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This issue covers 19 academic papers and research software resources added between September 21 and 27, 2026. Topics include cryo-EM sample preparation and radiation damage, crystallographic imaging and data processing, serotonin receptor drug design, in situ and time-resolved structural studies of cells, organic cation transport, cardiac fibrosis, drug targets, and retinoic acid. Highlights include acoustic manipulation and ice-thickness control, designs selective for receptor subtypes, and insights into transport mechanisms. The summaries are based on abstracts rather than full-text reviews. Inclusion dates are not publication dates, and the reported technical benefits and clinical potential require further validation.
This issue covers 19 scholarly publications and research software resources added to the Zotero personal library between September 21 and 27, 2026. Dates and ordering follow Beijing time and the time each item was added. Entries are grouped by topic and listed in reverse chronological order within each group; miscellaneous items appear at the end.
The summaries below were prepared by AI based on abstracts, with some abstracts supplemented from external sources; the full texts were not read in depth. Publication and issue dates follow the records and do not necessarily indicate publication this week. Book chapters and software resources are identified separately. A review on 5-HT7 appeared in an earlier issue and is included again because it was added to the library during this period.
Cryo-EM Sample Preparation and Radiation Damage (6 papers)
01 · Acoustofluidic cryo-EM enables in situ particle manipulation for uniform, high-quality cryo-EM specimens
Authors: Kaichun Yang, Wyatt Peele, Pengzhan Liu, Jianping Xia, Venkata Dandey, Ruoyu Zhong, Ke Jin, Kedar Sharma, Abigail J. Watson, Shujie Yang, Ying Chen, Aryan Agahtehrani, Shu Nakajima Lan, Peiran Zhang, Zhenhua Tian, Mingyuan Liu, Elizabeth Viverette, Xianchen Xu, Qian Wu, Mario J. Borgnia, Luke P. Lee, Tony Jun Huang
Uneven particle distribution during cryo-EM sample preparation reduces the number of usable particles and can compromise imaging, especially for dilute or unstable complexes. The authors introduce ACE, an acoustofluidic cryo-EM method that integrates contact-free acoustic manipulation into the standard plunge-freezing workflow. By vibrating the grid and generating localized acoustic flow, it redistributes particles within the sample. Experiments with liposomes and apoferritin showed up to a fourfold increase in local particle density under the tested conditions, while preserving structural integrity and improving image quality. The approach offers a way to actively adjust particle distribution during preparation, but the maximum gain comes from specific test systems and should not be assumed for all samples; the stability of each target complex also needs evaluation.
Highlight · Acoustic manipulation can redistribute particles locally before freezing, increasing usable particle density in specific samples.
Ice thickness directly affects cryo-EM image quality, but the instability of the liquid film before freezing makes it difficult to control precisely. The authors identify instability in films thinner than 100 nm as a key factor and use a designed graphene reservoir structure to spatially confine the film. Varying the reservoir depth allows the ice thickness to be tuned, producing confined ice layers that are relatively uniform and reproducible across larger areas. The abstract reports improved contrast, reduced motion and better orientation distributions across several macromolecular samples, helping with high-resolution reconstruction. The work links ice-thickness control to liquid-film stabilization, though specific benefits still need validation for each target particle, support material and preparation condition.
Highlight · Confining the liquid film with graphene structures shifts ice-thickness control from trial and error toward geometric constraint.
This review focuses on on-grid enrichment of low-abundance and challenging targets. Membrane proteins, endogenous complexes, chromatin-associated assemblies and transient signaling intermediates are often limited by sample availability, dissociation, denaturation and preferred orientation. Affinity-functionalized support films can selectively capture and enrich particles before vitrification, increasing local concentration and recovery; some implementations may also reduce exposure to the air–water interface. The authors compare platforms including Ni–NTA lipid monolayers, streptavidin grids, antibody supports, graphene-derived materials and magnetic nanoparticles, discussing their respective strengths and limitations. The broader shift is toward support films as active biochemical interfaces, but capture strategies must be matched to the target; enrichment cannot be assumed to preserve every aspect of the native state.
Highlight · Affinity grids turn support films into selective capture interfaces, expanding preparation options for scarce and unstable complexes.
04 · Chapter Fifteen - Radiation Damage in Electron Cryomicroscopy
Cryo-EM Part A Sample Preparation and Data Collection · Publication/issue date: 2010-01-01
Authors: Lindsay A. Baker, John L. Rubinstein
This book chapter reviews radiation damage in cryo-EM and how it limits resolution. The electron beam damages the sample even as it records signal: initial processes include ionization, bond breaking and radical formation, followed by the migration of secondary electrons and radicals that drive further reactions. Gas formation can cause more substantial morphological changes. This creates a fundamental trade-off between collecting enough statistical signal and limiting damage. The chapter addresses practical issues such as measuring electron exposure, estimating absorbed dose, accelerating voltage, sample temperature and exposure choices, and explains the importance of low temperatures and dose limits. It provides a framework for understanding imaging trade-offs—not a basis for treating lower temperatures or longer exposures as simple, guaranteed ways to improve structural quality.
Highlight · Radiation damage occurs throughout electron exposure, forcing a trade-off between signal statistics and sample preservation.
05 · Reducing the effects of radiation damage in cryo-EM using liquid helium temperatures
Proceedings of the National Academy of Sciences · Publication/issue date: 2025-04-29
Authors: Joshua L. Dickerson, Katerina Naydenova, Mathew J. Peet, Hugh Wilson, Biplob Nandy, Greg McMullan, Robert Morrison, Christopher J. Russo
Lowering sample temperature further should, in theory, reduce radiation damage, but earlier single-particle experiments at liquid-helium temperatures did not fully realize the expected gains. The authors identified and addressed factors that caused information loss under these conditions. Combining nanoscale electron-beam illumination with perforated gold supports yielded more information in every exposure frame than under liquid-nitrogen conditions. The study also notes that hole edges appear in images, damaged proteins tend to accumulate at those edges, and unnecessary irradiation of water and support foil should be minimized. The results show that the benefits of low temperatures depend on coordinating illumination, support and particle distribution—not temperature alone. These factors need to be considered together when designing new microscopes and sample carriers to harness the potential of reduced damage at lower temperatures.
