Structural Dynamics-Us最新文献

{"title":"Applications of visualization technology in the structural sciences.","authors":"Edward T Eng, Nichole R Valdez","doi":"10.1063/4.0000753","DOIUrl":"10.1063/4.0000753","url":null,"abstract":"<p><p>The structural sciences are undergoing a transformation driven by advancements in visualization technologies that aid researchers in understanding and communicating experimental data from complex molecular systems. New applications of integrative structural biological and biophysical approaches add a wide variety of complementary information from a broad range of scientific disciplines. These approaches extend structural biophysical methodologies to enable research by the incorporation of a variety of data streams and utilization of tools like molecular graphics, virtual reality, and machine learning. To redefine how structural data-particularly from cryo-electron microscopy and x-ray crystallography-are fed forward for scientific exploration and communication, the advances in tools for data visualization and interpretation have been critical. By bringing molecular systems into an interactive three-dimensional space, these novel technologies enhance research workflows, facilitate structure-based drug design, and create engaging educational experiences. Taken together, these visualization innovations are essential tools for advancing the field by making concepts more accessible and compelling.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"030901"},"PeriodicalIF":2.3,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12119125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175406","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}

{"title":"Recovering high-resolution information using energy filtering in MicroED.","authors":"Max T B Clabbers, Tamir Gonen","doi":"10.1063/4.0000755","DOIUrl":"10.1063/4.0000755","url":null,"abstract":"<p><p>Inelastic scattering poses a significant challenge in electron crystallography by elevating background noise and broadening Bragg peaks, thereby reducing the overall signal-to-noise ratio. This is particularly detrimental to data quality in structural biology, as the diffraction signal is relatively weak. These effects are aggravated even further by the decay of the diffracted intensities as a result of accumulated radiation damage, and rapidly fading high-resolution information can disappear beneath the noise. Loss of high-resolution reflections can partly be mitigated using energy filtering, which removes inelastically scattered electrons and improves data quality and resolution. Here, we systematically compared unfiltered and energy-filtered microcrystal electron diffraction data from proteinase K crystals, first collecting an unfiltered dataset followed directly by a second sweep using the same settings but with the energy filter inserted. Our results show that energy filtering consistently reduces noise, sharpens Bragg peaks, and extends high-resolution information, even though the absorbed dose was doubled for the second pass. Importantly, our results demonstrate that high-resolution information can be recovered by inserting the energy filter slit. Energy-filtered datasets showed improved intensity statistics and better internal consistency, highlighting the effectiveness of energy filtering for improving data quality. These findings underscore its potential to overcome limitations in macromolecular electron crystallography, enabling higher-resolution structures with greater reliability.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"034702"},"PeriodicalIF":2.3,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081369","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}

{"title":"First experiments with ultrashort, circularly polarized soft x-ray pulses at FLASH2.","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, M Braune, M Ilchen, S Savio, T Otto, K Tiedtke, V Scheppe, J Rönsch-Schulenberg, E Schneidmiller, C Schüßler-Langeheine, H A Dürr, M Beye, G Brenner, N Pontius","doi":"10.1063/4.0000298","DOIUrl":"https://doi.org/10.1063/4.0000298","url":null,"abstract":"<p><p>Time-resolved absorption spectroscopy and magnetic circular dichroism with circularly polarized soft x-rays (XAS and XMCD) are powerful tools to probe electronic and magnetic dynamics in magnetic materials element- and site-selectively. By employing these methods, groundbreaking results have been obtained, for instance, for magnetic alloys, which helped to fundamentally advance the field of ultrafast magnetization dynamics. At the free-electron laser facility FLASH, key capabilities for ultrafast XAS and XMCD experiments have recently improved. In an upgrade, an APPLE-III helical afterburner undulator was installed at FLASH2 in September 2023. This installation allows for the generation of circularly polarized soft x-ray pulses with a duration of a few tens of femtoseconds covering the <math> <mrow> <mrow> <msub><mrow><mi>L</mi></mrow> <mrow><mn>3</mn> <mo>,</mo> <mn>2</mn></mrow> </msub> </mrow> </mrow> </math> -edges of the important 3<i>d</i> transition metal elements with pulse energies of several <math><mi>μ</mi></math> J. Here, we present first experimental results with such ultrashort x-ray pulses from the FL23 beamline employing XMCD at the <math> <mrow> <mrow> <msub><mrow><mi>L</mi></mrow> <mrow><mn>3</mn> <mo>,</mo> <mn>2</mn></mrow> </msub> </mrow> </mrow> </math> -edges of the 3<i>d</i> metals, Co, Fe, and Ni. We obtain significant dichroic difference signals indicating a degree of circular polarization close to 100%. With the pulse-length preserving monochromator at beamline FL23 and an improved pump-laser setup, FLASH can offer important and efficient experimental instrumentation for ultrafast demagnetization studies and other investigations of ultrafast spin dynamics in 3<i>d</i> transition metals, multilayers, and alloys.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"034301"},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12065633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144041117","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}

