bims-toxgon 2025-12-14 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2025–12–14
29 papers selected by
Lakesh Kumar, BITS Pilani

Atomic models of the Toxoplasma cell invasion machinery.
An apicoplast-localized GTPase is essential for Toxoplasma gondii survival.
Evolutionarily convergent mechanism of formin regulation coordinates actin polymerization in apicomplexan parasites.
An atlas of novel microtubule-associated proteins in the malaria parasite Plasmodium falciparum.
Assessing the function of the alternative electron transport chain in the Cryptosporidium parvum mitosome.
Lysine Deacetylation: An Emerging Molecular Switch of Plant Light Signaling.
Metabolic needs and capabilities among Cryptosporidium species.
Free GPIs and Comparison of GPI Structures Among Species.
Independent nuclear and organellar mechanisms determine apicoplast fate in malaria parasites.
Caspase-8 expression in CD8+ T cells promotes pathogen restriction in the brain during Toxoplasma gondii infection.
Protein succinylation in tumors-from biology to clinical therapy.
Functional Characterization of VS-186B, a Novel HDAC Inhibitor with Anticancer Activity.
The phytochemical arbutin exerts potent anti-Toxoplasma effects through activation of cell-autonomous defense mechanisms while attenuating inflammation.
Microbial acetyl-CoA synthesis as an emerging metabolic and regulatory hub in plant-microbe interactions.
Internally quenched fluorescent peptides provide insights into underexplored and reversible post-translational modifications.
Metabolic mediators at the Nexus: How SAM, Acetyl-CoA, and NAD+ bridge phytohormone signaling and epigenetic regulation.
Metabolic costs and trade-offs of hypermetabolism in human motor neurons with ATP synthase deficiency.
HK1 and HK2 Beyond Glycolysis: Mitochondrial Interactions and Dual Roles in Metabolism and Cell Fate.
Characterization of the Regulatory AAA-ATPase Subunit Rpt3 in Plasmodium berghei as an Activator of Protein Phosphatase 1.
SUCLA2 Inhibited Lysine Succinylation of SHMT2 to Suppress Ferroptosis and Renal Interstitial Fibrosis.
Unveiling the Plasmodium inositol (pyro)phosphate pathway: Highlighting inositol polyphosphate multikinase as a novel therapeutic target for malaria.
Advances in MS-based glycomics for biomedical research.
Survival strategies of mycoplasmas: the critical role of post-translational modifications.
Mass spectrometry-based profiling of single-cell histone post-translational modifications to dissect chromatin heterogeneity.
Does peptidome mimicry shape host-parasite coevolution?
Bromodomain-Driven Regulation of Stem Cells: A Potential Target for Cancer Therapeutic Intervention.
Structure of Trypanosoma peroxisomal import complex unveils conformational heterogeneity.
Glutamine Promotes Myogenesis in Myoblasts Through Glutaminolysis-Mediated Histone H3 Acetylation That Enhances Myogenin Transcription.
Integrative modelling of biomolecular dynamics.

Nat Struct Mol Biol. 2025 Dec 09.

Atomic models of the Toxoplasma cell invasion machinery.

Jianwei Zeng, Yong Fu, Pengge Qian, Wei Huang, Qingwei Niu, Wandy L Beatty, Alan Brown, L David Sibley, Rui Zhang.

Apicomplexan parasites, responsible for toxoplasmosis, cryptosporidiosis and malaria, invade host cells through a unique gliding motility mechanism powered by actomyosin motors and a dynamic organelle called the conoid. Here, using cryo-electron microscopy, we determined structures of four essential complexes of the Toxoplasma gondii conoid: the preconoidal P2 ring, tubulin-based conoid fibers, and the subpellicular and intraconoidal microtubules. Our analysis identified 40 distinct conoid proteins, several of which are essential for parasite lytic growth, as revealed through genetic disruption studies. Comparative analysis of the tubulin-containing complexes sheds light on their functional specialization by microtubule-associated proteins, while the structure of the preconoidal ring pinpoints the site of actin polymerization and initial translocation, enhancing our mechanistic understanding of gliding motility and, therefore, parasite invasion.

DOI: https://doi.org/10.1038/s41594-025-01728-w
mSphere. 2025 Dec 09. e0071325

An apicoplast-localized GTPase is essential for Toxoplasma gondii survival.

Michael B Griffith, Morgan E Wagner, Victoria L Robinson, Aoife T Heaslip.

  The apicoplast is an essential organelle found in Apicomplexa, a large phylum of intracellular eukaryotic pathogens. The apicoplast produces metabolites that are utilized for membrane biogenesis and energy production. A majority of apicoplast-resident proteins are encoded by the nuclear genome and are trafficked to the apicoplast and are referred to as nuclear-encoded and apicoplast-trafficked (NEAT) proteins. In this study, we characterized a NEAT protein named TgBipA, which is a homolog of the highly conserved prokaryotic translational GTPase BipA. BipA is essential for bacterial survival in stress conditions and functions through interactions with the prokaryotic ribosome, although its role is not fully understood. Through genetic knockouts of TgBipA and immunofluorescence imaging, we show that the loss of TgBipA results in apicoplast genome replication defects, disruption of NEAT trafficking, loss of the apicoplast, and ultimately parasite death. Furthermore, we show through comparative studies that this phenotype closely resembles the delayed death phenomenon observed when inhibiting apicoplast translation. Finally, we show that TgBipA is an active GTPase in vitro, and its GTP hydrolysis activity is critical for its cellular function. Our findings demonstrate that TgBipA is a GTPase that has an essential role in apicoplast maintenance, providing new insights into the cellular processes of the organelle.IMPORTANCEToxoplasma gondii, and many other parasites in the phylum Apicomplexa, are pathogens with significant medical and veterinary importance. Most Apicomplexa contain a non-photosynthetic plastid organelle named the apicoplast. This organelle produces essential metabolites, and perturbation of apicoplast function results in parasite death. The apicoplast contains bacterial-like pathways for apicoplast genome replication and expression. Thus, the discovery of the apicoplast leads to optimism that this organelle would provide a wealth of anti-parasitic drug targets. Therefore, the identification and characterization of new apicoplast proteins could provide new opportunities for therapeutic development. In this study, we characterized the function of a protein called TgBipA, a homolog of a highly conserved bacterial GTPase BipA, which has been implicated in the maturation of the 50S ribosomal subunit and adaptation to cellular stress. We show that TgBipA is essential for apicoplast maintenance and parasite survival.

