bims-toxgon 2025-08-10 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2025–08–10
28 papers selected by
Lakesh Kumar, BITS Pilani

Structure and molecular composition of Toxoplasma gondii pellicle.
Function and interactions of a protein bridge between the inner membrane complex and subpellicular microtubules in Toxoplasma gondii.
Inflammation manipulation and a complement-centered reboot of the Toxoplasma gondii model of schizophrenia.
Structure-Based Drug Design of Novel Heterocyclic Scaffolds as TgCDPK1 Inhibitors.
Toxoplasma gondii-induced host's high secretion of 25-hydroxycholesterol for immunoprotection.
To be or not to be: how does the brain respond to different infectious agents?
Differentiation of Toxoplasma into latent forms is linked to central carbon metabolism and requires a GID/CTLH-type E3 ubiquitin ligase.
Nutrient acquisition at the membrane interface: Trypanosomatids subverting host defenses.
Trypanosoma cruzi membrane proteins and host cell invasion.
[Sirtuins: molecular-cellular mechanisms of chondrocyte aging.]
New derivatives of 6-nitrocoumarin-3-thiosemicarbazone exhibit improved antiparasitic activity in the placenta against Trypanosoma cruzi and Toxoplasma gondii.
The AMPK Pathway: Molecular Rejuvenation of Metabolism and Mitochondria.
HDACs repress runaway stress and cell identity to promote reprogramming in root regeneration.
Bromodomain proteins IBD1 and IBD2 link histone acetylation to SWR1- and INO80-mediated H2A.Z regulation in Tetrahymena.
KAT8-mediated MDH2 lactylation promotes renal cancer progression by enhancing mitochondrial function and stress resistance.
HDT2-mediated lysine deacetylation promotes phytochrome A degradation during photomorphogenesis in Arabidopsis.
HCF-1 as a key modulator of OGT function and O-GlcNAcylation in the liver.
Advantages of outcrossing in Plasmodium falciparum : insights from genetic crosses using fluorescent labelled parasites.
PACAP Inhibits TNF-α- Induced Senescence in Primary Chondrocytes by SIRT3: An Implication in Osteoarthritis.
Nuclear functional role of metabolic enzymes and related metabolites: focus on gene expression regulation.
Key proteins of the plasma membrane of Leishmania spp.
Assessing cellular metabolic dynamics with NAD(P)H fluorescence polarization imaging.
Research progress on the interaction between glucose metabolic reprogramming and lactylation in tumors.
Does sequence clustering confound AlphaFold2?
Parasite genome organization: come together, right now!
SIRT4-Mediated Deacetylation of PRDX3 Attenuates Liver Ischemia Reperfusion Injury by Suppressing Ferroptosis.
Net1 Controls Src Activation to Regulate Breast Cancer Cell Motility and Invasion.
Protein structure prediction and design for high-throughput computing.

Curr Top Membr. 2025 ;pii: S1063-5823(25)00004-3. [Epub ahead of print]95 133-157

Structure and molecular composition of Toxoplasma gondii pellicle.

Erica S Martins-Duarte.

  Toxoplasma gondii is one of the most successful protozoan parasites in the world, chronically infecting around 25-30 % of the human population. As a member of the phylum Apicomplexa, Toxoplasma has unique cellular structures, the best known being the apical complex and, no less notable, a trilaminar pellicle structure formed by the plasma membrane on top of a set of flattened membranous sacs (alveoli) called inner membrane complex. As an obligated intracellular pathogen, T. gondii pellicle contains an arsenal of proteins involved in host cell recognition and adhesion, which are crucial for cell invasion. Besides, the pellicle also houses molecular motor machinery that drives the parasite gliding motility. Thus, this chapter will dissect the structure of the pellicle and will also address its main molecular components.

Keywords:  Alveoli; Alveolin; Inner membrane complex; SRS proteins; Subpellicular network; Toxoplasmosis

DOI:  https://doi.org/10.1016/bs.ctm.2025.06.004
Mol Biol Cell. 2025 Aug 06. mbcE24100458

Function and interactions of a protein bridge between the inner membrane complex and subpellicular microtubules in Toxoplasma gondii.

Emily S Cheng, Andy S Moon, William D Barshop, James A Wohlschlegel, Peter J Bradley.

Toxoplasma gondii is an intracellular parasite that utilizes peripheral membrane and cytoskeletal structures for essential functions such as host cell invasion and replication. These include the inner membrane complex (IMC) and the underlying longitudinal subpellicular microtubules (SPMTs) that provide support for the IMC and give the parasite its distinctive crescent shape. While the IMC and SPMTs have been studied separately, the mechanisms linking these adjacent structures remain largely unknown. This study identifies a protein named IMT1 that localizes to the maternal IMC and SPMTs and appears to tether the IMC to the microtubules. We disrupt the IMT1 gene to assess function and then use deletion analyses and mutagenesis to reveal regions of the protein that are necessary for binding to the IMC cytoskeleton or SPMTs. Using proximity labelling, we identify candidate IMT1 interactors in the IMC or SPMTs. Exploration of these candidates reveals that the loss of IMT1 results in a dramatic reduction of the microtubule associated protein TLAP2 and that IMT1 binds directly to the cytoskeletal IMC proteins IMC1, IMC18 and IMC24. Together, these interactions reveal a novel bridge that connects two key cytoskeletal structures and provides new insight into the organization of the structural backbone of T. gondii.

DOI: https://doi.org/10.1091/mbc.E24-10-0458
Neurosci Biobehav Rev. 2025 Aug 01. pii: S0149-7634(25)00314-8. [Epub ahead of print] 106313

Inflammation manipulation and a complement-centered reboot of the Toxoplasma gondii model of schizophrenia.

Jianchun Xiao, Emily G Severance.

  The protozoan parasite, Toxoplasma gondii, has evolved a creative skillset to engage and sustain itself within a diversity of warm-blooded hosts. Progression to adulthood requires residence in the definitive host, Felidae, a taxonomic family encompassing the beloved, sometimes maligned, housecat. Humans are intermediate hosts, primarily infected following ingestion of foodstuffs containing T. gondii tissue cysts or T. gondii oocysts shed by cats. Although most human cases are asymptomatic, acute inflammation and deadly encephalopathies can result if the infection is congenital, or the host is immunocompromised. Increasingly, presumably benign asymptomatic infections are being investigated for behavioral outcomes and complex brain disorders such as schizophrenia. While not typically considered an inflammatory disorder, reports of muted idiopathic inflammation-like comorbidities in schizophrenia persist and cannot be discounted by the usual covariants, medications and metabolic factors. T. gondii's survival success may depend on its ability to regulate host inflammation and satisfy its own life-stage requirements for both motility and quiescence. Within the setting of this fluctuating inflammatory environment putatively controlled by T. gondii, other gene and environmental forces are also at work. We consider a model of schizophrenia centered on complement gene variants and the unique capacity for this set of immune pathways to perpetrate and perpetuate neurobiological dysfunction. We examine T. gondii's connections to the gut, to chronic stress, how its relationship with schizophrenia has matured, and how the boundaries between what qualifies as gene and environment have become blurred as we enter a new era of the microbiome and more personalized medicine.

