034301 (2025)]. 勘误：“在FLASH2上进行的超短圆偏振软x射线脉冲的首次实验”[结构]。[j].化学工程学报，2012,034301（2025）。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-05-07 eCollection Date: 2026-05-01 DOI: 10.1063/4.0000792

S Marotzke, D Gupta, R-P Wang, M Pavelka, S Dziarzhytski, C von Korff Schmising, S Jana, N Thielemann-Kühn, T Amrhein, M Weinelt, I Vaskivskyi, R Knut, D Engel, V Scheppe, M Braune, M Ilchen, S Savio, T Otto, K Tiedtke, S Alisauskas, A Tajalli, G Cirmi, H Cankaya, P Vagin, K Götze, J Rönsch-Schulenburg, E Schneidmiller, C Schüßler-Langeheine, H A Dürr, M Beye, G Brenner, N Pontius

引用次数: 0

Integrating metabolomics and histopathology: A method for metabolite recovery from fixed tissue specimens. 结合代谢组学和组织病理学：一种从固定组织标本中提取代谢物的方法。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-05-01 eCollection Date: 2026-03-01 DOI: 10.1063/4.0001205

Ivan Vučković, Ryan Meloche, Prasanna K Mishra, Song Zhang, Petras Dzeja, Maria V Irazabal, Slobodan Macura

{"title":"Integrating metabolomics and histopathology: A method for metabolite recovery from fixed tissue specimens.","authors":"Ivan Vučković, Ryan Meloche, Prasanna K Mishra, Song Zhang, Petras Dzeja, Maria V Irazabal, Slobodan Macura","doi":"10.1063/4.0001205","DOIUrl":"10.1063/4.0001205","url":null,"abstract":"Combined histopathological and metabolomic analysis of the same tissue specimen can reduce biological variability compared to independent analyses of similar samples. However, conventional workflows are incompatible: tissue fixation leads to metabolite loss through dilution and chemical reactions with fixative, while metabolomic extraction typically destroys the specimen. We propose a method that reconciles these conflicting requirements by enabling metabolite recovery from fixative while preserving tissue for histopathology. In this approach, tissue is initially fixed in a small volume of fixative; an aliquot of the fixative is then collected for nuclear magnetic resonance-based metabolomic analysis before additional fixative is added for standard processing. As a proof-of-concept, mouse kidneys from the same subject were analyzed using two protocols: standard perchloric acid extraction (ensuring complete metabolite recovery but destroying tissue) and metabolite extraction from fixative. Several metabolites were fully recoverable from the fixative, others partially, while some were lost due to chemical reactions. Despite some limitations, this strategy may be useful for analyzing precious specimens, such as human biopsies, that must remain intact for further studies. Moreover, using the same specimen for dual analyses reduces the number of animals required and enhances statistical robustness.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 3","pages":"034701"},"PeriodicalIF":2.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147822540","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

Poplar: A polarized neutron development beamline for polarization analysis and Larmor labeling techniques. 杨树：用于极化分析和拉莫尔标记技术的极化中子发展束线。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-04-24 eCollection Date: 2026-03-01 DOI: 10.1063/4.0000783

Fankang Li, Kaleb Burrage, Wei Lu, Dominic Giuliano, Arturo Diaz, Wei Tian, Doug Kyle, Lowell Crow

{"title":"Poplar: A polarized neutron development beamline for polarization analysis and Larmor labeling techniques.","authors":"Fankang Li, Kaleb Burrage, Wei Lu, Dominic Giuliano, Arturo Diaz, Wei Tian, Doug Kyle, Lowell Crow","doi":"10.1063/4.0000783","DOIUrl":"10.1063/4.0000783","url":null,"abstract":"A thermal neutron development beamline equipped with a Si monochromator has been commissioned at the HB-2D beam port of the High Flux Isotope Reactor at Oak Ridge National Laboratory. This instrument is dedicated to the development of neutron scattering methods and instrumentation, serving as a complement to the cold neutron development beamline CG-4B at the cold guide hall. Two incident wavelengths are available, 2.43 and 1.72 Å, with a flux of 1.75 and 1.28 <math><mrow><mo>×</mo> <mrow> <msup><mrow><mn>10</mn></mrow> <mn>5</mn></msup> </mrow> </mrow> </math> <math> <mrow> <mrow> <msup><mrow><mi>n</mi> <mo>/</mo> <mo>(</mo> <mtext>cm</mtext></mrow> <mn>2</mn></msup> </mrow> <mtext> </mtext> <mi>s</mi> <mo>)</mo></mrow> </math> , respectively. The instrument can be operated either in high-resolution or high-intensity mode through the horizontal bending of the monochromator. As the bending increases, the incident flux on the sample increases as a result of the additional lattice strain induced in the silicon wafers. With its mission centered on advancing neutron scattering instrumentation, the beamline has been named POPLAR, an acronym for polarized neutron development beamline for polarization analysis and Larmor labeling techniques.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 2","pages":"024301"},"PeriodicalIF":2.9,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147785729","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

A role of protein conformational dynamics in mammalian DNA methylation. 蛋白质构象动力学在哺乳动物DNA甲基化中的作用。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-04-24 eCollection Date: 2026-03-01 DOI: 10.1063/4.0001204