Keywords:  GTPase; Toxoplasma gondii; apicoplast

DOI:  https://doi.org/10.1128/msphere.00713-25
Sci Adv. 2025 Dec 12. 11(50): eaea2136

Evolutionarily convergent mechanism of formin regulation coordinates actin polymerization in apicomplexan parasites.

Pengge Qian, Yong Fu, Jianwei Zeng, Michael J Naldrett, Rui Zhang, L David Sibley.

Apicomplexan parasites rely on actin-based motility for host cell invasion and for their dissemination. Although previous studies implicate formin 1 (FRM1) in governing this process in Toxoplasma, the mechanisms that position it at the cell apex and regulate its activity during the transition from intracellular replication to active motility remain unclear. Here, we demonstrate that FRM1 is complexed with a protein methyl transferase that stabilizes it from degradation and positions it at the cell apex. Moreover, we identify a conserved intramolecular interaction within FRM1 that serves as a critical regulatory switch that is functionally conserved in Plasmodium and other apicomplexan parasites. Using structural modeling combined with biochemical assays, we define two regulatory elements located upstream of the FH2 domain that mediate autoinhibition. Repositioning these elements by activation of an intramolecular switch relieves autoinhibition and activates actin polymerization by the FH2 domain. Collectively, these findings elucidate how precise regulation of FRM1 coordinates actin polymerization, parasite motility and host cell invasion.

DOI: https://doi.org/10.1126/sciadv.aea2136
mBio. 2025 Dec 08. e0340725

An atlas of novel microtubule-associated proteins in the malaria parasite Plasmodium falciparum.

Korbinian Niedermüller, Nick Piwon, Joëlle Paolo Mesen-Ramirez, Leah Zink, Sarah Lemcke, Benjamin Liffner, Cláudia F Fernandes, Guilherme B Farias, Arne Alder, Christian Löw, Noa Dahan, Danny W Wilson, José Cubillán-Marín, Tim W Gilberger.

  Mature gametocytes of Plasmodium falciparum exhibit a characteristic falciform shape, which is conferred by a complex array of subpellicular microtubules (SPMTs) associated with the inner membrane complex (IMC). While several microtubule-associated proteins (MAPs) have been characterized in the related apicomplexan parasite Toxoplasma gondii, the identity and function of MAPs in Plasmodium remain poorly understood. Here, we employed proximity-dependent biotinylation (BioID) using PfSPM3, a subpellicular MAP, as a bait in order to identify proteins associated with P. falciparum gametocyte SPMTs. Mass spectrometry analysis revealed 37 high-confidence proteins in the immediate vicinity of PfSPM3 constituting its "proxiome." Using GFP tags on the endogenous proteins of 11 highly enriched candidates, we provide a spatial localization atlas of previously uncharacterized proteins. Notably, many of these putative MAPs showed a distinct localization to different structures within the SPMT network, highlighting its complexity in developing gametocytes. Among these, we demonstrate that functional knockout of one MAP, PF3D7_1003400, which exhibits a localization pattern consistent with positioning near the IMC suture/SPMT boundary, interferes with gametocytogenesis and prevents falciform gametocyte development. These findings provide the first atlas of the SPMT network required to coordinate cytoskeletal dynamics, IMC organization, and gametocyte development. Understanding these interactions offers new avenues for blocking gametocyte cytoskeleton development and malaria transmission.IMPORTANCETransmission of Plasmodium falciparum relies on the formation of falciform gametocytes, a process dependent on the dynamic interplay between subpellicular microtubules (SPMTs) and the inner membrane complex (IMC). In this study, we employed proximity-dependent biotinylation using PfSPM3, an SPMT-associated protein, as a bait. We present a comprehensive list of highly enriched proteins and a validation of the top candidates revealing novel components of the cytoskeleton of gametocytes that might play a role in their morphogenesis and transmission.

Keywords:  Plasmodium falciparum; gametocytes; inner membrane complex; microtubule-associated proteins; subpellicular microtubules

DOI:  https://doi.org/10.1128/mbio.03407-25
mBio. 2025 Dec 10. 16(12): e0112025

Assessing the function of the alternative electron transport chain in the Cryptosporidium parvum mitosome.

Silu Deng, Wandy Beatty, L David Sibley.

  Cryptosporidium parvum and C. hominis possess a remanent mitochondrion called the mitosome, which lacks DNA, the tricarboxylic acid cycle, a conventional electron transport chain, and ATP synthesis. The mitosome retains ubiquinone and iron-sulfur cluster biosynthesis pathways, which require protein import that relies on the membrane potential. It was previously proposed that the membrane potential may be generated by a transhydrogenase (TH) that pumps protons out of the mitosome. This pathway was also proposed to rely on an alternative oxidase (AOX) and type II NADH dehydrogenase (NDH2), which also exists in plants, some fungi, and several protozoan parasites. To examine this model, we determined the location and function of AOX and NDH2 in C. parvum. Surprisingly, we observed that NDH2 was localized to parasite surface membranes instead of the mitosome. Furthermore, a ∆ndh2 knockout (KO) strain was readily obtained, indicating that this protein is not essential for parasite growth. Although AOX exhibited a mitosome-like staining pattern, we readily obtained a ∆aox KO strain, which did not exhibit a difference in MitoTracker, indicating that AOX is likely not involved in membrane potential and is dispensable for parasite growth. The growth of the ∆aox strain was inhibited by the AOX inhibitors, salicylhydroxamic acid and 8-hydroxyquinoline, to the same extent as wild type, indicating that AOX is not the target of these inhibitors in C. parvum. Collectively, our studies indicate that NDH2 and AOX are non-essential genes in C. parvum, supporting an alternative mechanism for maintaining the mitosome membrane potential.
IMPORTANCE: Cryptosporidiosis is a leading cause of diarrhea in young children and immunocompromised individuals, particularly AIDS/HIV patients. The only FDA-approved drug against cryptosporidiosis, nitazoxanide, has limited effectiveness in immunocompromised patients and is not approved for use in children under 1 year. Genomic analysis and previous studies proposed an alternative respiration pathway involving alternative oxidase (AOX) and type II NAD(P)H dehydrogenase (NDH2), which are thought to generate the mitosome membrane potential in Cryptosporidium parvum. Additionally, AOX was nominated as potential drug targets, based on its absence in mammalian hosts and sensitivity of parasite growth to known inhibitors of AOX. However, our study demonstrated that NDH2 is not localized in the mitosome, AOX is non-essential for parasite growth, and knockout lines lacking this enzyme are equally sensitive to AOX inhibitors. These findings indicate that AOX and NDH2 are not ideal candidates for future drug development against cryptosporidiosis and force a re-evaluation of models of how the mitosome generates its membrane potential.