Keywords:  Genetics; Psychiatry; behavior; immunity; infection; microbiology; parasite

DOI:  https://doi.org/10.1016/j.neubiorev.2025.106313
ChemMedChem. 2025 Aug 08. e202500440

Structure-Based Drug Design of Novel Heterocyclic Scaffolds as TgCDPK1 Inhibitors.

Anoopjit Singh Kooner, Mariah Norman, Igi Vilza, Michael P Mannino, Mary Savari Dhason, Jon Helander, Shrushti Patil, L David Sibley, James W Janetka.

  Toxoplasmosis is caused by the protozoan parasite Toxoplasma gondii and poses grave health concern for immunocompromised patients. T. gondii has a family of calcium dependent protein kinases (CDPKs) that control a variety of critical processes. Among these, TgCDPK1 is required for parasite motility, cell invasion, and egress and hence is essential both for in vitro growth of T. gondii and to cause infections in animals. Using existing X-ray cocrystal structures of pyrazolopyrimidine (PP) inhibitors bound to TgCDPK1, six new chemical series of inhibitors are rationally designed. The synthesis of analogs based on the most promising novel series is pursued, which resulted in potent TgCDPK1 inhibitors that effectively block parasite growth in cells. The resulting lead compounds 44 and 45 belonging to the imidazopyrazine chemical series demonstrate the promising potential of this new class of inhibitors for the treatment and possible cure of the Toxoplasmosis.

Keywords:  calcium dependent protein kinase 1; kinase inhibitor; structure‐based drug design; toxoplasmosis

DOI:  https://doi.org/10.1002/cmdc.202500440
Parasit Vectors. 2025 Aug 04. 18(1): 333

Toxoplasma gondii-induced host's high secretion of 25-hydroxycholesterol for immunoprotection.

Zi-Han Yang, Wei-Ling Wu, Jia-Jia Zheng, Chi Zhang, Ying-Ying Lu, Hong-Juan Peng.

   BACKGROUND: Toxoplasma gondii, a parasitic protozoan affecting approximately one-third of global population, causes opportunistic toxoplasmosis. It penetrates barriers to immune-privileged sites, causing encephalitis, retinochoroiditis, and fetal damage. The infection may be linked to neurodegenerative and psychiatric disorders. The T. gondii-host interaction mechanism remains central to understanding its pathogenesis. The changes in small molecule metabolites after infection, which affects the central nervous system (CNS) normal function, have been poorly characterized.
METHODS: The metabolic alterations in brain tissues of sv129 mice infected by T. gondii at 9 days post-infection (DPI) were analyzed through untargeted metabolomic detection. Cholesterol metabolic reprogramming was assessed through analysis of related gene's transcription with quantitative reverse transcription polymerase chain reaction (qRT-PCR). The primary target cells responsible for cholesterol metabolic dysregulation were identified through detection of the secreted cytokines with enzyme-linked immunosorbent assay (ELISA). The T. gondii replication in host cells treated with 25-HC was evaluated using immunofluorescence assay (IFA). Transcriptomic analysis was performed to identify the differentially expressed genes (DEGs) in the host cells infected by T. gondii and/or treated with 25-HC, and the host cell M1 polarization was confirmed by qRT-PCR.
RESULTS: Brain metabolomic profiling identified 19 differentially expressed metabolites (including 25-HC), primarily involved in amino acid metabolism and cholesterol metabolism pathways (biosynthesis of primary bile acids and steroids). Toxoplasma gondii infection triggered host cholesterol metabolic reprogramming and promoted 25-HC secretion from glial cells, which indirectly inhibited T. gondii's proliferation in host cells. Transcriptomic analysis revealed that 25-HC upregulated the expression of chemokines, C-type lectin receptors, and inflammation-related genes. Notably, 25-HC was verified to confer host resistance against T. gondii infection by promoting microglial M1 polarization.
CONCLUSIONS: Our study demonstrated that T. gondii infection activates the CH25H-25-HC axis to induce microglial M1 polarization and cytokine secretion, thereby establishing an anti-Toxoplasma defense. These findings highlight the central role of cholesterol metabolism in T. gondii pathogenesis and provide innovative strategies for the diagnosis, prevention, and treatment of toxoplasmosis.

Keywords:  25-hydroxycholesterol; Cholesterol metabolism; Metabolomics; Microglia; Toxoplasma gondii; Transcriptomics

DOI:  https://doi.org/10.1186/s13071-025-06890-0
mSphere. 2025 Aug 05. e0032625

To be or not to be: how does the brain respond to different infectious agents?

Ushma Ruparel, Christopher J Tonkin.

  Toxoplasma gondii is an apicomplexan parasite that chronically infects approximately 30% of the global population. In healthy adults, infection is typically resolved within a few weeks, resulting in tissue cysts that persist in the central nervous system for the lifetime of the host. In immune-compromised patients, infection can manifest as toxoplasmic encephalitis and blindness. Additionally, there are several neurological and psychiatric associations with toxoplasmosis, including but not limited to epilepsy and bipolar disorder. This commentary reflects on recent work by Johnson and colleagues (H. J. Johnson, J. A. Kochanowsky, S. Chandrasekaran, C. A. Hunter, et al., mSphere 10:e00216-25, 2025, https://doi.org/10.1128/msphere.00216-25) investigating the difference in neuronal response to T. gondii compared to neurotropic West Nile and Zika viruses. They identify unique neurological and immune signatures associated with the different infections, as well as overlapping pathways enriched regardless of pathogen type. This study provides insights into host signaling pathways that can be manipulated for therapies against toxoplasmosis.

Keywords:  Toxoplasma; brain; flavivirus; immunity; infection; neuron

DOI:  https://doi.org/10.1128/msphere.00326-25
bioRxiv. 2025 Jul 28. pii: 2025.07.27.667068. [Epub ahead of print]

Differentiation of Toxoplasma into latent forms is linked to central carbon metabolism and requires a GID/CTLH-type E3 ubiquitin ligase.