Highlight · Imaging at liquid-helium temperatures benefits from nanoscale beam illumination and support design; cooling alone is not enough.
06 · Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins
Proceedings of the National Academy of Sciences · Publication/issue date: 2021-11-23
Authors: Joël S. Bloch, Somnath Mukherjee, Julia Kowal, Ekaterina V. Filippova, Martina Niederer, Els Pardon, Jan Steyaert, Anthony A. Kossiakoff, Kaspar P. Locher
Small membrane proteins are difficult to align in cryo-EM and need auxiliary structures that are both stable and easy to identify. The authors developed NabFab, which binds nanobody frameworks with high affinity while minimizing interference with nanobody–target interactions. Transplanting the recognition loops onto a compatible framework allows nanobodies from different sources and against different targets to use the same Fab module. The module adds mass and provides a fiducial marker; using it, the researchers resolved high-resolution structures of two small membrane proteins of about 50 kDa. An additional anti-Fab nanobody also helped with initial 3D reconstruction. The results demonstrate the module’s reusability, though its binding, rigidity and ability to preserve conformation should be checked for each new target.
Highlight · NabFab recognizes a common nanobody framework, providing a reusable mass and alignment aid for small membrane proteins.
Crystallographic Imaging and Data Processing (3 papers)
07 · Macromolecular diffractive imaging using imperfect crystals
Nature · Publication/issue date: 2016-02
Authors: Kartik Ayyer, Oleksandr M. Yefanov, Dominik Oberthür, Shatabdi Roy-Chowdhury, Lorenzo Galli, Valerio Mariani, Shibom Basu, Jesse Coe, Chelsie E. Conrad, Raimund Fromme, Alexander Schaffer, Katerina Dörner, Daniel James, Christopher Kupitz, Markus Metz, Garrett Nelson, Paulraj Lourdu Xavier, Kenneth R. Beyerlein, Marius Schmidt, Iosifina Sarrou, John C. H. Spence, Uwe Weierstall, Thomas A. White, Jay-How Yang, Yun Zhao, Mengning Liang, Andrew Aquila, Mark S. Hunter, Joseph S. Robinson, Jason E. Koglin, Sébastien Boutet, Petra Fromme, Anton Barty, Henry N. Chapman
Protein crystal structures are usually determined from Bragg diffraction, while the continuous diffraction produced by imperfect lattices is often ignored. Using photosystem II as an example, the authors show that positional disorder in a lattice can preserve additional molecular structural information rather than simply degrade data quality. They used the molecular envelope from conventional analysis as a constraint, advancing dimer imaging from information limited to about 4.5 Å by measurable Bragg peaks to about 3.5 Å. The results show that appropriate treatment of continuous diffraction may overcome resolution limits imposed by analyzing discrete diffraction peaks alone. The work reappraises the value of imperfect crystals, but its approach depends on the form of disorder and the overall molecular structure; it does not mean that any low-quality crystal will yield similar improvements.
Highlight · Continuous diffraction from lattice disorder can add structural information, giving imperfect crystals potential for high-resolution imaging.
Software resource: CrystalPilot is a browser-based interface for XDS crystallographic data processing, hosted on Zenodo; it is not a journal article. It brings project management, input-file editing, analysis of indexing and integration results, resolution-cutoff assessment and inspection of scaling results into one interface. Features include automated processing of single datasets or batches, frame viewing and Table 1 generation. A learning-oriented workflow is also part of its design. The available abstract mainly lists features and provides no independent performance comparisons or processing-accuracy data, so no claim is made here that it outperforms other interfaces. It may help reduce repetitive work and organize XDS processing steps, but data quality and parameter choices still need to be assessed from the outputs.
Highlight · CrystalPilot brings XDS project management, parameters, diagnostics and batch processing together in a browser interface.
Authors: A. Aydin, N. Fraikin, P. Lagoutte, C. Lesterlin, L. Terradot
mJuniper is a monomeric cyan fluorescent protein optimized for bacterial imaging. Its rapid maturation makes it suitable for time-course observations. The authors initially used it to improve the solubility of another target protein, but unexpectedly obtained a high-resolution crystal structure of mJuniper while attempting structural studies. The structure shows the typical β-barrel fold and two rotational isomeric states of the chromophore; the abstract links this difference to specific radiation damage occurring nearby. The work adds structural information about this imaging tool and also serves as a reminder that local conformational heterogeneity in crystals may reflect changes caused by the measurement process. It does not establish that both states represent the native functional distribution in the absence of irradiation.
Highlight · The unexpected mJuniper crystal structure provides a structural reference and shows that radiation damage can alter local chromophore conformation.
This review discusses the potential value of 5-HT7 receptor antagonism in depression research. The receptor is associated with mood, circadian rhythms and cognition, and signals mainly through the Gαs/cAMP pathway, although other coupling mechanisms have also been reported. The authors summarize evidence that selective antagonists produce antidepressant-like effects in rodent behavioral models and discuss how bioengineering platforms, human-relevant models and targeted delivery to the central nervous system could help clarify the mechanisms. They emphasize that the receptor is found in both peripheral and central tissues, making tissue selectivity important. Current evidence supports further investigation, but behavioral changes in animals cannot be equated directly with symptom improvement in patients and are not enough to define a clinical treatment strategy.
