Mariusz Mozajew, Maciej Sikora, Mateusz Fortunka, Agata P Perlinska, Anna Kluza, Szymon Niewieczerzal, Fernando Bruno da Silva, Maciej Lukaszewicz, Julia A Sikorska, Lena J Mikulska, Sophie E Jackson, Joanna I Sulkowska
{"title":"Unique features of EIGHT fold-Proteins with the most complex 8<sub>3</sub> knotted topology.","authors":"Mariusz Mozajew, Maciej Sikora, Mateusz Fortunka, Agata P Perlinska, Anna Kluza, Szymon Niewieczerzal, Fernando Bruno da Silva, Maciej Lukaszewicz, Julia A Sikorska, Lena J Mikulska, Sophie E Jackson, Joanna I Sulkowska","doi":"10.1073/pnas.2523017123","DOIUrl":"https://doi.org/10.1073/pnas.2523017123","url":null,"abstract":"<p><p>Herein, we present three crystal structures of the most complex knotted protein to date, an [Formula: see text] knot with eight crossings, which belongs to a clasp knot family. The fold of this protein is also unique, and we call it the EIGHT fold (Extraordinarily Intricate Globular Helical Tangled fold). The [Formula: see text] knot is found only in a certain group of bacteria, where it is strictly conserved, despite sequence identities as low as 10%. The [Formula: see text] structure shows a high level of internal symmetry, with structurally analogous halves. It is possible that the EIGHT fold evolved from a single unknotted \"half\" that duplicated and formed a complex protein. Based on an in vitro study of three selected [Formula: see text] proteins, we estimated their thermal and thermodynamic stability, and showed that they follow a two-state unfolding model under equilibrium conditions and their refolding occurs to a compact, nonnative state. Unfolding kinetics of [Formula: see text] knotted proteins reveal a complex, multiphase process spanning milliseconds to days. Six kinetic phases were resolved using stopped-flow fluorescence and far-ultraviolet absorbance circular dichroism spectroscopy, highlighting both rapid early events and slower rearrangements in secondary and tertiary structures. Finally, with a structure-based model, we showed that proteins with an [Formula: see text] knot can self-tie through a [Formula: see text] knotted intermediate state. They can also self-untie, albeit via an additional intermediate knot such as [Formula: see text]. Nevertheless, these proteins do not seem to fit with current folding theories known to date and require the development of a new approach.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 43","pages":"e2523017123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Umeshkumar Vekariya, Benjamin Lee Prather, Roland L Dunbrack, Rongsheng E Wang, Tomasz Skorski
{"title":"PSF3 recruits Polθ to stalled replication forks to promote DNA repair.","authors":"Umeshkumar Vekariya, Benjamin Lee Prather, Roland L Dunbrack, Rongsheng E Wang, Tomasz Skorski","doi":"10.1073/pnas.2613699123","DOIUrl":"https://doi.org/10.1073/pnas.2613699123","url":null,"abstract":"<p><p>DNA polymerase theta (Polθ) plays a pivotal role in the maintenance of stalled replication forks. However, little is known about how Polθ is recruited to the stalled forks. Here we show that PSF3, a member of GINS replicative complex, recruits Polθ to the stalled replication forks. Polθ, which is recruited by interacting with the C-terminal portion of PSF3, restarts the forks, exerts DNA double-strand break end-joining to repair the breaks resulting from collapsed forks in BRCA1/2-deficient and proficient tumor cells, and also fills single-stranded gaps on the replication fork lagging strand in BRCA1/2-deficient tumor cells. Thus, PSF3-Polθ interaction promotes the proliferation of homologous recombination-deficient and proficient tumor cells. Overall, this study highlights an important mechanism of Polθ recruitment to the stalled replication forks to maintain Polθ-dependent fork protection in tumor cells.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 43","pages":"e2613699123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Programmable chemoenzymatic synthesis of a keratan sulfate <i>N</i>-glycan library for glycocode decoding.","authors":"Kaixuan Wang, Wenjing Ma, Wei Zhang, Tianhui Hao, Mengjia Zhang, Wentao Li, Wei Zhao, Zhuojia Xu, Tiehai Li","doi":"10.1073/pnas.2621414123","DOIUrl":"https://doi.org/10.1073/pnas.2621414123","url":null,"abstract":"<p><p>Keratan sulfate (KS) is a unique and widely distributed glycosaminoglycans family implicated in diverse biological processes. KS features branched glycan architectures with diverse sialylation and sulfation patterns, encoding a vastly expanded chemical and biological space. The limited accessibility of well-defined structures has hindered precise investigations into