Alessandro D Uboldi, Sachin Khurana, Amalie A Jaywickrama, Sai Prasanna Lekkala-Lethakula, Amber Simonpietri, Karan Singh, Vinzenz Hofferek, Ushma Ruparel, Lachlan L Whitehead, Kelly L Rogers, Alexandra L Garnham, Nichollas Scott, Nicholas J Katris, Malcolm J McConville, David Komander, Simon A Cobbold, Christopher J Tonkin.

Toxoplasma and other Apicomplexan parasites, switch between different developmental stages to persist in and transmit between hosts. Toxoplasma can alternate between systemic tachyzoites and encysted bradyzoite forms found in the CNS and muscle tissues. How parasites sense these tissue types and trigger differentiation remains largely unknown. We show that Toxoplasma differentiation is induced under glucose-limiting conditions and using a CRISPR screen identify parasite genes required for growth under these conditions. From ∼25 identified genes important for differentiation we show that lactate and glutamine metabolism is linked to differentiation and demonstrate the importance of an E3 ubiquitin ligase complex, orthologous to glucose induced degradation deficient (GID) complex in yeast and CTLH complex in humans. We show that TgGID likely regulates translational repression of a key transcription factor required for differentiation, BFD1, through its 3' utr. Overall, this work provides important new insight into how these divergent parasites sense different host cell niches and trigger stage conversion through a ubiquitination-dependent program.

DOI: https://doi.org/10.1101/2025.07.27.667068
Curr Top Membr. 2025 ;pii: S1063-5823(25)00002-X. [Epub ahead of print]95 289-325

Nutrient acquisition at the membrane interface: Trypanosomatids subverting host defenses.

Romário Lopes Boy, Lucas Felipe Almeida Athayde, Nassib Saab Daniel, Maria Fernanda Laranjeira-Silva.

  Trypanosoma brucei, Trypanosoma cruzi, and Leishmania spp. are the trypanosomatid parasites responsible for some of the most significant neglected tropical diseases, such as trypanosomiases and leishmaniases, which impact millions of people globally. Alarmingly, some of these diseases have expanded into previously unaffected regions in recent years. These parasites alternate between invertebrate and vertebrate hosts during their life cycles, adapting to different environments and competing with their hosts for several nutrients. To survive, they have evolved complex strategies to acquire essential nutrients, often subverting host immune defenses and overcoming host-imposed nutritional barriers. This chapter explores the membrane-dependent mechanisms of nutrient sensing and uptake in T. brucei, T. cruzi, and Leishmania spp., with an emphasis on how these parasites adapt to nutrient-limited conditions within their host. Following an overview of the challenges posed by host imposed nutrient restrictions, we examine the parasites' membrane-associated processes and metabolic adaptations that enable their survival. The chapter spans a wide range of micro- and macronutrients-lipids, fatty acids, carbohydrates, amino acids, and metals-discussing the roles of membrane proteins in nutrient scavenging, the metabolic pathways they trigger, and their physiological importance for parasite survival, growth, and infectivity. Special attention is given to the mechanisms by which these parasites evade nutritional immunity, a host defense strategy that limits nutrient availability to pathogens. By shedding light on these nutrient acquisition strategies, this chapter aims to advance our understanding of host-parasite interactions and identify potential targets for therapeutic interventions aimed at the metabolic vulnerabilities of these parasites.

Keywords:  Amino acids; Carbohydrates; Fatty acids; Leishmania; Lipids; Metals; Parasites; Trypanosoma

DOI:  https://doi.org/10.1016/bs.ctm.2025.06.002
Curr Top Membr. 2025 ;pii: S1063-5823(25)00003-1. [Epub ahead of print]95 159-173

Trypanosoma cruzi membrane proteins and host cell invasion.

Luciana O Andrade.

  Trypanosoma cruzi can invade a wide range of non-professional phagocytic cells and does so by subverting the host cell membrane repair mechanism. For this, T. cruzi interacts with and signals to the host cell, leading to the recruitment and fusion of lysosomes to the plasma membrane, which ultimately culminates with the endocytosis of the parasite. To do so, parasite follows a series of steps that include attachment, signaling and formation of the parasitophorous vacuole. For each of these steps a set of proteins have been described to participate, which most likely contribute to its ability to invade different cell types. Besides, intracellular environment also modifies parasite protein expression profile, contributing to its adaptability to the host environment. This chapter will present the different aspects and proteins involved in each of the host cell infection steps.

Keywords:  T. cruzi; intracellular environment; invasion; lysosomes; protein expression

DOI:  https://doi.org/10.1016/bs.ctm.2025.06.003
Adv Gerontol. 2025 ;38(2): 213-221

[Sirtuins: molecular-cellular mechanisms of chondrocyte aging.]

V N Khabarov, E S Mironova, D Ngoc Hop.

More and more studies are focused on the functions of sirtuin proteins in the pathogenesis of joint diseases. Numerous experimental data illustrate the biological functions of sirtuins in the pathogenesis of osteoarthritis in terms of inflammation and cellular aging. The literature also mentions the role of sirtuins in the regulation of circadian rhythms, which have recently been recognized as one of the key aspects in the development of joint pathologies. Some representatives of the sirtuin protein family can participate in the regulation of mitochondrial functions. Over the past three decades, evidence has been obtained that sirtuins are not only important energy sensors, but also have protective properties against metabolic stress and premature aging of cells. Sirtuins regulate metabolism, inhibit apoptosis and autophagy of chondrocytes, and prevent aging of cartilage tissue by exhibiting their deacetylating function. This review shows the role and participation of sirtuins in various molecular signaling events that are associated with the suppression of the functional activity of chondrocytes with increasing age. Modern studies demonstrate the positive effect of sirtuins on the functional activity of chondrocytes and cartilage anabolism. The development of possible ways to regulate sirtuin activity is of considerable interest, which can lead to progress in the treatment of joint pathology.

Keywords: SIRT; cellular aging; chondrocytes; osteoarthritis; sirtuins
Antimicrob Agents Chemother. 2025 Aug 07. e0045425

New derivatives of 6-nitrocoumarin-3-thiosemicarbazone exhibit improved antiparasitic activity in the placenta against Trypanosoma cruzi and Toxoplasma gondii.

Esteban Rocha-Valderrama, Santiago Rostán, Mercedes Fernández, Ana Liempi, Christian Castillo, Graciela Mahler, Ambar Galarza-Jarrin, Jaime A Costales, Josué Pozo-Martínez, Claudio Olea-Azar, Lucía Otero, Mauricio Moncada-Basualto.

