Structural Dynamics-UsPub Date : 2026-08-20eCollection Date: 2026-07-01DOI: 10.1063/4.0001210
Anna De Falco, Ben Shurina, Rebecca Greene-Cramer, Theresa A Ramelot, Gaetano T Montelione
{"title":"Slowly exchanging bound states of SARS-CoV-2 3CL<sup>pro</sup>-inhibitor complexes revealed by <sup>19</sup>F NMR.","authors":"Anna De Falco, Ben Shurina, Rebecca Greene-Cramer, Theresa A Ramelot, Gaetano T Montelione","doi":"10.1063/4.0001210","DOIUrl":"https://doi.org/10.1063/4.0001210","url":null,"abstract":"<p><p>The SARS-CoV-2 virus causes COVID-19, and several of its gene products have been successfully targeted for antiviral drug development, including the 3C-like protease (3CL<sup>pro</sup>). The substrate-binding site of 3CL<sup>pro</sup> exhibits significant conformational plasticity. While available X-ray crystal structures reveal substantial loop variability and molecular dynamics simulations indicate that conformational heterogeneity persists in ligand-bound complexes, the slow-timescale thermodynamic and kinetic landscape of these complexes in solution remains incompletely defined. Using <sup>19</sup>F NMR spectroscopy, we characterize a slow-exchange conformational equilibrium in both the covalent nirmatrelvir (NMV) and noncovalent ensitrelvir (ENS) complexes of 3CL<sup>pro</sup>. For the wild-type 3CL<sup>pro</sup>-NMV complex at 298 K, joint dual-field line shape and exchange spectroscopy analysis resolves a millisecond-timescale exchange between two distinct states (population ratio ∼ 65:35; <i>k<sub>ex</sub></i> ≈ 52 s<sup>-1</sup>; ΔG<sup>‡</sup> ≈ 15 kcal mol<sup>-1</sup>). Co-existing bound states also persist in both the noncovalent NMV-[C145A] mutant (minor state population, <i>p<sub>B</sub></i> ≈ 18%) and wild-type ENS (<i>p<sub>B</sub></i> ≈ 38%) complexes, demonstrating that this slow-exchange heterogeneity is an intrinsic property of the ligated protease rather than a consequence of covalent attachment. These dynamics are not readily explained by available crystal structures or conventional microsecond molecular dynamics simulations, suggesting that in solution the inhibited enzyme samples alternative, energetically accessible conformations that are not fully represented in the crystal lattice. This study highlights the utility of solution-state <sup>19</sup>F NMR for quantifying low-energy conformational states relevant to drug-target energetics and inhibitor design.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 4","pages":"044701"},"PeriodicalIF":2.9,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13493197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148799684","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}
Structural Dynamics-UsPub Date : 2026-08-04eCollection Date: 2026-07-01DOI: 10.1063/4.0001216
Nele Stetzuhn, Emmanuelle Jal, Juliette Dubois, Boris Vodungbo, Flavio Capotondi, Emanuele Pedersoli, Matteo Pancaldi, Luca Gianessi, Claudio Masciovecchio, Ivaylo Nikolov, Giovanni Perosa, Dario De Angelis, Marco Malvestuto, Iuliia Bykova, Benedikt Rösner, Christian David, Jan Lüning, Angelo Giglia, Nicola Mahne, Deepika Gill, Sangeeta Sharma, Kirill I Bolotin, Clemens von Korff Schmising, Stefan Eisebitt
{"title":"Simultaneous two-color absorption dynamics in the van der Waals ferromagnet Fe<sub>3</sub>GeTe<sub>2</sub>.","authors":"Nele Stetzuhn, Emmanuelle Jal, Juliette Dubois, Boris Vodungbo, Flavio Capotondi, Emanuele Pedersoli, Matteo Pancaldi, Luca Gianessi, Claudio Masciovecchio, Ivaylo Nikolov, Giovanni Perosa, Dario De Angelis, Marco Malvestuto, Iuliia Bykova, Benedikt Rösner, Christian David, Jan Lüning, Angelo Giglia, Nicola Mahne, Deepika Gill, Sangeeta Sharma, Kirill I Bolotin, Clemens von Korff Schmising, Stefan Eisebitt","doi":"10.1063/4.0001216","DOIUrl":"10.1063/4.0001216","url":null,"abstract":"<p><p>For the integration of two-dimensional materials in future devices, a fundamental understanding of their response to external stimuli is needed. Toward this goal, we have investigated the electron and spin dynamics in the metallic van der Waals material Fe<sub>3</sub>GeTe<sub>2</sub> (FGT) in its paramagnetic state after ultrafast optical excitation. To this end, we have employed a zone plate streaking technique with probing energies in the extreme ultraviolet range, tuned to the Fe M<sub>2,3</sub> and Te N<sub>4,5</sub> absorption edges. This approach provides insights into energy-dependent charge dynamics with a sensitivity to transient absorption changes on