{"title":"Structures of myxobacterial phytochrome revealed by cryo-EM using the Spotiton technique and with x-ray crystallography.","authors":"Prabin Karki, David Menendez, William Budell, Shishir Dangi, Carolina Hernandez, Joshua Mendez, Srinivasan Muniyappan, Shibom Basu, Peter Schwander, Tek N Malla, Emina A Stojković, Marius Schmidt","doi":"10.1063/4.0000301","DOIUrl":"https://doi.org/10.1063/4.0000301","url":null,"abstract":"<p><p>Phytochromes are red-light photoreceptors first identified in plants, with homologs found in bacteria and fungi, that regulate a variety of critical physiological processes. They undergo a reversible photocycle between two distinct states: a red-light-absorbing Pr form and a far-red light-absorbing Pfr form. This Pr/Pfr photoconversion controls the activity of a C-terminal enzymatic domain, typically a histidine kinase (HK). However, the molecular mechanisms underlying light-induced regulation of HK activity in bacteria remain poorly understood, as only a few structures of unmodified bacterial phytochromes with HK activity are known. Recently, cryo-EM structures of a wild-type bacterial phytochrome with HK activity are solved that reveal homodimers in both the Pr and Pfr states, as well as a heterodimer with individual monomers in distinct Pr and Pfr states. Cryo-EM structures of a truncated version of the same phytochrome-lacking the HK domain-also show a homodimer in the Pfr state and a Pr/Pfr heterodimer. Here, we describe in detail how structural information is obtained from cryo-EM data on a full-length intact bacteriophytochrome, and how the cryo-EM structure can contribute to the understanding of the function of the phytochrome. In addition, we compare the cryo-EM structure to an unusual x-ray structure that is obtained from a fragmented full-length phytochrome crystallized in the Pr-state.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"034701"},"PeriodicalIF":2.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12048173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002301","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}

{"title":"GARFIELD, a toolkit for interpreting ultrafast electron diffraction data of imperfect quasi-single crystals.","authors":"Alexander Marx, Sascha W Epp","doi":"10.1063/4.0000286","DOIUrl":"https://doi.org/10.1063/4.0000286","url":null,"abstract":"<p><p>The analysis of ultrafast electron diffraction (UED) data from low-symmetry single crystals of small molecules is often challenged by the difficulty of assigning unique Laue indices to the observed Bragg reflections. For a variety of technical and physical reasons, UED diffraction images are typically of lower quality when viewed from the perspective of structure determination by single-crystal x-ray or electron diffraction. Nevertheless, time series of UED images can provide valuable insight into structural dynamics, providing that an adequate interpretation of the diffraction patterns can be achieved. Garfield is a collection of tools with a graphical user interface designed to facilitate the interpretation of diffraction patterns and to index Bragg reflections in challenging cases where other indexing tools are ineffective. To this end, Garfield enables the user to interactively create, explore, and optimize sets of parameters that define the diffraction geometry and characteristic properties of the sample.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 2","pages":"024103"},"PeriodicalIF":2.3,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12033043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005022","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}

{"title":"Aminoacyl-tRNA synthetase urzymes optimized by deep learning behave as a quasispecies.","authors":"Sourav Kumar Patra, Nicholas Randolph, Brian Kuhlman, Henry Dieckhaus, Laurie Betts, Jordan Douglas, Peter R Wills, Charles W Carter","doi":"10.1063/4.0000294","DOIUrl":"https://doi.org/10.1063/4.0000294","url":null,"abstract":"<p><p>Protein design plays a key role in our efforts to work out how genetic coding began. That effort entails urzymes. Urzymes are small, conserved excerpts from full-length aminoacyl-tRNA synthetases that remain active. Urzymes require design to connect disjoint pieces and repair naked nonpolar patches created by removing large domains. Rosetta allowed us to create the first urzymes, but those urzymes were only sparingly soluble. We could measure activity, but it was hard to concentrate those samples to levels required for structural biology. Here, we used the deep learning algorithms ProteinMPNN and AlphaFold2 to redesign a set of optimized LeuAC urzymes derived from leucyl-tRNA synthetase. We select a balanced, representative subset of eight variants for testing using principal component analysis. Most tested variants are much more soluble than the original LeuAC. They also span a range of catalytic proficiency and amino acid specificity. The data enable detailed statistical analyses of the sources of both solubility and specificity. In that way, we show how to begin to unwrap the elements of protein chemistry that were hidden within the neural networks. Deep learning networks have thus helped us surmount several vexing obstacles to further investigations into the nature of ancestral proteins. Finally, we discuss how the eight variants might resemble a sample drawn from a population similar to one subject to natural selection.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 2","pages":"024701"},"PeriodicalIF":2.3,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12033045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144047777","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}