  Congenital infections by Trypanosoma cruzi and Toxoplasma gondii pose significant clinical challenges due to the lack of safe and effective treatments. This study evaluates eight novel 6-nitrocoumarin-3-thiosemicarbazone derivatives in an ex vivo human placenta model, assessing their antiparasitic activity and impact on tissue integrity. Two therapeutic approaches were tested: pre-infection (preventive) and post-infection (therapeutic). In vitro and ex vivo assays revealed strong activity trends. Compound 7 was the most effective against T. cruzi (IC50 = 22.4 ± 0.8 µM, logP = 2.49), while compound 1 exhibited the highest activity against T. gondii (IC50 = 17.3 ± 0.5 µM, logP = 1.44). Unlike current treatments, none of the compounds induced placental tissue damage, preserving trophoblast function. Structure-activity relationship (SAR) analysis identified an inverse correlation between lipophilicity and antiparasitic activity in T. gondii, where polar compounds were more effective. In T. cruzi, higher lipophilicity favored trypanocidal activity, suggesting differential cell permeability mechanisms. Mechanistic studies using electrochemistry and electron spin resonance (ESR) demonstrated that nitro group bioreduction promotes ROS generation, explaining activity against T. cruzi. By contrast, lower ROS levels in T. gondii suggest alternative mechanisms. This study validates the ex vivo human placenta model as a clinically relevant platform for antiparasitic drug screening. The findings highlight 6-nitrocoumarin-3-thiosemicarbazones as promising early-stage candidates that warrant further optimization to develop safer and more effective therapies for congenital infections.

Keywords:  6-nitrocoumarin-3-thiosemicarbazone; Toxoplasma gondii; Trypanosoma cruzi; in vitro and ex vivo models

DOI:  https://doi.org/10.1128/aac.00454-25
Annu Rev Cell Dev Biol. 2025 Aug 06.

The AMPK Pathway: Molecular Rejuvenation of Metabolism and Mitochondria.

Nazma Malik, Reuben J Shaw.

Cells must constantly adapt their metabolism to the availability of nutrients and signals from their environment. Under conditions of limited nutrients, cells need to reprogram their metabolism to rely on internal stores of glucose and lipid metabolites. From the emergence of eukaryotes to the mitochondria as the central source of ATP to hundreds of other metabolites required for cellular homeostasis, survival, and proliferation, cells had to evolve sensors to detect even modest changes in mitochondrial function in order to safeguard cellular integrity and prevent energetic catastrophe. Homologs of AMP-activated protein kinase (AMPK) are found in all eukaryotic species and serve as an ancient sensor of conditions of low cellular energy. Here we explore advances in how AMPK modulates core processes underpinning the mitochondrial life cycle and how it serves to restore mitochondrial health in parallel with other beneficial metabolic adaptations.

DOI: https://doi.org/10.1146/annurev-cellbio-120420-094431
bioRxiv. 2025 Jul 29. pii: 2024.01.09.574680. [Epub ahead of print]

HDACs repress runaway stress and cell identity to promote reprogramming in root regeneration.

Ramin Rahni, Bruno Guillotin, Laura R Lee, Indie Suresh, Brandon M L Gorodokin, Graeme Vissers, Kenneth D Birnbaum.

The widespread regenerative capacity of plants is mediated by the ability of specialized cells to reprogram their fate, but the sequential cellular states of regenerating plant cells remain an open question. Here, we characterize the trajectory of cellular reprogramming using single-cell RNA/ATAC-seq, imaging, and mutant analysis. The earliest events were dependent on repressive chromatin modification, where Multiome and genetic analysis showed that Class I histone deacetylases (HDACs) HDA9 and HDA19 were needed to shut down old identities and to prevent a runaway stress response. Cell division mediates a second step needed for the acquisition of many new identity markers, where division rates were tuned by DOF transcription factor OBP1 accelerating and SMR5 , 7 , and 10 decelerating division rates hours later. The results show how plants actively mediate the loss of remnant identities within hours of injury and then tune cell division rates to rapidly reprogram cells to new identities.

DOI: https://doi.org/10.1101/2024.01.09.574680
Epigenetics Chromatin. 2025 Aug 06. 18(1): 51

Bromodomain proteins IBD1 and IBD2 link histone acetylation to SWR1- and INO80-mediated H2A.Z regulation in Tetrahymena.

Jyoti Garg, Alejandro Saettone, Syed Nabeel-Shah, Steven Dang, Abdul Hadi Khalid, Jérémy Loehr, Alexandra Petrova, James D Burns, Peter Karabatsos, Sherin Shibin, Suzanne Wahab, Sean D Taverna, Jack F Greenblatt, Jean-Philippe Lambert, Jeffrey Fillingham.

   BACKGROUND: INO80 and SWR1 are evolutionarily related ATP-dependent chromatin remodeling complexes that regulate the chromatin occupancy of the histone variant H2A.Z, playing critical roles in transcriptional regulation, genome replication, and DNA repair. While the H2A.Z-related functions of INO80 and SWR1 are well characterized in budding yeast and metazoans, much less is known about their composition and chromatin-targeting mechanisms outside of the Opisthokonts. We previously found that a distinct bromodomain-containing protein, IBD1, is involved in multiple chromatin-related complexes, including the SWR1-complex, in the ciliate protozoan Tetrahymena thermophila.
RESULTS: Here, we report that a closely related bromodomain-containing protein, IBD2, functions as an acetyl lysine reader module within a putative INO80 complex. Through iterative proteomic analyses, we show that the Tetrahymena INO80 complex retains several conserved subunits found in its yeast and metazoan counterparts. In vitro binding assays reveal that recombinant IBD2 preferentially recognizes acetylated histone H3 tails. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) demonstrates that IBD2 is enriched near transcription start sites and promoter regions. Notably, the IBD1 and IBD2 genomic binding profiles strongly correlate with that of H2A.Z (Hv1), supporting their functional association with the SWRI- and INO80-complexes.
CONCLUSIONS: Together, our findings support a model in which H2A.Z chromatin dynamics are modulated by SWR1- and INO80-complexes that are differentially recruited to chromatin via distinct bromodomain proteins that recognize specific histone acetylation marks.

Keywords:  Bromodomains; Chromatin remodeling; H2A.Z; INO80c; SWR1c; Transcription

DOI:  https://doi.org/10.1186/s13072-025-00614-5
Int J Biol Macromol. 2025 Aug 04. pii: S0141-8130(25)07128-4. [Epub ahead of print] 146571

KAT8-mediated MDH2 lactylation promotes renal cancer progression by enhancing mitochondrial function and stress resistance.