Keywords:  alternative oxidase; cryptosporidiosis; mitochondria; type II NADH dehydrogenase

DOI:  https://doi.org/10.1128/mbio.01120-25
Physiol Plant. 2025 Nov-Dec;177(6):177(6): e70685

Lysine Deacetylation: An Emerging Molecular Switch of Plant Light Signaling.

Minghui Xing, Kai Cheng, Xuejie Zhao, Xiao Zhang, Weiqiang Li, Xiaojian Yin.

  Lysine acetylation, dynamically regulated through the balanced activities of histone deacetylases (HDACs) and histone acetyltransferases (HATs), plays dual roles in chromatin regulation and post-translational regulation. In plant light signaling, HDACs are recruited by ELONGATED HYPOCOTYL 5 (HY5) and PHYTOCHROME-INTERACTING FACTORS (PIFs) to regulate light-responsive gene expression via histone deacetylation during seedling development. Recent studies have expanded this classical framework by revealing non-histone functions of HDACs. Their works demonstrate that two HDACs, HDT2 and HDA9, directly deacetylate the far-red photoreceptor phyA and the blue-light photoreceptor phot1, respectively, thereby modulating their stability and activity to downstream light signaling. These findings identify non-histone deacetylation as an emerging regulatory switch linking photoreceptor stability and activity to downstream light signaling and reveal pivotal non-histone roles of HDACs in photomorphogenesis and phototropism in Arabidopsis thaliana. In this minireview, we outline a multilayered regulatory network that integrates HDAC-mediated histone and non-histone deacetylation to coordinate transcriptional reprogramming with photoreceptor stability and activation, thereby ensuring precise and adaptable light responses in plants.

Keywords:  histone deacetylase; light signaling; lysine acetylation; photomorphogenesis; phototropism

DOI:  https://doi.org/10.1111/ppl.70685
Trends Parasitol. 2025 Dec 06. pii: S1471-4922(25)00328-9. [Epub ahead of print]

Metabolic needs and capabilities among Cryptosporidium species.

Rachel Humann, Dominique Soldati-Favre, Amandine Guérin.

  In the past decade, Cryptosporidium research has progressed considerably, often drawing on Toxoplasma gondii as a molecular model. Yet, accumulating evidence reveals that such cross-species extrapolation risks overlooking the distinctive biology of Cryptosporidium. Notably, marked metabolic differences exist not only between apicomplexans but also within the Cryptosporidium species, particularly between those infecting the stomach (C. andersoni, C. muris) and those targeting the intestines (C. parvum, C. hominis). Pathways such as polyamine and ceramide metabolism illustrate how earlier assumptions, combined with insufficient attention to species delineation, have led to an incomplete and sometimes inaccurate description of Cryptosporidium metabolism. This review examines metabolic needs and capabilities across several Cryptosporidium species to clarify evolutionary differences and highlight promising pathways for therapeutic intervention.

Keywords:  Cryptosporidium; apicomplexan; ceramide; metabolism; polyamine

DOI:  https://doi.org/10.1016/j.pt.2025.11.005
Int J Mol Sci. 2025 Nov 29. pii: 11592. [Epub ahead of print]26(23):

Free GPIs and Comparison of GPI Structures Among Species.

Stella Amarachi Ihim, Morihisa Fujita.

  Glycosylphosphatidylinositols (GPIs) are complex glycolipids that function as membrane anchors for a wide array of eukaryotic proteins, collectively referred to as GPI-anchored proteins (GPI-APs). These structures are critical for various cellular processes including signal transduction, host-pathogen interactions, and immune evasion. While GPI-APs have been extensively studied, increasing attention is being paid to non-protein-linked GPI, called free GPIs, which have been identified in both protozoan parasites and mammalian cells. In protozoa such as Trypanosoma brucei, Trypanosoma cruzi, Toxoplasma gondii, Plasmodium falciparum, and Leishmania spp., free GPIs play roles in virulence, immune modulation, and parasite survival. In mammals, free GPIs have been detected in several tissues and pathogenic conditions of paroxysmal nocturnal hemoglobinuria caused by PIGT mutation and rare blood group phenotypes. This review provides a comparative overview of the structure and biosynthesis of free GPIs and GPI-APs across species, highlighting unique adaptations in each. We also discuss the emerging physiological and pathological roles of free GPIs, proposing that these underexplored molecules may serve as important biomarkers and therapeutic targets. Understanding the diversity and function of free GPIs offers new insights into glycobiology and host-pathogen interactions.

Keywords:  GPI-anchored protein; Leishmania spp.; Plasmodium falciparum; Toxoplasma gondii; Trypanosoma brucei; Trypanosoma cruzi; biosynthesis; free GPI; mammalian cells

DOI:  https://doi.org/10.3390/ijms262311592
J Cell Biol. 2026 Feb 02. pii: e202504052. [Epub ahead of print]225(2):

Independent nuclear and organellar mechanisms determine apicoplast fate in malaria parasites.

Michal Shahar, Alia Qasem, Eshkar Shamay, Amanda Tissawak, Yariv Maron, Anat Florentin.

The apicoplast organelle of the malaria parasite, Plasmodium falciparum, is essential for parasite replication, though its cell cycle regulation remains poorly understood. We developed a dynamic live-imaging platform with analytical capabilities to track subcellular structures throughout the parasite's 48-h intraerythrocytic life cycle. Our analysis revealed four distinct morphological stages in apicoplast development that correlate with nuclear replication. We identified a critical "Crown" morphology stage required for nucleus-apicoplast attachment, where the apicoplast stretches across multiple nuclei, in close association with centriolar plaques. We measured DNA ploidy and replication dynamics of the nuclear and apicoplast genomes. Inhibition of nuclear DNA replication blocked apicoplast biogenesis at early stages, demonstrating dependence on S-phase initiation. Conversely, inhibiting apicoplast genome replication minimally affected organelle development but disrupted the Crown stage, preventing proper organelle segregation into daughter cells. These findings establish a central pathway connecting apicoplast development to the cell cycle and an independent mechanism governing organelle inheritance.