Highlight · Translational research on 5-HT7 antagonism needs to address human-relevant models, tissue selectivity and delivery.
Drug development based on classic psychedelics aims to preserve activity at 5-HT2A while avoiding activation of 5-HT2B, which is associated with heart valve risks. The authors compared ligand-binding pockets in the two receptor subtypes, used key differences to build a structure-guided model, and developed two series of candidates that act as 5-HT2A agonists and 5-HT2B antagonists. Cryo-EM structures of several receptor–ligand complexes support their explanation of subtype selectivity, and some candidates also showed antidepressant-like effects in animal models. By linking structural differences to functional selectivity, the study offers a strategy for reducing off-target receptor activity. However, receptor selectivity and animal behavior do not establish clinical safety or efficacy; more extensive validation is needed.
Highlight · Comparing the binding pockets of related receptors can guide candidates that combine 5-HT2A agonism with 5-HT2B antagonism.
Authors: Lingjie Tang, Xin Ji, Yumeng Wang, Dongmei Cao, Huiqiong Li, Licong He, Jianjun Cheng, Sheng Wang
This study further examines why similar ligands produce different functional effects at 5-HT2A and 5-HT2B. The authors systematically examined lateral and extended binding regions, finding that local steric hindrance and conformational constraints can affect ligand orientation and, in turn, receptor signaling. Based on these insights, they combined interactions with the binding regions and scaffold modifications across different chemical scaffolds to find designs that enhance 5-HT2A activation while limiting 5-HT2B activity. Cryo-EM structures of both receptors bound to representative candidates support the proposed mechanism. The work adds a structural rationale for subtype selectivity, but a plausible mechanism does not mean all adverse effects have been eliminated; therapeutic value will need to be assessed through broader pharmacological and clinical studies.
Highlight · Spatial constraints in the binding pocket affect signaling by shaping ligand orientation, offering a mechanistic framework for distinguishing 5-HT2A from 5-HT2B activation.
In Situ Cellular Structures and Time-Resolved Cryo-ET (2 papers)
13 · Single-cell visual proteomics of a minimal bacterium reveals structural coordination of gene expression machineries
Cell · Publication/issue date: 2026-09-25
Authors: Joseph M. Dobbs, Rasmus K. Jensen, Julia Mahamid
The study used cryo-electron tomography to examine native Mycoplasma pneumoniae cells and cells exposed to antibiotics, resolving 140 structural maps spanning translation initiation, elongation and recycling. In situ observations of several transcription–translation complexes led the authors to propose a translation reinitiation mechanism linked to “threading” and provided structural evidence for a supercomplex coordinating transcription, translation and membrane attachment. They also found many membrane-associated large ribosomal subunits, suggesting that their release from the membrane may be tied to the conditions that initiate another round of translation. By placing gene-expression machinery back in its cellular context, the work reveals multiple layers of coordination among processes; proposed explanations for reinitiation and membrane release should be distinguished from the structural features directly observed.
Highlight · In-cell structural maps connect transcription, translation and membrane attachment, revealing organization that isolated-molecule studies cannot capture.
14 · Strategies for time-resolved cryogenic electrontomography of transient cellular processes
Current Opinion in Structural Biology · Publication/issue date: 2026-12-01
Author: Arjen J. Jakobi
Cryo-electron tomography captures local cellular structures at the moment of vitrification, while time-resolved studies aim to relate these static observations to defined perturbations or stages of transient processes. This review outlines four experimental routes for introducing temporal information and discusses the conditions needed for reliable structural and temporal interpretation. Common requirements include being able to generate or identify the target state reproducibly and collecting enough samples to compare stages. The review also emphasizes that all methods face challenges in state selection, assigning timing and interpreting results. Its value lies in treating time-resolved cryo-ET as a matter of experimental design and sampling, rather than simply adding timestamps to tomograms. The abstract does not detail the four routes, so no specific categories are added here.
Highlight · Reliable time-resolved cryo-ET depends on identifiable states, clear temporal links and enough samples for comparison.
Authors: Yang Suo, Nicholas J. Wright, Hugo Guterres, Justin G. Fedor, Kevin John Butay, Mario J. Borgnia, Wonpil Im, Seok-Yong Lee
OCT1 and OCT2 mediate the uptake and clearance of various organic cations in the liver and kidneys, respectively, and are important in drug disposition and interactions. The authors resolved four cryo-EM structures of consensus variants of the two transporters in apo, substrate-bound and drug-bound conditions, covering outward-open and outward-closed states. Combined with functional assays, molecular docking and dynamics simulations, the study examines how each transporter accommodates structurally diverse cations and how its extracellular gate closes. The work provides structural principles for polyspecific substrate recognition and a reference for understanding transporter-related drug interactions. Because the study used consensus variants and a limited set of conformations, specific native transporters and drug combinations still need to be evaluated individually.
Highlight · Multiple OCT1/2 conformations link broad cation recognition to the mechanism of extracellular gate closure.
Authors: Binghong Xu, Shengjian Liang, Ziyu Wang, Xiaoyu Zhou, Liuying Wang, Qinqin Liang, Xiaoke Liu, Wei Guo, Sai Shi, Cheng Zhu, Sheng Ye, Zhiyong Lou, Yaxin Wang
OCTN1 transports ergothioneine and other metabolites, as well as various drugs, across membranes; its dysregulation is also associated with cancer-related processes. The authors determined cryo-EM structures of human OCTN1 in apo and ergothioneine-bound states, located the substrate-binding region and analyzed the conformational changes required for sodium-dependent transport. Structure-based virtual screening identified mebendazole as an inhibitor of the transporter, and experiments found that it suppressed the proliferation of cervical and lung cancer cells. The study thus connects substrate-recognition mechanisms with candidate drug screening and provides a basis for targeting this transporter. However, cell proliferation results do not demonstrate patient benefit, and the contribution of other drug targets and the drug’s effects in vivo still need to be distinguished.
