Structural Dynamics-Us最新文献

{"title":"Advances in structural science: Education, outreach, and research applications.","authors":"Charles Bou-Nader, Jamaine Davis, Louise N Dawe, David S Goodsell, James Kaduk, Bart Kahr, Helen Maynard-Casely, Brandon Q Mercado, Beata E Mierzwa, Olayinka Olatunji-Ojo, Allen Oliver, Christine Zardecki, Shao-Liang Zheng","doi":"10.1063/4.0000304","DOIUrl":"10.1063/4.0000304","url":null,"abstract":"<p><p>A fundamental challenge for specialists in any field is communicating the importance and intricacies of their work to those outside of it. The 2024 Transactions Symposium held at the 74th annual meeting of the American Crystallographic Association: Structural Science Society was designed to address two pivotal themes concerning the promotion and understanding of structural science: first, pedagogical approaches of teaching structural science, emphasizing the methodologies that enhance student learning and second, strategies to capture the interest of non-specialists and the general public. By reflecting on what makes experts passionate about their field and what they wish others understood about it, the symposium highlighted actionable insight into bridging gaps and fostering a broader appreciation for structural science.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"034101"},"PeriodicalIF":2.3,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12182285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144477389","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":"Advanced glycation end product (AGE) crosslinking of a bacterial protein: Are AGE-modifications going undetected in our studies?","authors":"Bonnie J Cuthbert, Steven J Jensen, Christopher S Hayes, Celia W Goulding","doi":"10.1063/4.0000754","DOIUrl":"10.1063/4.0000754","url":null,"abstract":"<p><p>The small reactive molecules, glyoxal (GO) and methylglyoxal (MGO), are common byproducts of metabolic processes. GO and MGO are known to modify proteins, DNA, and lipids, resulting in advance glycation end products (AGEs). AGEs are linked to numerous human diseases but are found across all three domains of life due to the widespread presence of GO and MGO. Recent structural studies have revealed that an antibacterial phospholipase toxin contains a methylglyoxal-derived imidazolium crosslink (MODIC). Unlike AGEs that are associated with human diseases and protein dysfunction, crosslinking is required for the toxin's enzymatic activity, indicating that MODIC acts as a bona fide post-translational modification to promote function. The MODIC-modified toxin represents the first structure in the protein data bank with an AGE-modification. However, because GO and MGO are present in all cells, AGE-modifications are likely more prevalent than currently reported but have gone undetected. We used the toxin's MODIC structural motif to query the protein data bank for other modified proteins. This search recovered the colicin Ia pore-forming toxin. Using the deposited crystal structure and structural data for colicin Ia, we were able to model glyoxal-derived imidazolium crosslink or MODIC modifications into the electron density map, suggesting that GO/MGO modifications may indeed be more common in bacterial proteins.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"031001"},"PeriodicalIF":2.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303374","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":"Statistically elucidated responses from low-signal contrast mechanisms in ultrafast electron microscopy.","authors":"Spencer A Reisbick, Alexandre Pofelski, Myung-Geun Han, Chuhang Liu, Eric Montgomery, Chunguang Jing, Kayla Callaway, John Cumings, June W Lau, Yimei Zhu","doi":"10.1063/4.0000751","DOIUrl":"10.1063/4.0000751","url":null,"abstract":"<p><p>The emergence of ultrafast electron microscopy (UEM) has enabled the discovery of strongly correlated dynamic mechanisms, including electron-phonon coupling, structural phase transitions, thermal transport, and electromagnetic deflection. Most UEM systems operate stroboscopically, meaning that the technique is susceptible to artifacts, mistakes, and misinterpretation of the data due to extensive experimental effort. In contrast to the ultrafast designation, data acquisition is extraordinarily slow because the electron beam has significantly reduced signal compared to traditional transmission electron microscopy due to pulsing the electron beam. Consequently, the sample may drift, tilt, or undergo irreversible structural changes that are independent of the time-resolved dynamics throughout the experimental time frame. Furthermore, these datasets require significant user interpretation that can be problematic when proper controls are not implemented thoroughly. Here, we demonstrate a new algorithm designed to separate ultrafast structural dynamics from long-term artifacts using a LiNbO₃ sample experiencing electrically driven surface acoustic wave propagation. Additionally, we provide examples of the impact of user bias when analyzing the data and provide a methodology, which enables the extraction of time-resolved responses when the image signal is extraordinarily low. Overall, the goal of this publication is to provide methods that validate the experimental results and reduce researcher biases during UEM data interpretation.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"034302"},"PeriodicalIF":2.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303375","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":"\"Everything's a sample\": Characterizing everyday materials using x-ray powder diffraction.","authors":"James A Kaduk","doi":"10.1063/4.0000756","DOIUrl":"10.1063/4.0000756","url":null,"abstract":"<p><p>We can learn something scientifically interesting about literally everything around us by examining it in a powder diffractometer. Comparing a macroscopic understanding of a material with the atomic-scale description proves to be a good way of generating excitement about our science among young people and the general public. I tell stories (case studies) about what can be learned by examining several classes of everyday materials: rocks (including slate and other flooring), water solids, rust and crud (including snow dirt), food (sugar, chocolate sandwich cookies, and peanut butter), medications (pain relief, decongestant, and pharmaceuticals), wood, and polymers.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 3","pages":"034501"},"PeriodicalIF":2.3,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12133226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217344","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":"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":2.9,"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":2.9,"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":"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":2.9,"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":"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":2.9,"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":"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":2.9,"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}