DOI: https://doi.org/10.1083/jcb.202504052
Sci Adv. 2025 Dec 12. 11(50): eadz4468

Caspase-8 expression in CD8+ T cells promotes pathogen restriction in the brain during Toxoplasma gondii infection.

Lydia A Sibley, Maureen N Cowan, Abigail G Kelly, NaaDedee A Amadi, Isaac W Babcock, Sydney A Labuzan, Michael A Kovacs, Samantha J Batista, John R Lukens, Tajie H Harris.

Cell death is an integral restriction mechanism against intracellular pathogens. We have previously reported extensive cell death in the brain during infection with the intracellular parasite, Toxoplasma gondii. Here, we focus on the role of caspase-8, a regulator of extrinsic apoptosis, during T. gondii infection. We find that Casp8-/-Ripk3-/- mice have increased brain parasite burden in comparison to controls and succumb to infection despite the generation of robust immune responses. We observed that neurons, astrocytes, and CD8+ T cells had high rates of parasite interactions in Casp8-/-Ripk3-/- mice compared to wild-type mice. While Casp8 deficiency in neurons and astrocytes did not affect control of infection, deletion of Casp8 in CD8+ T cells led to impaired survival, increased parasite burden, and direct infection of CD8+ T cells in the brain. We conclude that in addition to well-characterized effector functions, CD8+ T cells use caspase-8 to control T. gondii in the brain.

DOI: https://doi.org/10.1126/sciadv.adz4468
Int J Biol Macromol. 2025 Dec 06. pii: S0141-8130(25)10046-9. [Epub ahead of print] 149489

Protein succinylation in tumors-from biology to clinical therapy.

Huiling Li, Huijuan Zhang, Jing Zhu, Yu Tang, Jing An.

  Lysine succinylation is a recently identified post-translational modification (PTM) characterized by the transfer of a succinyl group (-CO-CH2-CH2-CO2H) to lysine residues, primarily mediated by succinyl-CoA. This modification plays a critical role in maintaining protein stability and function, and is involved in diverse biological processes, including energy metabolism, substrate transport, and signal transduction. Accumulating evidence indicates that lysine succinylation contributes to tumorigenesis and cancer progression, with both enzymatic and non-enzymatic mechanisms playing regulatory roles. This review summarizes recent advances in succinylation research within the context of tumor metabolism, the tumor immune microenvironment, and its interplay with other epigenetic modifications. Furthermore, we highlight current developments in anti-tumor therapeutics and succinylation inhibitors, aiming to provide novel insights into protein post-translational modifications and to support the identification of potential drug targets for clinical applications.

Keywords:  Cell metabolism; Epigenetic regulation; Immune microenvironment; Post-translational modification; Succinylation; Therapy

DOI:  https://doi.org/10.1016/j.ijbiomac.2025.149489
Int J Mol Sci. 2025 Nov 24. pii: 11354. [Epub ahead of print]26(23):

Functional Characterization of VS-186B, a Novel HDAC Inhibitor with Anticancer Activity.

Laura A Sanchez-Michael, Vijayalakshmi Sudarshan, Allison Elias, Denisse A Gutierrez, Jose A Lopez-Saenz, Jaqueline Pena-Zacarias, Gabriela C Torres, Armando Varela-Ramirez, Sujeet Kumar, Subhas S Karki, Renato J Aguilera.

  Histone acetylation and deacetylation are key regulators of gene expression and are frequently dysregulated in cancer, contributing to tumorigenesis and drug resistance. Overexpression of histone deacetylases (HDACs) in many cancer types leads to silencing of tumor suppressor genes and uncontrolled proliferation. Tumors often rely on epigenetic mechanisms to escape therapy and develop resistance. This study aimed to identify novel compounds that selectively target cancer cells while minimizing toxicity to non-cancerous cell lines. A series of novel HDAC inhibitors was evaluated using the Differential Nuclear Staining (DNS) assay, flow cytometry, and HDAC inhibition assays. These assays assessed cytotoxicity, selectivity, and mechanisms of cell death. Among seven compounds tested, VS-186B exhibited the highest cytotoxicity and Selective Cytotoxicity Index (SCI), particularly against the human Jurkat T-cell leukemia cell line. Flow cytometry experiments (Annexin V-FITC, ROS, JC-1, and Caspase-3/7 assays) revealed that VS-186B induced apoptosis. VS-186B was more cytotoxic than Curcumin and Vorinostat across most of the cell lines tested and was more specific to hematological cells. Connectivity Map (CMap) analysis showed strong similarity to genes affected by known HDAC inhibitors. Subsequently, HDAC enzymatic assays confirmed that VS-186B inhibits Class I and II HDACs in a dose-dependent manner. VS-186B exhibits promising anticancer potential as a selective HDAC inhibitor since it induces apoptosis in cancer cells without significant cytotoxicity to non-cancerous lines with a similar gene expression profile to known HDAC inhibitors. These findings support further development of VS-186B as an epigenetic treatment for leukemia/lymphoma.

Keywords:  HDAC inhibitor; Jurkat; Vorinostat; anti-cancer; apoptosis; curcumin; cytotoxicity; leukemia; selectivity

DOI:  https://doi.org/10.3390/ijms262311354
PLoS Negl Trop Dis. 2025 Dec 11. 19(12): e0013815

The phytochemical arbutin exerts potent anti-Toxoplasma effects through activation of cell-autonomous defense mechanisms while attenuating inflammation.

Zhuanzhuan Liu, Yulu Ma, Yaoyao Xiang, Yusi Shen, Longxiang Liao, Xiuwen Zhu, Zhen Shi, Yanxia Wei, Yanbo Kou, Yugang Wang.