Highlight · OCTN1 structures reveal ergothioneine recognition and offer a starting point for exploring links between transport inhibition and cancer cell growth.
17 · Targeting an atypical G protein–coupled receptor signaling pathway for cardiac fibrosis therapy
Science · Publication/issue date: 2026-09-24
Authors: Hao Zhang, Rabindra V. Shivnaraine, Lu Ren, Phung N. Thai, Remi Janicot, Wenjuan Zhu, Rihua Huang, Dirk H. Siepe, Chengyi Tu, Wenqiang Liu, Marcin Maziarz, Jonathan C. Deutsch, Yu Liu, Chun Liu, Danielle H. Shin, Hyeonyu Kim, Mark Chandy, Marian Kalocsay, Nipavan Chiamvimonvat, Mikel Garcia-Marcos, Brian K. Kobilka, Joseph C. Wu
The researchers built a drug-screening platform using cardiac cells derived from human induced pluripotent stem cells and tested candidates in primary fibroblasts, three-dimensional cardiac tissue and animal models of heart failure. The screen identified CGS15943, which inhibited fibroblast activation and fibrosis-related expression. Mechanistic analysis showed that although different adenosine receptors have distinct canonical Gα coupling modes, they can converge through Gβγ on PI3K–AKT and YAP signaling to form a profibrotic pathway. Combined blockade was more effective than targeting a single subtype, offering an explanation for previously inconsistent subtype studies. The findings support this shared signaling axis as a potential target, but improvements in cells and mice do not establish antifibrotic efficacy in people.
Highlight · Multiple adenosine receptors converge on profibrotic Gβγ signaling, providing a mechanistic basis for combined blockade.
Nature Reviews Drug Discovery · Publication/issue date: 2026-09-21
Authors: Liliana Halip, Sorin Avram, John P. Overington, Bissan Al-Lazikani, Ramona Curpan, Suman Sirimulla, Alexei Pushechnikov, Andrea Rosario Beccari, Nikolay Savchuck, Tudor I. Oprea
Over the past 25 years, genetics, genomics, proteomics and data technologies have transformed drug discovery, while therapeutic modalities have expanded beyond traditional small molecules and natural-product derivatives. This review surveys and quantifies changes in the drug-target landscape, covering the biomolecules through which drugs exert therapeutic effects and how the number and categories of targets have evolved. The authors’ analysis includes 686 biomolecules modulated by 1,702 drugs and discusses how new therapeutic modalities continue to shift the boundaries of druggability. These figures reflect the review’s own accounting framework, not the total number of all potential targets. The article is useful for understanding the long-term relationship between target selection and technological advances, rather than as treatment guidance for any single disease.
Highlight · New therapeutic modalities and omics technologies are expanding the target landscape, making druggability a moving concept.
Signal Transduction and Targeted Therapy · Publication/issue date: 2026-09-22
Authors: Maria Teresa De Angelis, Vincenzo Dattilo, Niccolò Vono, Valentina Lise, Michela Reda, Carmela De Marco, Antonia Rizzuto, Francesco Trapasso, Giuseppe Viglietto, Gianluca Santamaria
Retinoic acid, the active metabolite of vitamin A, is involved in embryonic development, adult tissue homeostasis and a range of disease processes. This review considers its synthesis, degradation, receptor signaling and pathway interactions across multiple organs, covering functions such as epithelial integrity, stem cells, immunity and metabolism. It emphasizes that retinoic acid’s role in cancer depends on context: it can promote differentiation, but under certain genetic and microenvironmental conditions may also support stemness. Organoids, single-cell analysis and spatial omics are revealing local and cell-type-specific responses, prompting the authors to propose a framework for retinoic acid states defined by tissue and disease stage. This may support stratified research, but broader therapeutic applications remain constrained by resistance, pharmacokinetics and tissue differences; successes in some settings cannot be generalized to all diseases.
Highlight · Retinoic acid’s effects depend on tissue, cell state and microenvironment; precision intervention requires identifying these differences.
This issue covers 19 scholarly publications and research software resources added to the Zotero personal library between September 21 and 27, 2026. Dates and ordering follow Beijing time and the time each item was added. Entries are grouped by topic and listed in reverse chronological order within each group; miscellaneous items appear at the end.
The summaries below were prepared by AI based on abstracts, with some abstracts supplemented from external sources; the full texts were not read in depth. Publication and issue dates follow the records and do not necessarily indicate publication this week. Book chapters and software resources are identified separately. A review on 5-HT7 appeared in an earlier issue and is included again because it was added to the library during this period.
Cryo-EM Sample Preparation and Radiation Damage (6 papers)
01 · Acoustofluidic cryo-EM enables in situ particle manipulation for uniform, high-quality cryo-EM specimens
Science Advances · Publication/issue date: 2026-09-25
Authors: Kaichun Yang, Wyatt Peele, Pengzhan Liu, Jianping Xia, Venkata Dandey, Ruoyu Zhong, Ke Jin, Kedar Sharma, Abigail J. Watson, Shujie Yang, Ying Chen, Aryan Agahtehrani, Shu Nakajima Lan, Peiran Zhang, Zhenhua Tian, Mingyuan Liu, Elizabeth Viverette, Xianchen Xu, Qian Wu, Mario J. Borgnia, Luke P. Lee, Tony Jun Huang
Uneven particle distribution during cryo-EM sample preparation reduces the number of usable particles and can compromise imaging, especially for dilute or unstable complexes. The authors introduce ACE, an acoustofluidic cryo-EM method that integrates contact-free acoustic manipulation into the standard plunge-freezing workflow. By vibrating the grid and generating localized acoustic flow, it redistributes particles within the sample. Experiments with liposomes and apoferritin showed up to a fourfold increase in local particle density under the tested conditions, while preserving structural integrity and improving image quality. The approach offers a way to actively adjust particle distribution during preparation, but the maximum gain comes from specific test systems and should not be assumed for all samples; the stability of each target complex also needs evaluation.