Yuangui Tang, Chenyun Dai, Huihui Yang, Xian Yang, Ziyu Chen, Jinxiu Dou, Liuxu Zhang, Tao Bai, Junfang Zheng.

  Non-histone proteins localized in membrane, cytosol and nucleus are lactylated to promote tumor progression. However, whether mitochondrial proteins undergo lactylation and contribute to tumor progression remains unexplored. Here, we identified multiple lactylated mitochondrial proteins in human renal cell carcinoma (RCC) cells using lactylome profiling. Among these, malate dehydrogenase 2 (MDH2)-the only lactylated protein in the tricarboxylic acid (TCA) cycle-emerged as a key target, with K239 as its lactylation site. MDH2K239la levels are regulated by KAT8 and SIRT3. Under low-glucose, high-lactate conditions mimicking the tumor microenvironment, MDH2K239la elevated the NADH/NAD+ ratio to drive ATP production and boosted NADPH generation to reduce ROS. This enables cells to alleviate oxidative stress, sustain mitochondrial function, and promote RCC malignancy in vitro and in vivo. Mechanistically, MDH2K239la enhances MDH2 enzymatic activity and strengthens its interaction with the citrate transporter SLC25A1. This facilitates citrate efflux, fueling IDH1-dependent NADPH production when lactate serves as an energy source. Collectively, we unveil a lactylation-dependent mechanism that reprograms mitochondrial metabolism to confer oxidative stress resistance and drive RCC progression. Targeting mitochondrial proteins lactylation, exemplified by MDH2K239la, represents a promising therapeutic strategy for RCC.

Keywords:  Lactylation; MDH2; RCC

DOI:  https://doi.org/10.1016/j.ijbiomac.2025.146571
Mol Plant. 2025 Aug 06. pii: S1674-2052(25)00268-0. [Epub ahead of print]

HDT2-mediated lysine deacetylation promotes phytochrome A degradation during photomorphogenesis in Arabidopsis.

Feng Zheng, Wenli Ou, Ling Deng, Yahan Wang, Hangcong Chen, Yiting Chen, Tao Peng, Yongyi Yang, Jaime A Teixeira da Silva, Xuncheng Liu.

  The switch from skotomorphogenesis to photomorphogenesis, a key developmental transition in the life cycle of seed plants, involves dramatic proteomic changes. Lysine acetylation (Lys-Ac) is an evolutionarily conserved and widely recognized post-translational modification that plays an important role in plant development, whereas its role in seedling deetiolation remains unclear. Here, we conducted a comparative lysine acetylomic analysis of etiolated Arabidopsis seedlings before and after red (R) light irradiation, revealing that exposure to R light mainly led to widespread protein lysine deacetylation during seedling deetiolation. Phytochrome A (phyA), the unique far-red (FR) light photoreceptor, was deacetylated at lysine 65 (K65) when etiolated seedlings were transferred to light. This residue served as a critical ubiquitination site that regulates phyA stability. Furthermore, K65 deacetylation facilitates phyA ubiquitination and 26S proteasome-mediated degradation, and is essential for the function of phyA in FR light signaling and seedling photomorphogenesis. We identified a plant-specific lysine deacetylase HDT2 that interacts with and deacetylates phyA in the nucleus, thereby promoting the ubiquitination and degradation of phyA during seedling deetiolation. Genetic analysis revealed that HDT2 plays a crucial role in phyA-mediated photomorphogenic growth. These findings suggest that lysine deacetylation of phyA by HDT2 plays an essential role in modulating phyA turnover in response to light, revealing that Lys-Ac is central to the rewiring of plants for photomorphogenic growth.

Keywords:  HDT2; light signal transduction; lysine deacetylase; lysine deacetylation; photomorphogenesis; phytochrome A

DOI:  https://doi.org/10.1016/j.molp.2025.08.002
Sci Rep. 2025 Aug 03. 15(1): 28328

HCF-1 as a key modulator of OGT function and O-GlcNAcylation in the liver.

Vaibhav Kapuria, Ayushma, Winship Herr, Shilpi Minocha.

  Host cell factor-1 (HCF-1) is a transcriptional coregulator essential for maintaining liver function and cellular metabolism. O-linked N-acetylglucosamine transferase (OGT) is a key nutrient-sensing enzyme that catalyzes protein O-GlcNAcylation, a critical post-translational modification regulating metabolic pathways. This study investigates the role of hepatocyte-specific depletion of HCF-1 in regulating OGT stability, activity, and cellular localization in hepatocytes. Using a transgenic mouse model with hepatocyte-specific HCF-1 deletion, we assessed the impact of HCF-1 loss on OGT expression and O-GlcNAcylation activity. OGT protein levels, mRNA expression, and cellular localization were evaluated using molecular and histological techniques. Comparisons were made with control mice and hepatocytes under nutrient-starved conditions. Hepatocyte-specific HCF-1 deletion led to progressive loss of HCF-1 protein and a concomitant decrease in OGT levels and global O-GlcNAcylation. Loss of HCF-1 did not alter OGT mRNA levels, suggesting post-translational regulation. Immunofluorescence revealed reduced nuclear OGT and O-GlcNAcylation, mimicking changes observed under fasting conditions. Isolated HCF-1-deficient hepatocytes showed impaired adhesion, further underscoring HCF-1's role in hepatocyte function. Notably, in heterozygous Hcfc1hepKO/ + females, HCF-1-negative hepatocytes displayed cytoplasmic O-GlcNAcylation, while HCF-1-positive cells maintained nuclear localization. HCF-1 is crucial for regulating OGT stability, activity, and nuclear localization in hepatocytes. These findings establish a mechanistic link between HCF-1 and OGT, highlighting their coordinated role in hepatic nutrient sensing and metabolic regulation.

Keywords:   O-GlcNAcylation; O‐linked N‐acetylglucosamine (O‐GlcNAc) transferase (OGT); Hepatocytes; Host cell factor-1; Liver; Nutrient sensing.

DOI:  https://doi.org/10.1038/s41598-025-11813-1
bioRxiv. 2025 Jul 31. pii: 2025.07.18.665596. [Epub ahead of print]

Advantages of outcrossing in Plasmodium falciparum : insights from genetic crosses using fluorescent labelled parasites.

Xue Li, Kathrin S Jutzeler, Biley A Abatiyow, Nastaran Rezakhani, Meseret T Haile, Amanda S Leeb, Hardik Patel, Stefan H I Kappe, François Nosten, Ian H Cheeseman, Michael T Ferdig, Timothy J C Anderson, Ashley M Vaughan, Sudhir Kumar.