BACKGROUND: Plant-derived natural products have emerged as promising candidates for developing novel anti-toxoplasmosis drugs. This study aimed to elucidate the role and mechanism of the phytochemical arbutin in the control of T. gondii infection.
METHODOLOGY/PRINCIPAL FINDINGS: The effect of arbutin on T. gondii infection and host inflammatory response was evaluated both in vitro and in vivo. RNA-seq was performed on mouse bone marrow-derived macrophage samples to identify potential arbutin-related biological processes and molecular targets that control T. gondii infection. These targets were further confirmed using target-specific activators or inhibitors. Our data indicated that arbutin has dual therapeutic effects against T. gondii infection through concurrently controlling parasite growth and mitigating infection-induced inflammation. Mechanistically, arbutin mediates restriction of intracellular labile iron pool in both immune and non-immune cells, thereby depriving the parasite of essential metal nutrients. In addition, in macrophages, arbutin not only inhibits infection-induced inflammatory response but also upregulates the expression of heme degrading enzyme heme oxygenase-1, which facilitates biliverdin production. Our data further demonstrated that biliverdin exhibits anti-T. gondii effector function. Furthermore, arbutin is also effective in reducing infection-related mortality in immunocompromised mice.
CONCLUSIONS/SIGNIFICANCE: Our data highlight arbutin's potential therapeutic value in fighting against acute hyperinflammatory phase of Toxoplasmosis even in immunocompromised host but also its limitation in establishing long-term immunity. Our study further suggests a potential direction for further development of effective drugs to prevent and treat toxoplasmosis by pharmacologically enhancing cell-autonomous defense mechanisms while suppressing inflammatory response.

DOI: https://doi.org/10.1371/journal.pntd.0013815
Microbiol Res. 2025 Dec 05. pii: S0944-5013(25)00372-6. [Epub ahead of print]304 128413

Microbial acetyl-CoA synthesis as an emerging metabolic and regulatory hub in plant-microbe interactions.

Yanan Zhou, Xue-Xian Zhang, Dandan Wang, Mengguang Zhao, Li Sun, Weiwei Huang, Zhihong Xie.

  Acetyl-CoA synthetase (ACS) is a well-characterized enzyme that catalyzes the ATP-dependent ligation of acetate and coenzyme A to produce acetyl-CoA, a central metabolite coordinating energy metabolism, carbon flux distribution, and post-translational protein modification. Recently, ACS has emerged as a metabolic nexus with broad implications for plant-microbe interactions in agriculture. Beyond its canonical role in primary metabolism, ACS governs diverse physiological processes in beneficial plant-associated microorganisms, including rhizosphere colonization, stress adaptation, secondary metabolite biosynthesis, and morphological development-all of which enhance plant growth and resilience. In contrast, in phytopathogens, ACS is closely related to the expression of virulence factors. Thus, ACS exerts a dual influence, shaping both mutualistic and antagonistic microbial lifestyles in planta. This review synthesizes recent advances in the structural and catalytic diversity of ACS, delineates its ecological and functional roles in agriculturally relevant microorganisms, and explores the environmental and host-derived signals that regulates its expression and activity. Particular attention is given to the interplay between ACS-mediated carbon metabolism and protein acetylation, which together modulate microbial physiology and plant-associated behaviors. ACS is thereby positioned as a strategic metabolic hub, providing a framework for future research at the interface of microbial metabolism, environmental adaptation, and plant health.

Keywords:  Acetyl-CoA synthetase (ACS); Agricultural applications; Plant-associated microorganisms; Plant-microbiome interaction; Rhizosphere colonization; Virulence regulation

DOI:  https://doi.org/10.1016/j.micres.2025.128413
Chem Sci. 2025 Dec 05.

Internally quenched fluorescent peptides provide insights into underexplored and reversible post-translational modifications.

Jordi C J Hintzen, Kamiel D Beckley, Emily L Goldberg, George M Burslem.

Internally quenched fluorescent (IQF) peptides offer a powerful, modular platform for studying the enzymatic dynamics of post-translational modifications (PTMs) on lysine and arginine. Here we report a versatile IQF system that enables monitoring of PTM installation and removal via proteolytic cleavage by trypsin. This platform is compatible with both native PTMs and PTM mimetics, including acetylation, various other acylations, mono-/di-/trimethylation and citrullination across both histone and non-histone derived peptide substrates. Using synthetically accessible thialysine and thiaarginine analogs, we developed cysteine conjugation chemistries to access a wide array of PTM mimics, including novel reagents for lysine lactylation, β-hydroxybutyrylation and methyl-acetylation. Application of the system revealed distinct substrate preferences and site-specific activities for enzymes such as SIRT3, HDAC2, HDAC6, KDM3A, KDM4A and PAD4. Notably, the system uncovered enzymatic selectivity for acyl chain type and methylation state and demonstrated resistance of the emerging PTM methyl-acetyllysine to erasers. The system was also used to study the recently reported reversibility of acylation modifications by HDAC2 and 6 and is capable of evaluating enzymatic crosstalk between neighboring post-translational modifications. Our platform's adaptability and readout simplicity offer a generalizable chemical biology toolkit for PTM profiling, enzyme characterization, and inhibitor discovery.

DOI: https://doi.org/10.1039/d5sc08759g
Curr Opin Plant Biol. 2025 Dec 11. pii: S1369-5266(25)00146-3. [Epub ahead of print]89 102832

Metabolic mediators at the Nexus: How SAM, Acetyl-CoA, and NAD+ bridge phytohormone signaling and epigenetic regulation.

Yue Yu, Kai Jiang.

  Plant hormones and epigenetic mechanisms coordinately regulate plant development and environmental adaptation through shared metabolic nodes. Metabolic intermediates such as S-adenosylmethionine (SAM), acetyl-CoA, and NAD+ serve dual functions in both hormone biosynthesis and epigenetic modifications. These metabolic nodes integrate energy status and hormonal signaling via three principal mechanisms: spatial relocalization of energy metabolism enzymes through subcellular compartmentalization, regulation of epigenetic modifying enzyme activities, and modulation of phytohormone biosynthesis. This review synthesizes recent advances elucidating the reciprocal regulatory interplay mediated by phytohormones, metabolic intermediates, and epigenetic modifications. We further propose that these metabolic intermediates may function as putative secondary messenger-like molecules, potentially bridging epigenetic regulatory networks with hormonal signaling cascades.

Keywords:  Epigenetic regulation; Metabolic intermediates; Phytohormones

DOI:  https://doi.org/10.1016/j.pbi.2025.102832
Commun Biol. 2025 Dec 11. 8(1): 1759

Metabolic costs and trade-offs of hypermetabolism in human motor neurons with ATP synthase deficiency.

Rubén Torregrosa-Muñumer, Jeremi Turkia, Rumeysa Ermiş, Jouni Kvist, Sandra Harjuhaahto, Jana Pennonen, Ville Hietakangas, Emil Ylikallio, Henna Tyynismaa.