Highlight · Acoustic manipulation can redistribute particles locally before freezing, increasing usable particle density in specific samples.
DOI: 10.1126/sciadv.aeh5900
02 · Control of ice thickness in cryo-EM via confinement
Nature Methods · Publication/issue date: 2026-09-25
Authors: Liming Zheng, Jiling Song, Xiaole Zhao, Jiacong Cao, Jie Xu, Zhengni Wang, Chenhui Zhang, Weiyu Sun, Buhang Chen, Xiaoyin Gao, Haonan Liu, Junhao Yang, Yu Xu, Luzhao Sun, Zhaohe Dai, Xiaoding Wei, Nan Liu, Hailin Peng, Hong-Wei Wang
Ice thickness directly affects cryo-EM image quality, but the instability of the liquid film before freezing makes it difficult to control precisely. The authors identify instability in films thinner than 100 nm as a key factor and use a designed graphene reservoir structure to spatially confine the film. Varying the reservoir depth allows the ice thickness to be tuned, producing confined ice layers that are relatively uniform and reproducible across larger areas. The abstract reports improved contrast, reduced motion and better orientation distributions across several macromolecular samples, helping with high-resolution reconstruction. The work links ice-thickness control to liquid-film stabilization, though specific benefits still need validation for each target particle, support material and preparation condition.
Highlight · Confining the liquid film with graphene structures shifts ice-thickness control from trial and error toward geometric constraint.
DOI: 10.1038/s41592-026-03244-1
03 · On-grid enrichment strategies in cryo-EM: affinity-functionalized supports for low-abundance and challenging targets
Acta Crystallographica Section D: Structural Biology · Publication/issue date: 2026-10-01
Authors: P. Mili, O. J. Chetia, U. Das
This review focuses on on-grid enrichment of low-abundance and challenging targets. Membrane proteins, endogenous complexes, chromatin-associated assemblies and transient signaling intermediates are often limited by sample availability, dissociation, denaturation and preferred orientation. Affinity-functionalized support films can selectively capture and enrich particles before vitrification, increasing local concentration and recovery; some implementations may also reduce exposure to the air–water interface. The authors compare platforms including Ni–NTA lipid monolayers, streptavidin grids, antibody supports, graphene-derived materials and magnetic nanoparticles, discussing their respective strengths and limitations. The broader shift is toward support films as active biochemical interfaces, but capture strategies must be matched to the target; enrichment cannot be assumed to preserve every aspect of the native state.
Highlight · Affinity grids turn support films into selective capture interfaces, expanding preparation options for scarce and unstable complexes.
DOI: 10.1107/S2059798326009605
04 · Chapter Fifteen - Radiation Damage in Electron Cryomicroscopy
Cryo-EM Part A Sample Preparation and Data Collection · Publication/issue date: 2010-01-01
Authors: Lindsay A. Baker, John L. Rubinstein
This book chapter reviews radiation damage in cryo-EM and how it limits resolution. The electron beam damages the sample even as it records signal: initial processes include ionization, bond breaking and radical formation, followed by the migration of secondary electrons and radicals that drive further reactions. Gas formation can cause more substantial morphological changes. This creates a fundamental trade-off between collecting enough statistical signal and limiting damage. The chapter addresses practical issues such as measuring electron exposure, estimating absorbed dose, accelerating voltage, sample temperature and exposure choices, and explains the importance of low temperatures and dose limits. It provides a framework for understanding imaging trade-offs—not a basis for treating lower temperatures or longer exposures as simple, guaranteed ways to improve structural quality.
Highlight · Radiation damage occurs throughout electron exposure, forcing a trade-off between signal statistics and sample preservation.
DOI: 10.1016/S0076-6879(10)81015-8
05 · Reducing the effects of radiation damage in cryo-EM using liquid helium temperatures
Proceedings of the National Academy of Sciences · Publication/issue date: 2025-04-29
Authors: Joshua L. Dickerson, Katerina Naydenova, Mathew J. Peet, Hugh Wilson, Biplob Nandy, Greg McMullan, Robert Morrison, Christopher J. Russo
Lowering sample temperature further should, in theory, reduce radiation damage, but earlier single-particle experiments at liquid-helium temperatures did not fully realize the expected gains. The authors identified and addressed factors that caused information loss under these conditions. Combining nanoscale electron-beam illumination with perforated gold supports yielded more information in every exposure frame than under liquid-nitrogen conditions. The study also notes that hole edges appear in images, damaged proteins tend to accumulate at those edges, and unnecessary irradiation of water and support foil should be minimized. The results show that the benefits of low temperatures depend on coordinating illumination, support and particle distribution—not temperature alone. These factors need to be considered together when designing new microscopes and sample carriers to harness the potential of reduced damage at lower temperatures.
Highlight · Imaging at liquid-helium temperatures benefits from nanoscale beam illumination and support design; cooling alone is not enough.