the KS biological functions. Here we report a programmable chemoenzymatic platform for assembling a 106-membered library of KS <i>N</i>-glycans and their nonsulfated counterparts, featuring length-variable oligo-<i>N</i>-acetyllactosamine (LacNAc) extensions and encompassing diverse sulfation and sialylation patterns. The synthetic strategy integrates length-controlled iterative glycosylation to assemble versatile precursors, orthogonal deprotection for site-specific sulfation, and modular enzyme-driven diversification. Glycan microarray analysis of this comprehensive library reveals that glycan-protein recognition is governed by the interplay of sulfation and sialylation patterns, oligo-LacNAc chain length, and terminal epitope presentation, providing insight into the functional versatility of KS glycans.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 43","pages":"e2621414123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Harnessing autoantibodies to target pathogenic plasma cells.","authors":"Julia I Ellyard, Anselm Enders","doi":"10.1073/pnas.2631232123","DOIUrl":"https://doi.org/10.1073/pnas.2631232123","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 43","pages":"e2631232123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaochao Tan, Shike Wang, Sieun Lee, Guan-Yu Xiao, Derrick L Cardin, Dakai Zhang, Yuting Xu, Chao Wu, Biyao Zhou, William K Russell, Guangwei Du
{"title":"PLD1-driven oncogenic secretion creates a therapeutic vulnerability in chromosome 3q-amplified NSCLC.","authors":"Xiaochao Tan, Shike Wang, Sieun Lee, Guan-Yu Xiao, Derrick L Cardin, Dakai Zhang, Yuting Xu, Chao Wu, Biyao Zhou, William K Russell, Guangwei Du","doi":"10.1073/pnas.2532484123","DOIUrl":"https://doi.org/10.1073/pnas.2532484123","url":null,"abstract":"<p><p>Chromosome 3q (3q) amplification is a frequent event in non-small cell lung cancer (NSCLC) and other cancer types, yet therapeutic strategies targeting oncogenic drivers within this amplicon have been unsuccessful. Our study revealed that the 3q amplicon encodes multiple Golgi-related proteins, including Phospholipase D1 (PLD1), which catalyzes the production of a potential oncogenic lipid, phosphatidic acid. We found that PLD1 is highly expressed in 3q-amplified NSCLC (3q-NSCLC) and its enzymatic activity is further boosted by coamplified PLD1 activator, ARF-like GTPase 14. High PLD1 activity is essential for 3q-NSCLC growth and metastasis. Mechanistically, PLD1 drives secretion of oncogenic factors via the carriers from the trans Golgi network to the cell surface pathway to support tumor growth. Transferrin receptor 1 (TFRC), which encodes a membrane protein, is coamplified with PLD1 and overexpressed in 3q-NSCLC. A TFRC antibody-drug conjugate (ADC) carrying a PLD1 inhibitor exhibited potential antitumor activity in mouse models. These findings establish PLD1 as a promoter of 3q-NSCLC and provide proof of concept for the development of PLD1-targeted therapies, including ADC-based approaches, for this challenging cancer subtype.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 43","pages":"e2532484123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The honey bee stinger: An unusual pump with collapsible double pistons.","authors":"Fiorella Ramirez-Esquivel, Claudia Klose, Hyun Chai Lee, Quinn Graco, Ajay Narendra, Sridhar Ravi","doi":"10.1073/pnas.2603916123","DOIUrl":"https://doi.org/10.1073/pnas.2603916123","url":null,"abstract":"<p><p>Most stinging animals deliver venom by contracting muscles around a venom reservoir, but honey bees employ a fundamentally different strategy. The stingers of worker bees have the unique ability to autotomize, separating from the body, to continue to sting independently. Despite more than a century of anatomical descriptions, the mechanics of venom pumping have remained unresolved due to the challenges of observing them in action. We recorded high-speed videos of active, autotomized stingers, combined with micro computed tomography-based three-dimensional reconstruction to characterize the biomechanics of stinging in the honey bee <i>Apis mellifera</i>. We reveal that the stinger functions as a unique double-piston micro-pump. Two lancets, each possessing a deformable valve, slide in antiphase within a bulb chamber. These valves dynamically deform to alternately form a seal during the downstroke and collapse during the upstroke, enabling pressure generation for pumping while potentially minimizing backflow during refilling. The inverted tear-drop shape of the bulb facilitates refill even while pumping proceeds. We explored valve deformations and flow behavior by constructing a dynamically scaled physical model of the bulb chamber confirming key features of the pumping cycle and propose mechanisms for valve deformations. The double piston design adds significant design complexity but enables continuous venom delivery in a compact, autonomous unit. These findings provide deeper understanding of venom pumping in honey bees and other Hymenoptera. This study also provides evidence of an axial piston pump within a biological system and offers inspiration for the design of microfluidic pumping devices.