the order of <math><mrow><mo>∼</mo> <mrow> <msup><mrow><mn>10</mn></mrow> <mrow><mo>-</mo> <mn>4</mn></mrow> </msup> </mrow> </mrow> </math> . We find a slow carrier relaxation time at both elemental edges-up to <math><mrow><mo>(</mo> <mn>2.2</mn> <mo>±</mo> <mn>0.6</mn> <mo>)</mo> <mtext> ps</mtext></mrow> </math> in Te and exceeding several picoseconds in Fe-which is surprising for a metal. To elucidate the complex time-resolved response, we also employ static x-ray absorption spectroscopy at the corresponding elemental edges, in which we find a double feature at the Fe M<sub>2,3</sub> edge. We attribute this to different Fe sites in the pristine material and an oxidized surface layer, and we propose that the time-resolved absorption dynamics show a mixture of signals stemming from the different species. Additionally, we conducted time-resolved x-ray magnetic circular dichroism measurements in FGT at room temperature. We do not find clear evidence of the previously observed light-induced ferromagnetic order above <math> <mrow> <mrow> <msub><mrow><mi>T</mi></mrow> <mi>C</mi></msub> </mrow> </mrow> </math> . Our study lays the groundwork for a deeper understanding of charge and spin dynamics in FGT after optical excitation as part of a roadmap for 2D spintronics.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 4","pages":"044501"},"PeriodicalIF":2.9,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13437137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148674325","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}
Structural Dynamics-UsPub Date : 2026-07-30eCollection Date: 2026-07-01DOI: 10.1063/4.0001219
Jongbum Na, Minchan Jeong, Jin Hae Kim
{"title":"Structural heterogeneity of iron-sulfur cluster scaffold protein IscU: Metamorphic or partially folded?","authors":"Jongbum Na, Minchan Jeong, Jin Hae Kim","doi":"10.1063/4.0001219","DOIUrl":"10.1063/4.0001219","url":null,"abstract":"<p><p>The scaffold protein IscU plays a central role in iron-sulfur (Fe-S) cluster assembly and transfer. Despite extensive structural and biochemical research, the conformational nature of IscU remains unclear. IscU has been proposed as a metamorphic protein that interconverts between structured (S) and disordered (D) states. However, its conformational heterogeneity has often been interpreted as a consequence of intrinsic marginal stability, with the D-state described as an unfolded and functionally irrelevant state. These contrasting views highlight the fundamental challenge in defining the structural identity of IscU. In this review, we provide a comprehensive overview of the structural heterogeneity of IscU and examine how intrinsic and extrinsic factors shape the conformational equilibrium between the S- and D-states. Furthermore, we consider how these conflicting interpretations could be reconciled within an ensemble-based framework. In addition, we highlight promising approaches for characterizing the structurally elusive D-state, including high-pressure nuclear magnetic resonance, single-molecule Förster resonance energy transfer, native ion mobility mass spectrometry, and artificial intelligence-based structural analysis, all of which provide new opportunities for probing low-populated and transient conformational states. Collectively, these perspectives suggest that the functional behavior of IscU is closely linked to its conformational heterogeneity and that a conformational landscape view may provide a more integrated understanding of its role in Fe-S cluster biosynthesis.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 4","pages":"041301"},"PeriodicalIF":2.9,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13423590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148632320","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}
Structural Dynamics-UsPub Date : 2026-07-22eCollection Date: 2026-07-01DOI: 10.1063/4.0001206
Laurenz Kremeyer, David Cai, Malik Lahlou, Sebastian Hammer, Raphael Schwenzer, Bradley J Siwick
