Structural Dynamics-Us最新文献

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 2.3 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":"https://doi.org/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":2.3,"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 2.3 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":"https://doi.org/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":2.3,"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 2.3 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":"https://doi.org/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":2.3,"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 2.3 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 2.3 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":"https://doi.org/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":2.3,"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 2.3 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":"https://doi.org/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":2.3,"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

Integrating neutron vibrational spectroscopy and computer simulation to elucidate structure and dynamics of hydrogen. 结合中子振动光谱和计算机模拟来阐明氢的结构和动力学。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-03-02 eCollection Date: 2026-03-01 DOI: 10.1063/4.0000790

Yongqiang Cheng, Anibal J Ramirez-Cuesta, Murillo L Martins, Chang Liu

{"title":"Integrating neutron vibrational spectroscopy and computer simulation to elucidate structure and dynamics of hydrogen.","authors":"Yongqiang Cheng, Anibal J Ramirez-Cuesta, Murillo L Martins, Chang Liu","doi":"10.1063/4.0000790","DOIUrl":"https://doi.org/10.1063/4.0000790","url":null,"abstract":"Understanding the structure and dynamics of hydrogen is critically important, yet direct experimental measurements are often challenging. Hydrogen interacts only weakly with common probing particles such as photons and electrons, and strong nuclear quantum effects can produce large nonthermal and anisotropic atomic displacements. Neutron scattering, however, provides a uniquely powerful approach due to the strong and distinct interactions of neutrons with atomic hydrogen, molecular hydrogen, and deuterium. Beyond neutron diffraction, which enables direct determination of hydrogen and deuterium positions, neutron vibrational spectroscopy-particularly when combined with computer simulations and modeling-offers unparalleled insights into hydrogen structure and dynamics that are inaccessible by other techniques. In this paper, after briefly summarizing the theoretical foundations, we review recent advances in applying neutron vibrational spectroscopy and computational methods to hydrogen-containing materials, ranging from molecular hydrogen adsorption to organic, inorganic, and hybrid compounds with diverse hydrogen local structure. Finally, we discuss opportunities offered by the recent progress in machine learning to further enhance the capabilities of this method.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 2","pages":"021301"},"PeriodicalIF":2.3,"publicationDate":"2026-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12956373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147356319","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

Photoelectron spectroscopy and circular dichroism of an open-shell organometallic camphor complex. 开壳有机金属樟脑配合物的光电子能谱和圆二色性。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-02-17 eCollection Date: 2026-01-01 DOI: 10.1063/4.0000791

Viktoria K Brandt, Michele Pugini, Nikolas Kaltsoyannis, Gustavo A Garcia, Ivan Powis, Laurent Nahon, Dominik Stemer

{"title":"Photoelectron spectroscopy and circular dichroism of an open-shell organometallic camphor complex.","authors":"Viktoria K Brandt, Michele Pugini, Nikolas Kaltsoyannis, Gustavo A Garcia, Ivan Powis, Laurent Nahon, Dominik Stemer","doi":"10.1063/4.0000791","DOIUrl":"https://doi.org/10.1063/4.0000791","url":null,"abstract":"We present an investigation of one-photon valence-shell photoelectron spectroscopy and photoelectron circular dichroism (PECD) for the chiral molecule (1R,4R)-3-(heptafluorobutyryl)-(+)-camphor (HFC) and its europium complex Eu(III) tris[3-(heptafluorobutyryl)-(1R,4R)-camphorate] (Eu-HFC3), the latter of which constitutes the heaviest organometallic molecule for which PECD has yet been measured. We discuss the role of keto-enol tautomerism in HFC, both as a free molecule and complexed in Eu-HFC3. PECD is a uniquely sensitive probe of molecular chirality and structure such as absolute configuration, conformation, isomerization, and substitution, and is, in principle, well suited to unambiguously resolving tautomers; however, modeling remains challenging. For small organic molecules, theory is generally capable of accounting for experimentally measured PECD asymmetries, but significantly poorer agreement is typically achieved for the case of large open-shell systems. Here, we report PECD asymmetries, ranging up to <math><mrow><mo>∼</mo> <mn>8</mn> <mi>%</mi></mrow> </math> for HFC and <math><mrow><mo>∼</mo> <mn>7</mn> <mi>%</mi></mrow> </math> for Eu-HFC3, of similar magnitude to those reported previously for smaller isolated chiral molecules, indicating that PECD remains a practical experimental technique for the study of large, complicated chiral systems.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 1","pages":"014301"},"PeriodicalIF":2.3,"publicationDate":"2026-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12916143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146229246","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

Crystal structure of apo human spermidine synthase reveals dynamic rearrangement at the active site. 载子人亚精胺合成酶的晶体结构揭示了活性位点的动态重排。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-01-16 eCollection Date: 2026-01-01 DOI: 10.1063/4.0001199

Omowumi O Fagbohun, Molly A Canfield, Jonathan A Clinger

{"title":"Crystal structure of apo human spermidine synthase reveals dynamic rearrangement at the active site.","authors":"Omowumi O Fagbohun, Molly A Canfield, Jonathan A Clinger","doi":"10.1063/4.0001199","DOIUrl":"10.1063/4.0001199","url":null,"abstract":"Polyamines are polycations involved in both differentiation and proliferation of cells. Highly conserved polyamine biosynthetic enzymes are involved in the synthesis of polyamines. Spermidine synthase (SPDS) is an important enzyme in the polyamine biosynthetic pathway, and it is an aminopropyl-transferase that catalyzes the synthesis of the polyamine, spermidine, from putrescine and decarboxylated S-adenosine methionine. Spermidine has a variety of biological roles, including the formation of eIF5A, regulating autophagy, and stabilizing DNA and RNA. While there are numerous structures of human SPDS in complex with its substrates, products, or inhibitors, and numerous apo structures from various species, there is no structure of the apo form of human SPDS reported to date. In this study, the crystal structure of apo human SPDS was determined at 1.95 Å resolution. Comparison of the inherently flexible gatekeeping loop in the apo human structure with apo homologues revealed species-specific differences in loop conformation, indicating dynamics. Significant conformational change was observed in active site residues that are involved in catalysis when the apo human structure was compared to human ligand-bound complexes. These findings provide structural insights into the conformational dynamics and ligand-binding properties of spermidine synthase.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 1","pages":"014701"},"PeriodicalIF":2.3,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12812037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145999501","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

Farewell and thank you note. 再见，谢谢你。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2026-01-07 eCollection Date: 2026-01-01 DOI: 10.1063/4.0001202

George N Phillips

引用次数: 0