Hypermetabolism, a futile cycle of energy production and consumption, has been proposed as an adaptative response to deficiencies in mitochondrial oxidative phosphorylation. However, the cellular costs of hypermetabolism remain largely unknown. Here we studied the consequences of hypermetabolism in human motor neurons harboring a heteroplasmic mutation in MT-ATP6, which impairs ATP synthase assembly. Respirometry, metabolomics, and proteomics analyses of the motor neurons showed that elevated ATP production rates were accompanied with increased demand for acetyl-Coenzyme A (acetyl-CoA) and depleted pantothenate (vitamin B5), and the proteome was remodeled to support the metabolic adaptation. Mitochondrial membrane potential and coupling efficiency remained stable, and the therapeutic agent avanafil did not affect metabolite levels. However, a redistribution of acetyl-CoA usage resulted in metabolic trade-offs, including reduced histone acetylation and altered maintenance of the neurotransmitter acetylcholine, revealing potential vulnerabilities in motor neurons. These findings advance the understanding of cellular metabolic consequences imposed by hypermetabolic conditions.

DOI: https://doi.org/10.1038/s42003-025-09149-7
Adv Biol (Weinh). 2025 Dec 12. e00472

HK1 and HK2 Beyond Glycolysis: Mitochondrial Interactions and Dual Roles in Metabolism and Cell Fate.

Noemi Anna Pesce, Giulia Seminara, Giuseppe Giarrusso, Marianna Flora Tomasello.

  HK1 and HK2 are increasingly recognized not only as glycolytic enzymes but also as key modulators of mitochondrial function and cell fate through dynamic interactions with VDAC. This review explores how HK-VDAC complexes support metabolic flexibility, regulate apoptosis, and coordinate glycolytic and mitochondrial activity across diverse physiological and pathological conditions. We incorporate recent reinterpretations of the Warburg effect, emphasizing how spatial and functional reorganization of HK supports proliferative metabolism beyond classical models of mitochondrial dysfunction. Importantly, the HK-VDAC interaction is dynamically regulated by post-translational modifications and signaling pathways that control its stability and mitochondrial anchoring. Disruption of these regulatory mechanisms can impair the balance between glycolytic and mitochondrial metabolism, contributing to disease progression. Emerging evidence links altered HK-VDAC interactions to the metabolic and apoptotic imbalances observed in cancer, neurodegeneration, and aging. By integrating insights from structural biology, bioenergetics, and disease models, we highlight mitochondrial HK anchoring as a central hub for metabolic adaptation and stress response.

Keywords:  HK‐VDAC; Warburg effect; aging; apoptosis; cancer; metabolism; mitochondria

DOI:  https://doi.org/10.1002/adbi.202500472
Int J Mol Sci. 2025 Dec 03. pii: 11720. [Epub ahead of print]26(23):

Characterization of the Regulatory AAA-ATPase Subunit Rpt3 in Plasmodium berghei as an Activator of Protein Phosphatase 1.

Claudianne Lainé, Caroline De Witte, Alain Martoriati, Amaury Farce, Inès Metatla, Ida Chiara Guerrera, Katia Cailliau, Jamal Khalife, Christine Pierrot.

  The 26S proteasome is the main proteolytic machinery involved in protein degradation, thereby contributing to the homeostasis and stress response of eukaryotic cells. This macromolecular complex consists of a 20S core particle assembled with one or two 19S regulatory particles. Here, we describe the Plasmodium berghei (Pb) proteasome AAA-ATPase regulatory subunit Rpt3 and demonstrate its binding to the Protein Phosphatase 1 catalytic subunit (PP1c), which is one of the major and essential parasite phosphatases. The PbRpt3 protein enhances the activity of PP1c both in vitro and in a Xenopus oocyte heterologous model. Further investigation of this model suggests that the PbRpt3-PP1c interaction may occur outside of the proteasome, and it reveals that the RVxF motifs of PbRpt3 are involved in its binding and regulatory function. Moreover, the ATP-binding capacity of PbRpt3 may also contribute to its phosphatase regulatory activity. In the parasite, reverse genetic studies suggest an essential role for PbRpt3 during erythrocytic cycle of P. berghei, and an interactome analysis confirmed that PbRpt3 belongs to the 19S regulatory particle of the proteasome and may interact with proteins previously shown to be involved in phospholipid binding.

Keywords:  19S regulatory particle; Plasmodium; Protein Phosphatase 1; Rpt3; proteasome

DOI:  https://doi.org/10.3390/ijms262311720
FASEB J. 2025 Dec 15. 39(23): e71314

SUCLA2 Inhibited Lysine Succinylation of SHMT2 to Suppress Ferroptosis and Renal Interstitial Fibrosis.

Huiyan Lyu, Donghua Hou, Yadong Liu, Jiaojiao Wang, Manshu Sui.

  Renal interstitial fibrosis (RIF) is a common pathway to end-stage renal diseases progressing towards renal failure. Angiotensin II (Ang II), as the core effector molecule of the renin-angiotensin system (RAS), is widely recognized as a key factor promoting RIF. Succinyl-CoA ligase subunit-beta (SUCLA2) can reversibly convert succinyl CoA into succinate and participates in many biological processes. This research was designed to explore the roles and mechanisms of SUCLA2 in RIF. Ang II-induced mouse model and HK-2 cell model were established. Ang II induced significant histological damage and interstitial fibrosis in mouse kidneys. SUCLA2 mRNA and protein levels were decreased, but lysine succinylation levels were increased in renal tissues of Ang II-induced mice and Ang II-treated HK-2 cells. Overexpression of SUCLA2 inhibited Ang II-induced ferroptosis, along with decreased lysine succinylation and succinyl-CoA levels. SUCLA2 negatively regulated lysine succinylation of SHMT2. Furthermore, SHMT2 desuccinylation by sirtuin 5 (SIRT5) inhibited Ang II-induced ferroptosis, and the inhibitory effect of SUCLA2 overexpression on Ang II-induced ferroptosis was restored by SHMT2 silencing. In vivo, the delivery of adeno-associated virus-mediated SUCLA2-expressing vector into mouse kidneys alleviated Ang II-induced histological damage and interstitial fibrosis. Our research has revealed SUCLA2 inhibited lysine succinylation of SHMT2 to repress renal cell ferroptosis and interstitial fibrosis.