{"title":"Prospects for direct electron detectors in ultrafast electron diffraction and scattering experiments.","authors":"Laurenz Kremeyer, David Cai, Malik Lahlou, Sebastian Hammer, Raphael Schwenzer, Bradley J Siwick","doi":"10.1063/4.0001206","DOIUrl":"10.1063/4.0001206","url":null,"abstract":"<p><p>Ultrafast electron diffraction and phonon-diffuse scattering [UED(S)] experiments make use of photo-induced changes to electron scattering intensity across 2D detectors to report on a very wide range of dynamic structural phenomena in molecules and materials. Hybrid pixel counting detectors (HPCDs) are a promising technology for improved sensitivity and signal-to-noise in UED(S) experiments, as they offer near-zero readout noise and dark counts with the possibility of new acquisition modalities (e.g., shot-to-shot normalization) due to their high frame rates. However, it is well known that HPCDs suffer from count losses at high electron fluxes even in CW beam applications. How this translates to ultrashort electron pulse exposures has yet to be determined and is critical to understanding the application of this technology to ultrafast electron scattering experiments. Here, we show that count losses are significantly exacerbated in ultrafast (pulsed) experiments and that HPCDs require unconventional data handling and saturate above <math><mrow><mo>≈</mo> <mn>2</mn></mrow> </math> electrons per pixel per pulse. This count-rate limitation presents a severe constraint on electron bunch charge when interrogating single crystal samples. Normalization strategies to optimize signal-to-noise in UED(S) and a complete model for measurement uncertainties using HPCDs are developed and tested using a large dataset. Finally, we suggest ways HPCDs could be better adapted to ultrashort pulsed beam experiments.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 4","pages":"044302"},"PeriodicalIF":2.9,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13391233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148563391","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}
Structural Dynamics-UsPub Date : 2026-07-13eCollection Date: 2026-07-01DOI: 10.1063/4.0001209
Carl E Jensen, Christoph Emeis, Stephan Jauernik, Petra Hein, Fabio Caruso, Michael Bauer
{"title":"Coherent phonon-driven band renormalizations in 1<i>T'</i>-MoTe<sub>2</sub>.","authors":"Carl E Jensen, Christoph Emeis, Stephan Jauernik, Petra Hein, Fabio Caruso, Michael Bauer","doi":"10.1063/4.0001209","DOIUrl":"10.1063/4.0001209","url":null,"abstract":"<p><p>Here, we investigate phonon mode- and electron band-selective electron-phonon couplings in centrosymmetric 1<i>T</i>'-MoTe<sub>2</sub> using time- and angle-resolved photoemission spectroscopy combined with frequency-domain analysis. Femtosecond near-infrared pulses excite coherent <math> <mrow> <mrow> <msub><mrow><mi>A</mi></mrow> <mi>g</mi></msub> </mrow> </mrow> </math> -symmetric phonon modes at 2.34, 3.34, and 3.86 THz, which manifest as oscillatory modulations in photoemission intensity and binding energy across the valence bands. Pixel-wise Fourier analysis using recently developed methodologies reveals pronounced band selectivity with distinct coupling strengths for different electronic states and phonon modes, enabling the evaluation of band-renormalization amplitudes in the range of few meV. <i>Ab initio</i> calculations qualitatively reproduce the experimentally observed coupling patterns and relative trends, demonstrating the capability of combined experimental and theoretical approaches to resolve ultrafast electron-phonon interactions in quantum materials.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 4","pages":"044301"},"PeriodicalIF":2.9,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13364501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148438573","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}
Structural Dynamics-UsPub Date : 2026-06-15eCollection Date: 2026-05-01DOI: 10.1063/4.0001213
Stephanann M Costello, Zeina C Sleiman, John N Glushka, Breeanna R Urbanowicz, Arthur S Edison
{"title":"<sup>13</sup>C NMR as a foundation for machine learning models of polysaccharides.","authors":"Stephanann M Costello, Zeina C Sleiman, John N Glushka, Breeanna R Urbanowicz, Arthur S Edison","doi":"10.1063/4.0001213","DOIUrl":"10.1063/4.0001213","url":null,"abstract":"<p><p>Polysaccharide structural assignment via nuclear magnetic resonance (NMR) spectroscopy remains an analytical challenge due to spectral overlap because of limited chemical shift dispersion. This challenge is exacerbated by the wide-spread use of proton (<sup>1</sup>H) detection. Progress has also been hindered by the dispersed nature of carbohydrate databases and the restricted applicability of most prediction tools, which provide limited atom-specific residue discrimination in larger polymers. These limitations hamper the efficient characterization of glycosyltransferase (GT) activity, which