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 43","pages":"e2603916123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149168539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nishant Joshi, Xuan Yan, Niccoló Calcini, Payam Safavi, Asli Ak, Koen Kole, Sven van der Burg, Tansu Celikel, Fleur Zeldenrust
{"title":"Neuromodulatory control of cortical function: Cell-type-specific regulation of neuronal information transfer.","authors":"Nishant Joshi, Xuan Yan, Niccoló Calcini, Payam Safavi, Asli Ak, Koen Kole, Sven van der Burg, Tansu Celikel, Fleur Zeldenrust","doi":"10.1073/pnas.2609893123","DOIUrl":"https://doi.org/10.1073/pnas.2609893123","url":null,"abstract":"<p><p>Neuromodulatory systems such as dopamine and acetylcholine enable cortical circuits to rapidly shift between behavioral states, yet it remains unclear how receptor-specific signaling reshapes what single neurons compute. Here, we combined whole-cell recordings from excitatory and inhibitory neurons in layer 2/3 of mouse somatosensory cortex with information-theoretic analyses under frozen-noise stimulation. We quantified stimulus-to-spike information transfer and profiled each neuron across four functional domains: passive membrane biophysics, action potential dynamics, intrinsic adaptation currents, and input feature selectivity captured by spike-triggered averages. Activation of D1, D2, or M1 receptors revealed three main findings. First, neuromodulators altered fractional information and firing output in a cell-type- and receptor-specific manner, demonstrating selective regulation of encoding. Second, unsupervised clustering based on functional attribute sets showed that receptor activation reorganizes baseline functional grouping, consistent with a dynamic computational phenotype. Third, multiset correlation and factor analysis revealed that neuromodulation systematically reorganizes covariance among functional domains. In excitatory neurons, dopaminergic activation decreased coordination between input feature selectivity and other functional properties while strengthening coordination among response-based features such as spike dynamics and adaptation. Inhibitory neurons, by contrast, generally exhibited increased coordination across domains. In unison, these findings identify neuromodulation as a reconfiguration signal that reshapes not only individual cellular properties, but also the statistical architecture linking them across the recorded cohort, thereby revealing a higher-dimensional mode of single-neuron regulatory control in the cortex.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 43","pages":"e2609893123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fanjie Meng, George A Pantelopulos, Jae-Yeol Kim, Robert B Best, Hoi Sung Chung
{"title":"Heterogeneous amyloid β dimerization revealed by single-molecule FRET and MD simulation.","authors":"Fanjie Meng, George A Pantelopulos, Jae-Yeol Kim, Robert B Best, Hoi Sung Chung","doi":"10.1073/pnas.2618695123","DOIUrl":"https://doi.org/10.1073/pnas.2618695123","url":null,"abstract":"<p><p>The correlation between specific amyloid fibril polymorphs and diseases suggests that characterization of heterogeneity in the aggregation process is key to understanding disease mechanisms. In this work, we use single-molecule Förster resonance energy transfer (FRET) spectroscopy and molecular dynamics (MD) simulation to quantitatively characterize dimerization of amyloid β (Aβ), the first step of the aggregation process. We find that dimerization is extremely rare, with a high dissociation constant of >16 mM, yet there are multiple dimer states with distinct FRET efficiencies and stabilities, many of which survive for milliseconds to seconds. The dimer population increases with the increasing ionic strength and decreasing pH, indicating the importance of nonspecific electrostatic interactions in dimer formation. MD simulations with enhanced sampling demonstrate the formation of diverse bound states having a range of FRET efficiencies and flexible N termini, compatible with the experimental observations. There are conformational clusters represented by the formation of three mixed parallel/antiparallel β strands forming Greek key-like motifs and the formation of antiparallel β strands, which may be representative of dimers with longer and shorter lifetimes, respectively, observed in the FRET experiment. This structural and kinetic heterogeneity, resulting from transient interactions, reflects the rugged energy landscape of amyloid formation and may be related to the great diversity of fibrils ultimately formed in the aggregation process.