DOI: 10.1073/pnas.2421538122
06 · Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins
Proceedings of the National Academy of Sciences · Publication/issue date: 2021-11-23
Authors: Joël S. Bloch, Somnath Mukherjee, Julia Kowal, Ekaterina V. Filippova, Martina Niederer, Els Pardon, Jan Steyaert, Anthony A. Kossiakoff, Kaspar P. Locher
Small membrane proteins are difficult to align in cryo-EM and need auxiliary structures that are both stable and easy to identify. The authors developed NabFab, which binds nanobody frameworks with high affinity while minimizing interference with nanobody–target interactions. Transplanting the recognition loops onto a compatible framework allows nanobodies from different sources and against different targets to use the same Fab module. The module adds mass and provides a fiducial marker; using it, the researchers resolved high-resolution structures of two small membrane proteins of about 50 kDa. An additional anti-Fab nanobody also helped with initial 3D reconstruction. The results demonstrate the module’s reusability, though its binding, rigidity and ability to preserve conformation should be checked for each new target.
Highlight · NabFab recognizes a common nanobody framework, providing a reusable mass and alignment aid for small membrane proteins.
DOI: 10.1073/pnas.2115435118
Crystallographic Imaging and Data Processing (3 papers)
07 · Macromolecular diffractive imaging using imperfect crystals
Nature · Publication/issue date: 2016-02
Authors: Kartik Ayyer, Oleksandr M. Yefanov, Dominik Oberthür, Shatabdi Roy-Chowdhury, Lorenzo Galli, Valerio Mariani, Shibom Basu, Jesse Coe, Chelsie E. Conrad, Raimund Fromme, Alexander Schaffer, Katerina Dörner, Daniel James, Christopher Kupitz, Markus Metz, Garrett Nelson, Paulraj Lourdu Xavier, Kenneth R. Beyerlein, Marius Schmidt, Iosifina Sarrou, John C. H. Spence, Uwe Weierstall, Thomas A. White, Jay-How Yang, Yun Zhao, Mengning Liang, Andrew Aquila, Mark S. Hunter, Joseph S. Robinson, Jason E. Koglin, Sébastien Boutet, Petra Fromme, Anton Barty, Henry N. Chapman
Protein crystal structures are usually determined from Bragg diffraction, while the continuous diffraction produced by imperfect lattices is often ignored. Using photosystem II as an example, the authors show that positional disorder in a lattice can preserve additional molecular structural information rather than simply degrade data quality. They used the molecular envelope from conventional analysis as a constraint, advancing dimer imaging from information limited to about 4.5 Å by measurable Bragg peaks to about 3.5 Å. The results show that appropriate treatment of continuous diffraction may overcome resolution limits imposed by analyzing discrete diffraction peaks alone. The work reappraises the value of imperfect crystals, but its approach depends on the form of disorder and the overall molecular structure; it does not mean that any low-quality crystal will yield similar improvements.
Highlight · Continuous diffraction from lattice disorder can add structural information, giving imperfect crystals potential for high-resolution imaging.
DOI: 10.1038/nature16949
Additional abstract source
08 · CrystalPilot: a browser interface for XDS crystallographic data processing
Zenodo (software resource) · Publication/issue date: 2026-09-26
Author: Mikael Elias
Software resource: CrystalPilot is a browser-based interface for XDS crystallographic data processing, hosted on Zenodo; it is not a journal article. It brings project management, input-file editing, analysis of indexing and integration results, resolution-cutoff assessment and inspection of scaling results into one interface. Features include automated processing of single datasets or batches, frame viewing and Table 1 generation. A learning-oriented workflow is also part of its design. The available abstract mainly lists features and provides no independent performance comparisons or processing-accuracy data, so no claim is made here that it outperforms other interfaces. It may help reduce repetitive work and organize XDS processing steps, but data quality and parameter choices still need to be assessed from the outputs.
Highlight · CrystalPilot brings XDS project management, parameters, diagnostics and batch processing together in a browser interface.
DOI: 10.5281/zenodo.22980310
09 · Serendipitous crystal structure of mJuniper, a rationally designed cyan fluorescent protein
Acta Crystallographica Section F: Structural Biology Communications · Publication/issue date: 2026-10-01
Authors: A. Aydin, N. Fraikin, P. Lagoutte, C. Lesterlin, L. Terradot
mJuniper is a monomeric cyan fluorescent protein optimized for bacterial imaging. Its rapid maturation makes it suitable for time-course observations. The authors initially used it to improve the solubility of another target protein, but unexpectedly obtained a high-resolution crystal structure of mJuniper while attempting structural studies. The structure shows the typical β-barrel fold and two rotational isomeric states of the chromophore; the abstract links this difference to specific radiation damage occurring nearby. The work adds structural information about this imaging tool and also serves as a reminder that local conformational heterogeneity in crystals may reflect changes caused by the measurement process. It does not establish that both states represent the native functional distribution in the absence of irradiation.
Highlight · The unexpected mJuniper crystal structure provides a structural reference and shows that radiation damage can alter local chromophore conformation.
DOI: 10.1107/S2053230X26009052
Serotonin Receptors and Neuropsychiatric Drugs (3 papers)
10 · Potential role of 5-HT7 receptor antagonists in the treatment of depression: Pharmacological and bioengineering perspectives
Progress in Neuro-Psychopharmacology and Biological Psychiatry · Publication/issue date: 2026-08-30
Authors: Arghya Kusum Dhar, Ruchi Keswani, Kuttiappan Anitha, Gauri Pathak, Aryaa Nigade, Shvetank Bhatt
This review discusses the potential value of 5-HT7 receptor antagonism in depression research. The receptor is associated with mood, circadian rhythms and cognition, and signals mainly through the Gαs/cAMP pathway, although other coupling mechanisms have also been reported. The authors summarize evidence that selective antagonists produce antidepressant-like effects in rodent behavioral models and discuss how bioengineering platforms, human-relevant models and targeted delivery to the central nervous system could help clarify the mechanisms. They emphasize that the receptor is found in both peripheral and central tissues, making tissue selectivity important. Current evidence supports further investigation, but behavioral changes in animals cannot be equated directly with symptom improvement in patients and are not enough to define a clinical treatment strategy.