depends on defining donor-acceptor substrate pairs and accurately identifying corresponding products. Here, we demonstrate the utility of high field <sup>13</sup>C-detected NMR for the assignment of two homohexamers. Laminarihexaose and xylohexaose were analyzed using 2D heteronuclear correlation and correlation via long-range coupling (COLOC) experiments to evaluate whether complete residue level assignments could be achieved. The COLOC experiment revealed long range correlations that were not resolved using heteronuclear multiple bond correlation, and the 1D <sup>13</sup>C spectra provided exceptional resolution, including distinct shoulders corresponding to residue specific chemical shift differences previously assumed to be indistinguishable. These findings suggest that high field <sup>13</sup>C NMR can provide the nuanced atom level information required to train machine learning models for predicting chemical shift assignments of large, complex, and highly degenerate polysaccharides. Such models offer a promising framework for rapid structural identification of GT reaction products, enabling progress of high throughput characterization of plant derived polysaccharides central to renewable biomaterial development.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 3","pages":"034302"},"PeriodicalIF":2.9,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148333771","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}
Structural Dynamics-UsPub Date : 2026-06-11eCollection Date: 2026-05-01DOI: 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":"<p><p>Strain engineering in epitaxial Bi(111) films on Si(111) enables temperature-tunable phonon frequencies through thermal expansion mismatch. Using <i>in situ</i> 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 <i>c</i>-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 <i>c</i>-axis, being insensitive to the in-plane lattice parameter and thereby enabling targeted control of phonon frequencies.</p>","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}
Structural Dynamics-UsPub Date : 2026-06-04eCollection Date: 2026-05-01DOI: 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
{"title":"Report of high data rate macromolecular crystallography (HDRMX) meeting, 23 July 2025.","authors":"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","doi":"10.1063/4.0001196","DOIUrl":"10.1063/4.0001196","url":null,"abstract":"<p><p>This paper is a report of the High Data Rate Macromolecular Crystallography workshop held on 23 July 2025 as part of the 2025 meeting of the American Crystallographic Association in Lombard, IL, USA, 18-23 July 2025. This report summarizes the discussions, questions, action items, and recommendations that arose from the meeting and includes links to the presentations. The sessions were moderated by Aaron S. Brewster and Graeme Winter. There was particularly lively discussion about the possible need for lossy compression as data rates increase, as multimodal experiments become more popular and as research budgets are squeezed.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 3","pages":"034301"},"PeriodicalIF":2.9,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148333789","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}
Structural Dynamics-UsPub Date : 2026-05-22eCollection Date: 2026-05-01DOI: 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":"<p><p>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 BRD4<sup>BD2</sup> 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 BRD4<sup>BD2</sup> 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 BRD4<sup>BD2</sup>. 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.</p>","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}
Structural Dynamics-UsPub Date : 2026-05-07eCollection Date: 2026-05-01DOI: 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
{"title":"Erratum: \"First experiments with ultrashort, circularly polarized soft x-ray pulses at FLASH2\" [Struct. Dyn. <b>12</b>, 034301 (2025)].","authors":"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","doi":"10.1063/4.0000792","DOIUrl":"10.1063/4.0000792","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1063/4.0000298.].</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"13 3","pages":"039901"},"PeriodicalIF":2.9,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13293236/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148333797","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}