Jikui Song

{"title":"A role of protein conformational dynamics in mammalian DNA methylation.","authors":"Jikui Song","doi":"10.1063/4.0001204","DOIUrl":"10.1063/4.0001204","url":null,"abstract":"DNA methylation at the C-5 position of cytosine is an important epigenetic mechanism underpinning various cellular functions, such as heterochromatin assembly, gene expression, and cell fate determination. In mammals, DNA methylation mainly occurs in the context of CpG dinucleotide contexts. Establishment and maintenance of mammalian DNA methylation is orchestrated by two groups of functionally distinct enzymes: de novo DNA methyltransferases DNMT3A and DNMT3B and maintenance DNA methyltransferase DNMT1. For proper genomic methylation, both de novo and maintenance DNMTs are subjected to multilayered regulation by the chromatin environment, such as histone modifications and the methylation stiate of the CpG dinucleotide. Furthermore, DNA methylation is critically regulated by the accessory proteins of DNMTs, such as DNMT3L and DNMT3B3 for de novo methylation and E3 ubiquitin ligase UHRF1 for maintenance DNA methylation. Increasing structural, biochemical and cellular evidence has unveiled the intricate interplay between the conformational dynamics of DNMTs and their target specification in governing the dynamic DNA demethylation across the genome. This review focuses on recent advances in structural and functional understanding of DNMTs, emphasizing how the interplay between their intramolecular and intermolecular interactions modulates the conformational dynamics and function of the individual DNA methylation machinery, thereby shaping the dynamic DNA methylation landscape across the mammalian genome.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 2","pages":"021302"},"PeriodicalIF":2.9,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109025/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147786502","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: Celebrating the work and achievements of Joachim Stöhr. 前言：庆祝约阿希姆的工作和成就Stöhr。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-04-17 eCollection Date: 2026-03-01 DOI: 10.1063/4.0001212

Stefan Eisebitt, Hermann Dürr, Jan Lüning

引用次数: 0

Structural basis of the oligomerization of anti-silencer Ler from enterohemorrhagic E. coli (EHEC). 肠出血性大肠杆菌（EHEC）抗消音器Ler寡聚的结构基础。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-04-14 eCollection Date: 2026-03-01 DOI: 10.1063/4.0001203

Guanghao Wang, Bo Duan, Bin Xia

{"title":"Structural basis of the oligomerization of anti-silencer Ler from enterohemorrhagic E. coli (EHEC).","authors":"Guanghao Wang, Bo Duan, Bin Xia","doi":"10.1063/4.0001203","DOIUrl":"10.1063/4.0001203","url":null,"abstract":"The locus of enterocyte effacement-encoded regulator (Ler) is a master transcriptional activator essential for the virulence of enterohemorrhagic and enteropathogenic Escherichia coli. Although Ler shares homology with the global silencer H-NS, it functions uniquely as an anti-silencer, a role strictly dependent on its oligomerization state. However, the structural mechanism governing Ler assembly remains poorly understood. In this study, we have characterized the N-terminal oligomerization domain (Ler1-74) of Ler using solution NMR spectroscopy and biophysical assays, and found that Ler1-74 shows concentration-dependent oligomerization. We demonstrate that Ler oligomerization is driven by two distinct interfaces with contrasting dynamic properties. We determined the solution structure of the Ler18-74 dimer, revealing a stable, anti-parallel \"tail-to-tail\" interface (dimer Site-2, residues 35-66) stabilized by a hydrophobic core. In contrast, the N-terminal interface (dimer Site-1, residues 12-33) forms a highly dynamic \"head-to-head\" dimer, which undergoes significant conformational exchange and exhibits concentration- and temperature-dependent dimerization. Based on these findings, we propose a structural model wherein Ler forms supramolecular assemblies through the propagation of alternating stable (Site-2) and dynamic (Site-1) interactions. This architecture, while reminiscent of H-NS, displays distinct stability features that may underlie Ler's specific anti-silencing function in bacterial pathogenesis.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 2","pages":"024702"},"PeriodicalIF":2.9,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13078945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147693107","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

Solution characterization of TraW, a regulatory protein of the F plasmid type 4 secretion system. F质粒4型分泌系统调节蛋白TraW的溶液表征。

IF 2.9 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-03-17 eCollection Date: 2026-03-01 DOI: 10.1063/4.0001201

Christina S Rodriguez, Gerald F Audette

{"title":"Solution characterization of TraW, a regulatory protein of the F plasmid type 4 secretion system.","authors":"Christina S Rodriguez, Gerald F Audette","doi":"10.1063/4.0001201","DOIUrl":"10.1063/4.0001201","url":null,"abstract":"Bacterial conjugation facilitates horizontal gene transfer through the Type IV Secretion System (T4SS), a complex nanomachine central to antibiotic resistance dissemination. This study investigates the structure and dynamics of TraW, a key F-plasmid conjugative protein. TraW, in conjugation with the protein TrbC, is critical for F-pilus biogenesis and mating pair stabilization. Using biophysical, computational, and structural methods, including CD, NMR, SAXS, and native mass spectrometry, we characterize TraW as a modular protein with a stable C-terminal domain and a flexible N-terminal region. The full-length construct exhibits higher conformational adaptability and transient dimerization, whereas truncation enhances compactness and monomeric stability. AlphaFold modeling and SAXS analyses reveal that this flexibility, rather than intrinsic disorder, enables TraW to modulate inter-protein interactions essential for T4SS assembly and function. These findings establish TraW as a dynamic adaptor protein and highlight how flexibility fine-tunes structural plasticity in conjugative machinery.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 2","pages":"024701"},"PeriodicalIF":2.9,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12999216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147487863","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