Highlight · Translational research on 5-HT7 antagonism needs to address human-relevant models, tissue selectivity and delivery.
DOI: 10.1016/j.pnpbp.2026.111915
11 · Structure-based design of subtype-selective psychedelic analogs
Nature Communications · Publication/issue date: 2026-09-17
Authors: Huiqiong Li, Lingjie Tang, Jinfeng Zhang, Bing Meng, Dongmei Cao, Yujin Chen, Jing Yu, Huan Wang, Zhi-Jie Liu, Sheng Wang, Jianjun Cheng
Drug development based on classic psychedelics aims to preserve activity at 5-HT2A while avoiding activation of 5-HT2B, which is associated with heart valve risks. The authors compared ligand-binding pockets in the two receptor subtypes, used key differences to build a structure-guided model, and developed two series of candidates that act as 5-HT2A agonists and 5-HT2B antagonists. Cryo-EM structures of several receptor–ligand complexes support their explanation of subtype selectivity, and some candidates also showed antidepressant-like effects in animal models. By linking structural differences to functional selectivity, the study offers a strategy for reducing off-target receptor activity. However, receptor selectivity and animal behavior do not establish clinical safety or efficacy; more extensive validation is needed.
Highlight · Comparing the binding pockets of related receptors can guide candidates that combine 5-HT2A agonism with 5-HT2B antagonism.
DOI: 10.1038/s41467-026-77658-y
12 · Mechanistic Basis for 5-HT2AR Over 5-HT2BR Activation
Nature Communications · Publication/issue date: 2026-09-17
Authors: Lingjie Tang, Xin Ji, Yumeng Wang, Dongmei Cao, Huiqiong Li, Licong He, Jianjun Cheng, Sheng Wang
This study further examines why similar ligands produce different functional effects at 5-HT2A and 5-HT2B. The authors systematically examined lateral and extended binding regions, finding that local steric hindrance and conformational constraints can affect ligand orientation and, in turn, receptor signaling. Based on these insights, they combined interactions with the binding regions and scaffold modifications across different chemical scaffolds to find designs that enhance 5-HT2A activation while limiting 5-HT2B activity. Cryo-EM structures of both receptors bound to representative candidates support the proposed mechanism. The work adds a structural rationale for subtype selectivity, but a plausible mechanism does not mean all adverse effects have been eliminated; therapeutic value will need to be assessed through broader pharmacological and clinical studies.
Highlight · Spatial constraints in the binding pocket affect signaling by shaping ligand orientation, offering a mechanistic framework for distinguishing 5-HT2A from 5-HT2B activation.
DOI: 10.1038/s41467-026-77659-x
In Situ Cellular Structures and Time-Resolved Cryo-ET (2 papers)
13 · Single-cell visual proteomics of a minimal bacterium reveals structural coordination of gene expression machineries
Cell · Publication/issue date: 2026-09-25
Authors: Joseph M. Dobbs, Rasmus K. Jensen, Julia Mahamid
The study used cryo-electron tomography to examine native Mycoplasma pneumoniae cells and cells exposed to antibiotics, resolving 140 structural maps spanning translation initiation, elongation and recycling. In situ observations of several transcription–translation complexes led the authors to propose a translation reinitiation mechanism linked to “threading” and provided structural evidence for a supercomplex coordinating transcription, translation and membrane attachment. They also found many membrane-associated large ribosomal subunits, suggesting that their release from the membrane may be tied to the conditions that initiate another round of translation. By placing gene-expression machinery back in its cellular context, the work reveals multiple layers of coordination among processes; proposed explanations for reinitiation and membrane release should be distinguished from the structural features directly observed.
Highlight · In-cell structural maps connect transcription, translation and membrane attachment, revealing organization that isolated-molecule studies cannot capture.
DOI: 10.1016/j.cell.2026.08.054
14 · Strategies for time-resolved cryogenic electrontomography of transient cellular processes
Current Opinion in Structural Biology · Publication/issue date: 2026-12-01
Author: Arjen J. Jakobi
Cryo-electron tomography captures local cellular structures at the moment of vitrification, while time-resolved studies aim to relate these static observations to defined perturbations or stages of transient processes. This review outlines four experimental routes for introducing temporal information and discusses the conditions needed for reliable structural and temporal interpretation. Common requirements include being able to generate or identify the target state reproducibly and collecting enough samples to compare stages. The review also emphasizes that all methods face challenges in state selection, assigning timing and interpreting results. Its value lies in treating time-resolved cryo-ET as a matter of experimental design and sampling, rather than simply adding timestamps to tomograms. The abstract does not detail the four routes, so no specific categories are added here.
Highlight · Reliable time-resolved cryo-ET depends on identifiable states, clear temporal links and enough samples for comparison.
DOI: 10.1016/j.sbi.2026.103385
Organic Cation Transport (2 papers)
15 · Molecular basis of polyspecific drug and xenobiotic recognition by OCT1 and OCT2
Nature Structural & Molecular Biology · Publication/issue date: 2023-07
Authors: Yang Suo, Nicholas J. Wright, Hugo Guterres, Justin G. Fedor, Kevin John Butay, Mario J. Borgnia, Wonpil Im, Seok-Yong Lee
OCT1 and OCT2 mediate the uptake and clearance of various organic cations in the liver and kidneys, respectively, and are important in drug disposition and interactions. The authors resolved four cryo-EM structures of consensus variants of the two transporters in apo, substrate-bound and drug-bound conditions, covering outward-open and outward-closed states. Combined with functional assays, molecular docking and dynamics simulations, the study examines how each transporter accommodates structurally diverse cations and how its extracellular gate closes. The work provides structural principles for polyspecific substrate recognition and a reference for understanding transporter-related drug interactions. Because the study used consensus variants and a limited set of conformations, specific native transporters and drug combinations still need to be evaluated individually.