Malaria parasites are obligately sexual hermaphrodite protozoans with gamete fusion occurring in the mosquito midgut, followed by meiosis and recombination. Malaria parasite populations show a spectrum of populations structures ranging from predominantly selfing to highly outcrossed. However, the fitness consequences of selfing and outcrossing for malaria parasites are poorly understood. This project was designed to investigate the dynamics of gamete fusion within the mosquito midgut and the relative fitness of selfed and outcrossed zygotes. We generated florescent-labelled clones of NF54 (mCherry), an African parasite, and NHP4026 (GFP), a Thai parasite, crossed these parasites, and scored genotypes of 8540 oocysts from 435 mosquitoes sampled from 7 to 14 days post infection. We observed decreasing proportions of outcrossed oocysts and increasing levels of inbreeding over the course of the infection in two independently replicated crosses. These results are consistent with the faster maturation of transmissible sporozoites derived from outcrossed compared with selfed oocysts. Our results suggest a substantial outcrossing advantage, perhaps because this allows for the removal of deleterious mutations accumulated during asexual parasite replication in the vertebrate host. We also found that selfed NF54 oocysts were larger than outcrossed or selfed NHP4026 oocysts, which may influence production of sporozoites and onward transmission. We conclude that fluorescent labelled parasites provide clear resolution of mating patterns, temporal dynamics and transmission potential of malaria parasites in mosquitoes. Importantly, faster maturation of outcrossed parasites can maximize levels of recombination in transmitted malaria parasite populations.

DOI: https://doi.org/10.1101/2025.07.18.665596
Clin Exp Pharmacol Physiol. 2025 Sep;52(9): e70062

PACAP Inhibits TNF-α- Induced Senescence in Primary Chondrocytes by SIRT3: An Implication in Osteoarthritis.

Xuewu Zhou, Kangquan Shou, Hao Yao.

  Osteoarthritis (OA) is a degenerative joint disease closely associated with aging, in which chondrocyte senescence plays a critical role in cartilage degradation. Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide known for its anti-inflammatory and cytoprotective effects; however, its role in chondrocyte senescence remains poorly understood. This study investigated the protective effects of PACAP38 on tumour necrosis factor-α (TNF-α)- induced chondrocyte senescence and the underlying mechanisms. Intracellular reactive oxygen species (ROS) levels were measured using 2',7'-dichlorodihydrofluorescein diacetate (DCFH-DA) staining, oxidative DNA damage was assessed by 8-hydroxy-2'-deoxyguanosine (8-OHdG) enzyme-linked immunosorbent assay (ELISA), and senescence markers were evaluated by senescence-associated β-galactosidase (SA-β-Gal) staining, telomerase activity assay, and telomere length analysis. Gene and protein expression were examined via real-time polymerase chain reaction (PCR) and Western blotting. We found that PACAP type I receptor (PAC1R), the receptor for PACAP, was expressed in both murine and human chondrocytes and was downregulated by TNF-α stimulation. PACAP38 treatment significantly reduced ROS and 8-OHdG levels, restored telomerase activity and telomere length, and decreased SA-β-Gal activity. Mechanistically, PACAP38 upregulated sirtuin 3 (SIRT3), a mitochondrial deacetylase that regulates oxidative stress and metabolism, while suppressing acetylated p53 (ac-p53) and plasminogen activator inhibitor-1 (PAI-1) expression. Furthermore, PACAP38 reversed TNF-α-induced dephosphorylation of AMP-activated protein kinase alpha (AMPK-α) and its downstream target acetyl-CoA carboxylase (ACC). Importantly, inhibition of AMPK by compound C abolished these protective effects, confirming the essential role of the AMPK-SIRT3 signalling pathway. In conclusion, our findings demonstrate that PACAP38 mitigates TNF-α-induced chondrocyte senescence via activation of the AMPK-SIRT3 signalling axis, suggesting a potential therapeutic strategy for OA.

Keywords:  AMPK; PACAP; SIRT3; chondrocyte; osteoarthritis; senescence

DOI:  https://doi.org/10.1111/1440-1681.70062
Mol Metab. 2025 Aug 06. pii: S2212-8778(25)00140-1. [Epub ahead of print] 102233

Nuclear functional role of metabolic enzymes and related metabolites: focus on gene expression regulation.

Simona Todisco, Dominga Iacobazzi, Anna Santarsiero, Paolo Convertini, Vittoria Infantino.

   BACKGROUND: Many biological processes from physiological development to different pathological conditions are closely linked to dynamic energetic metabolism and its dysregulations. Mounting evidence shows that metabolic rewiring allows cells to adapt to stress conditions, changes in extracellular cues, and nutritional fluctuations in a timely and precise manner by modulating gene expression. Recent studies reveal non-strictly metabolic functions of metabolic enzymes and related metabolites often confined to the nucleus. Indeed, beyond the diffusion of metabolites through nuclear pores, several metabolic enzymes translocate to the nucleus during cellular differentiation, macrophage activation, tumorigenesis, and so on.
SCOPE OF REVIEW: This review aims to outline recent advances in the nuclear functions of metabolic enzymes, focusing on gene expression regulation through transcription factors and epigenetic mechanisms.
MAJOR CONCLUSIONS: The nuclear localization of metabolic enzymes and metabolites underlines the dual role of metabolism as both a driver and a controller of cellular processes by linking energy metabolism directly to gene expression and cellular reprogramming. The main involvement of respiratory enzymes in nuclear functions suggests a ready interplay between energy status and transcriptional regulation. We trust that these insights will contribute to a more extensive knowledge of the cellular and nuclear landscape and could inspire future investigations on metabolic-mediated gene regulation mechanisms with the aim of developing more effective therapies against diseases.

Keywords:  epigenetics; gene expression regulation; metabolic enzymes; metabolites; nuclear translocation

DOI:  https://doi.org/10.1016/j.molmet.2025.102233
Curr Top Membr. 2025 ;pii: S1063-5823(25)00008-0. [Epub ahead of print]95 249-265

Key proteins of the plasma membrane of Leishmania spp.

Ramon Vieira Nunes, Bruna Rodrigues de Almeida, Hélida Monteiro de Andrade.