Keywords:  Ang II; SHMT2; SUCLA2; ferroptosis; lysine succinylation; renal interstitial fibrosis

DOI:  https://doi.org/10.1096/fj.202502544RR
PLoS One. 2025 ;20(12): e0338411

Unveiling the Plasmodium inositol (pyro)phosphate pathway: Highlighting inositol polyphosphate multikinase as a novel therapeutic target for malaria.

Abigail Obuobi, Neils B Quashie, Nancy Odurowah Duah-Quashie, Jon R Sayers.

Plasmodium falciparum malaria is fatal if left untreated. Treatment is hampered by drug-resistant variants of the malaria parasite, highlighting the need to explore unique pathways for the development of new drugs with different mechanisms of action. Kinases in the inositol phosphate signaling pathway (IPP), and its products play many important roles in energy metabolism and signal transduction, making them attractive drug targets. In this exploratory study we investigated the potential of P. falciparum IPP as a novel and attractive pathway for antimalarial drug discovery, employing a combined in silico and molecular approach. The sequences and structures of the putative P. falciparum inositol phosphate kinases were characterized in silico. Experimental validation across laboratory strains and a clinical isolate confirmed the p.Pro375Gln substitution in IPMK1, providing the first evidence of this variant in field isolates. We provide molecular evidence of the existence of IPP genes in P. falciparum and suggest that targeting this pathway could be detrimental to the parasite. We identify P. falciparum inositol polyphosphate multikinase (IPMK) as a promising drug target due to its unique sequence and structural characteristics. These results serve as a guide for future experimental validation.

DOI: https://doi.org/10.1371/journal.pone.0338411
Anal Methods. 2025 Dec 10.

Advances in MS-based glycomics for biomedical research.

Joy Solomon, Akeem Sanni, Waziha Purba, Odunayo Oluokun, Sarah Sahioun, Mojibola Fowowe, Ayobami Oluokun, Ahmed Hussein, Yehia Mechref.

Glycosylation is a highly complex and functionally diverse post-translational modification that modulates protein folding, stability, cell signaling, and immune response. Aberrant glycosylation is associated with numerous diseases, including cancer, neurodegenerative disorders, and infections, making glycans attractive targets for biomarker discovery and therapeutic development. Mass spectrometry (MS) has become a widely used analytical tool, for glycomics analysis due to its high sensitivity, specificity, and structural resolution. This review highlights advances in MS-based glycomics, encompassing sample preparation, ionization techniques, and fragmentation strategies. Quantitative strategies, including stable isotope labeling, isobaric tagging, and label-free approaches, are also examined for their roles in precise glycan quantification. The review also explores bioinformatics tools and the growing integration of artificial intelligence and machine learning for glycan structure prediction and data interpretation.

DOI: https://doi.org/10.1039/d5ay01169h
Front Cell Infect Microbiol. 2025 ;15 1688880

Survival strategies of mycoplasmas: the critical role of post-translational modifications.

Tingting Li, Hongxia Yuan, Wenjun Zhang, Fangyi Guo.

  Mycoplasmas are unique prokaryotic pathogens distinguished by their lack of a cell wall. These microorganisms are widespread in nature and can cause severe infections, leading to substantial tissue damage. Recent advances in mycoplasmology, driven by developments in molecular biology and proteomics, have provided novel insights into their pathogenicity and pathogenic mechanisms. However, critical knowledge gaps remain in understanding their biology. Emerging evidence highlights the crucial role of protein post-translational modifications (PTMs) in regulating mycoplasma physiology, including virulence, metabolic adaptation, and persistence. Investigating mycoplasma PTMs in greater depth promises to expand our understanding of their pathogenic strategies and may reveal new targets for therapeutic intervention against mycoplasma-associated diseases.

Keywords:  acetylation; glycosylation; mycoplasmas; phosphorylation; post-translational modifications

DOI:  https://doi.org/10.3389/fcimb.2025.1688880
Nat Commun. 2025 Dec 12. 16(1): 11100

Mass spectrometry-based profiling of single-cell histone post-translational modifications to dissect chromatin heterogeneity.

Ronald Cutler, Laura Corveleyn, Claudia Ctortecka, Francesca LiCausi, Joshua Cantlon, Alvaro Sebastian Vaca Jacome, Dieter Deforce, Jan Vijg, Maarten Dhaenens, Malvina Papanastasiou, Steven A Carr, Simone Sidoli.

Single-cell proteomics confidently quantifies cellular heterogeneity, however quantification of post-translational modifications, such as those deposited on histone proteins, remains elusive. Here, we develop a robust mass spectrometry-based method for the unbiased analysis of single-cell histone post-translational modifications (sc-hPTM). sc-hPTM identifies both single- and combinatorial histone post-translational modifications (67 peptidoforms in total), which includes nearly all frequently studied histone post-translational modifications with comparable reproducibility to traditional bulk experiments. As a proof of concept, we treat cells with sodium butyrate, a histone deacetylase inhibitor, and demonstrate that our method can i) distinguish between treated and untreated cells, ii) identify sub-populations of cells with heterogeneous response to the treatment, and iii) reveal differential co-regulation of histone post-translational modifications in the context of drug treatment. The sc-hPTM method enables comprehensive investigation of chromatin heterogeneity at single-cell resolution and provides a further understanding of the histone code.

DOI: https://doi.org/10.1038/s41467-025-66031-0
Trends Parasitol. 2025 Dec 05. pii: S1471-4922(25)00325-3. [Epub ahead of print]

Does peptidome mimicry shape host-parasite coevolution?

Jaroslav Flegr.

  The peptidome mimicry hypothesis (PMH) builds on the principle that vertebrate immunity recognizes peptides absent from the host proteome. It extends this idea to predict host-parasite coevolution outcomes, systematic 'missing peptides', the narrow host specificity of many parasites, and the higher susceptibility of some interspecies hybrids to infection. PMH proposes that long-term coevolution reduces parasite peptide vocabularies and drives convergence toward host repertoires - a pattern that can help to infer a parasite's original host. For example, analyses of SARS-CoV-2 peptide vocabularies have been used to reconstruct the virus's likely host-switching history. Beyond theory, PMH provides an independent and effective way to nominate immunogenic peptide targets for vaccine design, complementary to existing prediction methods.

Keywords:  MHC; T cell epitopes; adaptive immunity; antigen presentation; evolution; host specificity

DOI:  https://doi.org/10.1016/j.pt.2025.11.002
Stem Cell Rev Rep. 2025 Dec 09.

Bromodomain-Driven Regulation of Stem Cells: A Potential Target for Cancer Therapeutic Intervention.