Highlight · Multiple OCT1/2 conformations link broad cation recognition to the mechanism of extracellular gate closure.
DOI: 10.1038/s41594-023-01017-4
16 · Structural and mechanistic insights into OCTN1-mediated transport and cancer cell proliferation
Nature Communications · Publication/issue date: 2026-09-14
Authors: Binghong Xu, Shengjian Liang, Ziyu Wang, Xiaoyu Zhou, Liuying Wang, Qinqin Liang, Xiaoke Liu, Wei Guo, Sai Shi, Cheng Zhu, Sheng Ye, Zhiyong Lou, Yaxin Wang
OCTN1 transports ergothioneine and other metabolites, as well as various drugs, across membranes; its dysregulation is also associated with cancer-related processes. The authors determined cryo-EM structures of human OCTN1 in apo and ergothioneine-bound states, located the substrate-binding region and analyzed the conformational changes required for sodium-dependent transport. Structure-based virtual screening identified mebendazole as an inhibitor of the transporter, and experiments found that it suppressed the proliferation of cervical and lung cancer cells. The study thus connects substrate-recognition mechanisms with candidate drug screening and provides a basis for targeting this transporter. However, cell proliferation results do not demonstrate patient benefit, and the contribution of other drug targets and the drug’s effects in vivo still need to be distinguished.
Highlight · OCTN1 structures reveal ergothioneine recognition and offer a starting point for exploring links between transport inhibition and cancer cell growth.
DOI: 10.1038/s41467-026-77727-2
Other Papers (3 papers)
17 · Targeting an atypical G protein–coupled receptor signaling pathway for cardiac fibrosis therapy
Science · Publication/issue date: 2026-09-24
Authors: Hao Zhang, Rabindra V. Shivnaraine, Lu Ren, Phung N. Thai, Remi Janicot, Wenjuan Zhu, Rihua Huang, Dirk H. Siepe, Chengyi Tu, Wenqiang Liu, Marcin Maziarz, Jonathan C. Deutsch, Yu Liu, Chun Liu, Danielle H. Shin, Hyeonyu Kim, Mark Chandy, Marian Kalocsay, Nipavan Chiamvimonvat, Mikel Garcia-Marcos, Brian K. Kobilka, Joseph C. Wu
The researchers built a drug-screening platform using cardiac cells derived from human induced pluripotent stem cells and tested candidates in primary fibroblasts, three-dimensional cardiac tissue and animal models of heart failure. The screen identified CGS15943, which inhibited fibroblast activation and fibrosis-related expression. Mechanistic analysis showed that although different adenosine receptors have distinct canonical Gα coupling modes, they can converge through Gβγ on PI3K–AKT and YAP signaling to form a profibrotic pathway. Combined blockade was more effective than targeting a single subtype, offering an explanation for previously inconsistent subtype studies. The findings support this shared signaling axis as a potential target, but improvements in cells and mice do not establish antifibrotic efficacy in people.
Highlight · Multiple adenosine receptors converge on profibrotic Gβγ signaling, providing a mechanistic basis for combined blockade.
DOI: 10.1126/science.aej5896
18 · The evolving landscape of drug targets
Nature Reviews Drug Discovery · Publication/issue date: 2026-09-21
Authors: Liliana Halip, Sorin Avram, John P. Overington, Bissan Al-Lazikani, Ramona Curpan, Suman Sirimulla, Alexei Pushechnikov, Andrea Rosario Beccari, Nikolay Savchuck, Tudor I. Oprea
Over the past 25 years, genetics, genomics, proteomics and data technologies have transformed drug discovery, while therapeutic modalities have expanded beyond traditional small molecules and natural-product derivatives. This review surveys and quantifies changes in the drug-target landscape, covering the biomolecules through which drugs exert therapeutic effects and how the number and categories of targets have evolved. The authors’ analysis includes 686 biomolecules modulated by 1,702 drugs and discusses how new therapeutic modalities continue to shift the boundaries of druggability. These figures reflect the review’s own accounting framework, not the total number of all potential targets. The article is useful for understanding the long-term relationship between target selection and technological advances, rather than as treatment guidance for any single disease.
Highlight · New therapeutic modalities and omics technologies are expanding the target landscape, making druggability a moving concept.
DOI: 10.1038/s41573-026-01530-3
19 · Retinoic acid in health and disease
Signal Transduction and Targeted Therapy · Publication/issue date: 2026-09-22
Authors: Maria Teresa De Angelis, Vincenzo Dattilo, Niccolò Vono, Valentina Lise, Michela Reda, Carmela De Marco, Antonia Rizzuto, Francesco Trapasso, Giuseppe Viglietto, Gianluca Santamaria
Retinoic acid, the active metabolite of vitamin A, is involved in embryonic development, adult tissue homeostasis and a range of disease processes. This review considers its synthesis, degradation, receptor signaling and pathway interactions across multiple organs, covering functions such as epithelial integrity, stem cells, immunity and metabolism. It emphasizes that retinoic acid’s role in cancer depends on context: it can promote differentiation, but under certain genetic and microenvironmental conditions may also support stemness. Organoids, single-cell analysis and spatial omics are revealing local and cell-type-specific responses, prompting the authors to propose a framework for retinoic acid states defined by tissue and disease stage. This may support stratified research, but broader therapeutic applications remain constrained by resistance, pharmacokinetics and tissue differences; successes in some settings cannot be generalized to all diseases.
Highlight · Retinoic acid’s effects depend on tissue, cell state and microenvironment; precision intervention requires identifying these differences.
DOI: 10.1038/s41392-026-03055-y