  The initial interaction between host cells and Leishmania infective rforms is dependent on surface proteins from both organisms. Membrane proteins are fundamental molecules that perform a variety of functions, including recognition, adhesion, and host cell penetration, as well as nutrient and enzyme transport and cell signaling. Several Leishmania plasma membrane proteins play critical roles in host interaction, parasite survival, and virulence during the early stages of infection. Among them, the most prominent is GP63, which confers resistance to complement-mediated lysis and induces macrophage phagocytosis. Another important surface protein, prohibitin, has a role in macrophage infection and has demonstrated the ability to generate a humoral response in human patients, making it a potential diagnostic marker. Furthermore, prohibitin is considered a promising target for vaccination against L. infantum. The kinetoplastid membrane protein 11 (KMP11) has also been identified as a potential B- and T-cell immunogen during infection. The analysis of the membrane proteome profile of Leishmania promastigotes could offer a more comprehensive understanding of host-parasite interactions and Leishmania biology. Despite membrane proteins constituting 20-30 % of the proteome in most organisms, there are relatively few proteomic studies on Leishmania parasites that focus on membrane-associated proteins, even though these proteins are potential drug targets. This review provides a survey of the current knowledge regarding the composition of plasma membrane focusing, in alphabetical order, on those proteins that are best characterized in terms of functionality in Leishmania.

Keywords:  Leishmania; Plasma membrane; Proteome

DOI:  https://doi.org/10.1016/bs.ctm.2025.06.008
bioRxiv. 2025 Jul 31. pii: 2025.07.28.667273. [Epub ahead of print]

Assessing cellular metabolic dynamics with NAD(P)H fluorescence polarization imaging.

Lu Ling, Jack C Crowley, Matthew L Tan, Jennie A M R Kunitake, Adrian A Shimpi, Rebecca M Williams, Lara A Estroff, Claudia Fischbach, Warren R Zipfel.

Altered metabolism enables adaptive advantages for cancer, driving the need for improved methods for non-invasive long-term monitoring of cellular metabolism from organelle to population level. Here we present two-photon steady-state fluorescence polarization ratiometric microscopy (FPRM), a label-free imaging method that uses nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) autofluorescence as a functional readout of cellular metabolism. The method is simple to implement and operates an order of magnitude faster than the NAD(P)H-fluorescence lifetime imaging microscopy (FLIM) imaging modality, reducing cytotoxic stress while providing long-term monitoring capacity. FPRM enables high-resolution dynamic tracking of NAD(P)H signals with subcellular details and we have established a set of instrument-independent ratiometric parameters that correlates NAD(P)H signals with metabolic status during pharmaceutical and environmental perturbations. We further integrated FPRM readouts with other parameters such as cell shape and migration on 2D and 3D collagen matrices, demonstrating the technique's versatility across bioengineered platforms for cancer metabolism research.

DOI: https://doi.org/10.1101/2025.07.28.667273
Front Immunol. 2025 ;16 1595162

Research progress on the interaction between glucose metabolic reprogramming and lactylation in tumors.

Yi Yang, Yi Wu, Hui Chen, Zehai Xu, Ruisi Lu, Sijie Zhang, Rui Zhan, Qinghua Xi, Yunfeng Jin.

  Glucose metabolic reprogramming describes the alterations in intracellular metabolic pathways in response to variations in the body's internal environment. This metabolic reprogramming has been the subject of extensive research. The primary function is to enhance glycolysis for rapid ATP production, even with sufficient oxygen, leading to a significant accumulation of lactic acid, which subsequently affects the functions of tumor cells and immune cells within TME. Lactylation represents a newly identified post-translational modification (PTM) that occurs due to lactate accumulation and is observed in various proteins, encompassing both histone and non-histone types. Lactylation alters the spatial configuration of proteins, influences gene transcription, and thereby regulates gene expression. This modification serves as a significant epigenetic regulatory factor in numerous diseases. Glucose metabolic reprogramming and lactylation are intricately linked in the process of tumorigenesis. Glucose reprogramming activates essential enzymes, including hexokinase 2 (HK2), pyruvate kinase M2 (PKM2), and lactate dehydrogenase A (LDHA), through transcription factors such as HIF-1α and c-Myc, thereby enhancing glycolysis and lactate accumulation. Lactate functions as a metabolite and signaling molecule, acting as a substrate for lactylation facilitated by histone acetyltransferases such as CBP/p300. This epigenetic modification inhibits antitumor immunity through the upregulation of oncogenic signaling pathways, the induction of M2-type macrophage polarization, and the dysfunction of T-cells. Glucose metabolic reprogramming not only influences lactate synthesis but also provides sufficient substrates for lactate modification. The two factors jointly affect gene expression and protein function, acidify the tumor microenvironment, regulate immune evasion, and promote carcinogenesis. This review systematically details the mechanisms of lactylation and glucose metabolic reprogramming, their impacts on immune cells within the tumor microenvironment, and their interrelations in tumor progression, immunity, and inflammation.

Keywords:  glucose metabolic reprogramming; immune cells; lactate; lactylation; macrophage; posttranslational modification; tumor microenvironment

DOI:  https://doi.org/10.3389/fimmu.2025.1595162
J Mol Biol. 2025 Aug 06. pii: S0022-2836(25)00442-5. [Epub ahead of print] 169376

Does sequence clustering confound AlphaFold2?

Hannah K Wayment-Steele, Sergey Ovchinnikov, Lucy Colwell, Dorothee Kern.

  Predicting multiple conformational states of proteins represents a significant open challenge in structural biology. Increasingly many methods have been reported for perturbing and sampling AlphaFold2 (AF2) [1] to achieve multiple conformational states. However, if multiple methods achieve similar results, that does not in itself invalidate any method, nor does it answer why these methods work. Interpreting why deep learning models give the results they do is a critically important endeavor for future model development and appropriate usage. To help the field continue to try to answer these questions, this work addresses misunderstandings and inaccurate conclusions in refs. [2-6]. Deep learning methods development moves quickly, and by no means did we think that the implementation of AF-Cluster in [7] would be the final word on how to sample multiple conformations. However, Porter et al.'s primary critique, that AF-Cluster does not use local evolutionary couplings in its MSA clusters, is incorrect. We report here further analysis that underscores our original finding that local evolutionary couplings do indeed play an important role in AF-Cluster predictions, and refute all false claims made against [7].

Keywords:  AlphaFold2; clustering; conformational ensembles; evolutionary couplings; metamorphic proteins

DOI:  https://doi.org/10.1016/j.jmb.2025.169376
Trends Parasitol. 2025 Aug 07. pii: S1471-4922(25)00199-0. [Epub ahead of print]

Parasite genome organization: come together, right now!

Parul Singh, Leon Walther, Maureen D Cabahug, Joana R C Faria, Jessica M Bryant.