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 43","pages":"e2618695123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Transient ATM inhibition enhances knock-in efficiency in hematopoietic stem cells by attenuating the DNA damage response.","authors":"Munkh-Erdene Natsagdorj, Hiromasa Hara, Kohei Iida, Yuji Kashiwakura, Nemekhbayar Baatartsogt, Enkhzaya Ganzorig, Daniele Canarutto, Sandra Pinho, Luigi Naldini, Tsukasa Ohmori, Yutaka Hanazono, Fumio Nakahara","doi":"10.1073/pnas.2531364123","DOIUrl":"https://doi.org/10.1073/pnas.2531364123","url":null,"abstract":"<p><p>Precise genome editing in hematopoietic stem cells (HSCs) holds great potential for treating inherited blood disorders; however, low knock-in (KI) efficiency and loss of functional HSCs after genome editing remain major obstacles. Here, we demonstrate that transient inhibition of Ataxia-Telangiectasia Mutated (ATM) kinase markedly enhanced KI efficiency in mouse HSCs genome-edited with Cas9/ribonucleoprotein (RNP) and AAV donor DNA. Phosphoproteomic and capillary western blot analyses revealed that ATM inhibition suppressed aberrant Cas9-AAV-induced ATM activation and the subsequent DNA damage response, reduced p53-dependent apoptosis, and enhanced survival of KI HSCs. In serial transplantation assays, ATM inhibition preserved long-term engrafting KI HSCs, increasing their frequency from ~0.3 to 40% in secondary recipients, an over 100-fold improvement. Furthermore, in an X-linked severe combined immunodeficient mouse model, ATM inhibition increased KI efficiency and restored T- and B cell differentiation. Comprehensive safety analyses, including long-read nanopore sequencing, amplicon deep sequencing, whole genome sequencing and clonal tracking, did not detect increased genomic alterations, chromosomal abnormalities, or clonal expansion following transient ATM inhibition. Taken together, these findings establish transient ATM inhibition as an effective strategy to enhance KI-mediated genome editing while maintaining the long-term repopulating capacity of HSCs.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 43","pages":"e2531364123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mechanism of HIV-1 capsid rupture and uncoating by reverse transcription.","authors":"Kuntal Ghosh, Manish Gupta, Gregory A Voth","doi":"10.1073/pnas.2617714123","DOIUrl":"https://doi.org/10.1073/pnas.2617714123","url":null,"abstract":"<p><p>One of the key events in the HIV-1 life cycle is reverse transcription (RT), during which single-stranded viral RNA (ssRNA) is converted into double-stranded DNA (dsDNA). This process occurs inside the mature HIV-1 capsid and, once it reaches a critical threshold, drives capsid rupture. This uncoating is essential for infection because it releases viral genetic material into the host cell nucleus. Despite its importance, many mechanistic details of this process remain to be fully understood. To address this gap, we develop a multiscale computational method for simulating RT inside the capsid, termed Coarse-Grained Kinetic Monte Carlo (CG-KMC). CG-KMC stochastically adds deoxynucleotide triphosphates (dNTPs) to the coarse-grained RNA model, enabling stepwise growth of DNA inside the HIV-1 capsid. We implement this method within an integrative coarse-grained framework that combines a \"bottom-up\" capsid model with a \"top-down\" representation of the viral RNA/DNA genome. Our simulations phenomenologically capture and predict diverse capsid rupture pathways during RT. The resulting ruptured structures closely match previously identified cryo-ET images. We further perform an extensive analysis of the rupture process, examining its mechanistic and kinetic aspects as well as the role of capsid-DNA interactions. Our findings illuminate how different capsid-DNA conditions give rise to distinct rupture pathways, which differ from ruptures due to simple outward pressure expansion models from within the capsid.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"123 43","pages":"e2617714123"},"PeriodicalIF":9.5,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149228594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}