{"title":"Femtosecond charge and spin dynamics in a Co₅₀Pt₅₀ alloy.","authors":"Martin Pavelka, Simon Marotzke, Ru-Pan Wang, Mohamed F Elhanoty, Günter Brenner, Siarhei Dziarzhytski, Somnath Jana, W Dieter Engel, Clemens V Korff Schmising, Deeksha Gupta, Igor Vaskivskyi, Tim Amrhein, Nele Thielemann-Kühn, Martin Weinelt, Ronny Knut, Juliane Rönsch-Schulenberg, Evgeny Schneidmiller, Christian Schüßler-Langeheine, Martin Beye, Niko Pontius, Oscar Grånäs, Hermann A Dürr","doi":"10.1063/4.0000297","DOIUrl":"https://doi.org/10.1063/4.0000297","url":null,"abstract":"<p><p>The use of advanced x-ray sources plays a key role in the study of dynamic processes in magnetically ordered materials. The progress in x-ray free-electron lasers enables the direct and simultaneous observation of the femtosecond evolution of electron and spin systems through transient x-ray absorption spectroscopy and x-ray magnetic circular dichroism, respectively. Such experiments allow us to resolve the response seen in the population of the spin-split valence states upon optical excitation. Here, we utilize circularly polarized ultrashort soft x-ray pulses from the new helical afterburner undulator at the free-electron laser FLASH in Hamburg to study the femtosecond dynamics of a laser-excited CoPt alloy at the Co L₃-edge absorption. Despite employing a weaker electronic excitation level, we find a comparable demagnetization for the Co 3<i>d</i>-states in CoPt compared to previous measurements on CoPd. This is attributed to the distinctly different spin-orbit coupling between 3<i>d</i> and 4<i>d</i> vs 3<i>d</i> and 5<i>d</i> elements in the corresponding alloys and multilayers.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 2","pages":"024303"},"PeriodicalIF":2.3,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12033042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020103","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}

{"title":"Defects in magnetic domain walls after single-shot all-optical switching.","authors":"Daniel Metternich, Kai Litzius, Sebastian Wintz, Kathinka Gerlinger, Sascha Petz, Dieter Engel, Themistoklis Sidiropoulos, Riccardo Battistelli, Felix Steinbach, Markus Weigand, Steffen Wittrock, Clemens von Korff Schmising, Felix Büttner","doi":"10.1063/4.0000287","DOIUrl":"https://doi.org/10.1063/4.0000287","url":null,"abstract":"<p><p>Helicity-independent all-optical switching (HI-AOS) is the fastest known way to switch the magnetic order parameter. While the switching process of extended areas is well understood, the formation of domain walls enclosing switched areas remains less explored. Here, we study domain walls around all-optically nucleated magnetic domains using x-ray vector spin imaging and observe a high density of vertical Bloch line defects. Surprisingly, the defect density appears to be independent of optical pulse parameters, significantly varies between materials, and is only slightly higher than in domain walls generated by field cycling. A possible explanation is given by time-resolved Kerr microscopy, which reveals that magnetic domains considerably expand after the initial AOS process. During this expansion, and likewise during field cycling, domain walls propagate at speeds above the Walker breakdown. Micromagnetic simulations suggest that at such speeds, domain walls accumulate defects when moving over magnetic pinning sites, explaining similar defect densities after two very different switching processes. The slightly larger defect density after AOS compared to field-induced switching indicates that some defects are created already when the domain wall comes into existence. Our work shows that engineered low-pinning materials are a key ingredient to uncover the intrinsic dynamics of domain wall formation during ultrafast all-optical switching.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 2","pages":"024504"},"PeriodicalIF":2.3,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12009145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020100","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}

{"title":"Unraveling atomic complexity from frozen samples.","authors":"Yasmeen N Ruma, Brent L Nannenga, Tamir Gonen","doi":"10.1063/4.0000303","DOIUrl":"https://doi.org/10.1063/4.0000303","url":null,"abstract":"<p><p>Cryo-electron microscopy (cryo-EM) is a significant driver of recent advances in structural biology. Cryo-EM is comprised of several distinct and complementary methods, which include single particle analysis, cryo-electron tomography, and microcrystal electron diffraction. In this Perspective, we will briefly discuss the different branches of cryo-EM in structural biology and the current challenges in these areas.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 2","pages":"020901"},"PeriodicalIF":2.3,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12009148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144035598","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}

{"title":"A new chapter for RCSB Protein Data Bank Molecule of the Month in 2025.","authors":"Janet Iwasa, David S Goodsell, Stephen K Burley, Christine Zardecki","doi":"10.1063/4.0000302","DOIUrl":"https://doi.org/10.1063/4.0000302","url":null,"abstract":"<p><p>The online Molecule of the Month series authored by David S. Goodsell and published by the Research Collaboratory for Structural Biology Protein Data Bank at PDB101.RCSB.org has highlighted stories about the biomolecular structures driving fundamental biology, biomedicine, bioenergy, and biotechnology since January 2000. A new chapter begins in 2025: Janet Iwasa has taken over as the series creator of stories about critically important biological macromolecules in a rapidly changing world.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 2","pages":"021101"},"PeriodicalIF":2.3,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12009144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144026339","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}