  Links between genome organization and transcription have been extensively studied in model eukaryotes; however, recent application of state-of-the-art chromosome conformation capture techniques to kinetoplastid and Plasmodium parasites has revealed fascinating and divergent architectural mechanisms underlying gene regulation. Trypanosomes assemble nuclear compartments to fine-tune transcription and splicing of variant surface glycoprotein genes. Plasmodium utilizes specific protein complexes to cluster variant surface antigen genes for their epigenetic regulation and genetic diversity. Recent studies have also observed coalescence of genes transcribed by RNAPII in Trypanosoma brucei and active stage-specific genes in Plasmodium falciparum, which could facilitate bursts of transcription in the dynamic parasite life cycle. Thus, connections between genome architecture and gene regulation are emerging as crucial to parasite survival and pathogenesis.

Keywords:  Plasmodium; chromatin; epigenetics; genome organization; nuclear compartments; transcription; trypanosome

DOI:  https://doi.org/10.1016/j.pt.2025.07.010
Int J Biol Sci. 2025 ;21(10): 4663-4682

SIRT4-Mediated Deacetylation of PRDX3 Attenuates Liver Ischemia Reperfusion Injury by Suppressing Ferroptosis.

Qiwen Yu, Dongjing Yang, Binli Ran, Jie Pan, Yaodong Song, Mengwei Cui, Qianqian He, Chaopeng Mei, Haifeng Wang, Huihui Li, Guanghui Li, Yinuo Meng, Fazhan Wang, Wenzhi Guo, Changju Zhu, Sanyang Chen.

  Liver ischemia-reperfusion injury (LIRI) is an important cause of the clinical prognosis of liver transplantation. Despite Sirtuin 4 (SIRT4) is involved in various post-translational modifications, its role in LIRI is unclear. This research aimed to investigate the influence of SIRT4 on the pathogenesis of LIRI. To this end, SIRT4 knockout (KO) and liver-specific overexpression mice, as well as alpha mouse liver 12 (AML12) cells, were employed. We showed that SIRT4 expression was downregulated in mice with LIRI or AML12 cells exposed to hypoxia-reoxygenation (H/R) injury, as well as in the liver tissue of liver transplant patients. SIRT4 KO exacerbated liver injury and ferroptosis; conversely, liver-specific SIRT4 overexpression in mice produced the opposite results. Furthermore, the ferroptosis inhibitor ferrostatin-1 mitigated the exacerbation of liver injury and ferroptosis caused by SIRT4 KO. Mechanistically, SIRT4 interacted with peroxiredoxins 3 (PRDX3) and deacetylated it at lysine 92, leading to the inhibition of ferroptosis. Furthermore, the protective effect of SIRT4 on LIRI was dependent on PRDX3 deacetylation at lysine 92. Additionally, liver-targeted lipid nanoparticles (LNPs)-sirt4 mRNA alleviated LIRI and ferroptosis in mice. Taken together, our findings highlight the SIRT4-PRDX3 axis as a key regulator and potential therapeutic target for LIRI.

Keywords:  PRDX3; SIRT4; deacetylation; ferroptosis; liver ischemia reperfusion injury

DOI:  https://doi.org/10.7150/ijbs.114510
Mol Cell Biol. 2025 Aug 05. 1-19

Net1 Controls Src Activation to Regulate Breast Cancer Cell Motility and Invasion.

Yan Zuo, Heather S Carr, Wen Li, Songlin Zhang, Jeffrey A Frost.

  The cytoplasmic tyrosine kinase Src supports many phenotypes in cancer cells, including proliferation, migration and invasion, survival, and metastasis. We have previously shown that Src promotes cytoplasmic localization of the RhoGEF Net1, where it stimulates RhoA activation, breast cancer cell motility, and extracellular matrix invasion. In the present work, we show that the Net1 expression in human breast tumors correlates with Src phosphorylation on its activating site Y419. We also show in human breast cancer cell lines that endogenous Net1 and Src interact, and that Net1 expression is required for full Src activation. Net1 must localize to the cytosol to promote Src activation, but surprisingly, the catalytic activity of Net1 toward Rho GTPases is not necessary for Src activation. Instead, Net1 requires interaction with the scaffolding protein Dlg1. Dlg1 knockdown prevents Src activation by Net1 and precludes interaction between Net1 and Src. Moreover, Net1 knockdown cooperates with small molecule inhibition of Src to inhibit breast cancer cell motility and extracellular matrix invasion. These data show a previously unrecognized relationship between Net1 and Src in human breast tumors and breast cancer cell lines, and suggest that therapeutic targeting of Net1 may be of benefit in breast cancers with elevated Src activity.

Keywords:  Dlg1; Net1; RhoA; Src; breast cancer; invasion

DOI:  https://doi.org/10.1080/10985549.2025.2536115
bioRxiv. 2025 Jul 22. pii: 2025.07.18.665594. [Epub ahead of print]

Protein structure prediction and design for high-throughput computing.

Vinay Saji Mathew, Gretta D Kellogg, William Km Lai.

Recent advances in structural biology and machines learning have resulted in a revolution in molecular biology. This revolution is driven by protein structure prediction and design tools such as Alphafold3, Chai-1, and Boltz-2 which are now able to accurately model protein structures as well as predict protein-complex formation with a variety of substrates at atomic resolution (i.e., DNA, RNA, small ligands, post-translational modifications). The impact of these protein-structure prediction algorithms has been matched by the emergence of in silico protein design platforms (RFdiffusion), which now promise to revolutionize synthetic biology and novel disease therapeutics. Despite their potential to transform molecular biology, the adoption of these algorithms is hindered in part, not only by their high computational requirements, but also by the difficulty in deploying these algorithms on available systems. To help address these barriers, we developed containerized solutions for AlphaFold3, Chai-1, Boltz-2, and RFdiffusion, optimized across a variety of computational architectures (e.g., x86 and ARM). Additionally, we present OmniFold, an optimized wrapper-platform with automatic QC report generation that enables AlphaFold3, Chai-1, and Boltz-2 to perform simultaneously while more efficiently utilizing GPU systems. Precompiled containers and their definition files are available as open source through Sylabs and GitHub. We hope that these containers and repos will help to facilitate reproducibility, accessibility, and accelerate scientific discovery.
Availability and implementation: Source code for containers is available at: https://github.com/EpiGenomicsCode/ProteinStruct-Containers https://github.com/EpiGenomicsCode/ProteinDesign-Containers https://github.com/EpiGenomicsCode/OmniFold.

DOI: https://doi.org/10.1101/2025.07.18.665594