Muthuvel Jothi, Anil Kumar Devakrishnan, Krishna Kumar Haridhasapavalan.

  All cells within an organism share identical genetic material, yet epigenetic mechanisms determine stem cell fate by precisely regulating transcriptional programs. Histone acetylation is a key epigenetic modification that establishes an open chromatin structure, which is recognized by proteins involved in modulating chromatin dynamics essential for stem cell functions. Bromodomain (BrD)-containing proteins specifically recognize acetylated lysines on histones and act as critical epigenetic regulators within larger protein complexes. This review comprehensively describes the BrD protein family, highlighting their structural classifications and diverse functions, and explores their critical roles in regulating stem cell pluripotency and differentiation, and their implications in cancer development. Dysregulated BrD proteins can drive cancer by increasing stem cell-like features and tumor heterogeneity, making them a potential target for cancer treatment. Furthermore, this review emphasizes BrD inhibitors as promising therapeutic targets capable of targeting cancer stem cells and potentially mitigating cancer progression. Understanding the detailed functions and regulatory pathways of BrD proteins may open new avenues for improved cancer stem cell-targeted therapies.

Keywords:  Bromodomain; Bromodomain inhibitors; Cancer stem cells; Epigenetic regulators; Histone acetylation

DOI:  https://doi.org/10.1007/s12015-025-11029-w
Nat Commun. 2025 Dec 11.

Structure of Trypanosoma peroxisomal import complex unveils conformational heterogeneity.

Ravi R Sonani, Artur Blat, Malgorzata Jemiola-Rzeminska, Oskar Lipinski, Stuti N Patel, Tabassum Sood, Grzegorz Dubin.

Peroxisomes are membrane enclosed organelles hosting diverse metabolic processes in eukaryotic cells. Having no protein synthetic abilities, peroxisomes import all required enzymes from the cytosol through a peroxin (Pex) import system. Peroxisome targeting sequence 1 (PTS1)-tagged cargo is recognized by cytosolic receptor, Pex5. The cargo-Pex5 complex docks at the peroxisomal membrane translocon, composed of Pex14 and Pex13, facilitating translocation into the peroxisomal lumen. Despite its significance, the structural basis of the process is only partially understood. Here, we characterize the cargo-Pex5-Pex14NTD ternary complex from Trypanosoma cruzi. Cryo-electron microscopy maps enabled model building for Pex5 (residues 327-462 and 487-653) bound to malate dehydrogenase (MDH; residues 1-323) cargo tetramer and Pex14NTD (residues 21-85). The model provides insight into conformational heterogeneity and identifies secondary interfaces. Specifically, we observe that orientations of Pex5 relative to MDH span a 17° angle. Additionally, PTS1- and Wxxx(F/Y)-independent contact surfaces are observed at MDH-Pex5 and Pex5-Pex14NTD interfaces, respectively. Mutational analysis indicates that the non-PTS1 MDH-Pex5 interface does not significantly contribute to the affinity, but limits the conformational heterogeneity of MDH-Pex5 interface. The Pex5-Pex14NTD interface constitutes an extended binding site of Pex14NTD over Pex5. We discuss the implications of these findings for understanding peroxisomal import mechanism.

DOI: https://doi.org/10.1038/s41467-025-66207-8
Nutrients. 2025 Nov 24. pii: 3673. [Epub ahead of print]17(23):

Glutamine Promotes Myogenesis in Myoblasts Through Glutaminolysis-Mediated Histone H3 Acetylation That Enhances Myogenin Transcription.

Masaru Takatoya, Tomoya Kasugai, Daichi Arai, Urara Kasuga, Chisato Miyaura, Michiko Hirata, Yoshifumi Itoh, Tsukasa Tominari, Yoshitsugu Aoki, Masaki Inada.

  Background/Objectives: Plasma glutamine levels in skeletal muscle change in response to exercise intensity and duration, both in physiological and pathological states. Glutamine contributes to muscle differentiation and regeneration; however, the mechanisms underlying this process remain unclear. This study investigated the role of glutamine glutaminolysis in myogenic differentiation, with a focus on epigenetic regulation of myogenin gene expression. Methods: C2C12 myoblasts were differentiated into myotubes using media containing various concentrations of glutamine, glutamate, or dimethyl 2-oxoglutarate (DM-α-KG), a cell-permeable analog of α-ketoglutarate. Results: Glutamine, glutamate, and DM-α-KG promoted C2C12 myoblast differentiation in a concentration-dependent manner, whereas the glutaminase inhibitor CB-839 suppressed differentiation. 4 mM glutamine increased myogenin mRNA expression by about 5-fold. CB-839 also inhibited glutamine-induced expression of myogenin but did not influence the effects of glutamate or DM-α-KG. Furthermore, glutamine increased histone H3 lysine 27 acetylation (H3K27ac) by about two-fold, whereas CB-839 (200 nM) and A-485 (10 µM), a CBP/p300 histone acetyltransferase inhibitor, reduced H3K27ac levels by about half. These results indicate that glutamine not only serves as a structural amino acid for muscle formation but also enhances myogenin transcription through epigenetic mechanisms. Conclusions: This report demonstrates glutaminolysis-dependent histone H3 acetylation, which induces myogenin transcription in myoblasts. These results, connecting glutamine supplementation during resistance training, may make it an effective strategy to accelerate muscle regeneration.

Keywords:  C2C12 myoblast; epigenetic regulation; glutamine; glutaminolysis; histone H3 acetylation

DOI:  https://doi.org/10.3390/nu17233673
Curr Opin Struct Biol. 2025 Dec 09. pii: S0959-440X(25)00213-1. [Epub ahead of print]96 103195

Integrative modelling of biomolecular dynamics.

Daria Gusew, Carl G Henning Hansen, Kresten Lindorff-Larsen.

Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with invaluable insights, they do not directly reveal that molecules are inherently dynamic. Advances in time-dependent and time-resolved experimental methods have made it possible to capture the dynamics of biomolecules at increasingly higher spatial and temporal resolutions. To complement these, computational models can represent the structural and dynamical behaviour of biomolecules at atomistic resolution and femtosecond timescale, and are therefore useful to interpret these experiments. Here, we review the progress in integrating simulations with dynamical experiments, focusing on the combination of simulations with time-resolved and time-dependent experimental data.

DOI: https://doi.org/10.1016/j.sbi.2025.103195