PONDR-FIT: a meta-predictor of intrinsically disordered amino acids

JMJD1C forms condensate to facilitate a RUNX1-dependent gene expression program shared by multiple types of AML cells

JMJD1C (Jumonji Domain Containing 1C), a member of the lysine demethylase 3 (KDM3) family, is universally required for the survival of several types of acute myeloid leukemia (AML) cells with different genetic mutations, representing a therapeutic opportunity with broad application. Yet how JMJD1C regulates the leukemic programs of various AML cells is largely unexplored. Here we show that JMJD1C interacts with the master hematopoietic transcription factor RUNX1, which thereby recruits JMJD1C to the genome to facilitate a RUNX1-driven transcriptional program that supports leukemic cell survival. The underlying mechanism hinges on the long N-terminal disordered region of JMJD1C, which harbors two inseparable abilities: condensate formation and direct interaction with RUNX1. This dual capability of JMJD1C may influence enhancer-promoter contacts crucial for the expression of key leukemic genes regulated by RUNX1. Our findings demonstrate a previously unappreciated role for the non-catalytic function of JMJD1C in transcriptional regulation, underlying a mechanism shared by different types of leukemias.

Targeting the Exonic Circular OGT RNA/O-GlcNAc Transferase/Forkhead Box C1 Axis Inhibits Asparagine- and Alanine-Mediated Ferroptosis Repression in Neuroblastoma Progression

The disruption of ferroptosis, an emerging form of programmed cell death, is crucial in the development and aggressiveness of tumors. Meanwhile, the mechanisms and treatments that control ferroptosis in neuroblastoma (NB), a prevalent extracranial cancer in children, are still unknown. In this study, forkhead box C1 (FOXC1) and O-GlcNAc transferase (OGT) are identified as regulators of asparagine- and alanine-mediated ferroptosis repression in NB. Mechanistically, OGT facilitates FOXC1 stabilization via inducing O-GlcNAcylation in liquid condensates to increase the expression of asparagine synthetase (ASNS) and glutamate pyruvate transaminase 2 (GPT2), resulting in asparagine and alanine biogenesis, and subsequent synthesis of cystathionine β-synthase (CBS) or ferritin heavy chain 1 (FTH1). Meanwhile, exonic circular OGT RNA (ecircOGT) is able to encode a novel protein (OGT-570aa) containing domain essential for binding of OGT to FOXC1, which competitively decreases the OGT-FOXC1 interaction. Preclinically, miconazole nitrate facilitates the interaction of OGT-570aa with FOXC1, suppresses ferroptosis resistance of NB cells, and inhibits their growth, invasion, and metastasis. In clinical NB cases, higher OGT, FOXC1, ASNS, GPT2, CBS, or FTH1 levels are correlated with worse survival, while lower ecircOGT or OGT-570aa expression is associated with tumor progression. These results indicate that targeting the ecircOGT/OGT/FOXC1 axis inhibits asparagine- and alanine-mediated ferroptosis repression in NB progression.

Mineralocorticoid receptor phase separation modulates cardiac preservation

Heart transplantation is the gold standard treatment for patients with end-stage heart failure. However, there is a shortage of donor hearts available. The short tolerable cold ischemic time for delivering donor hearts to matching recipients is closely responsible for this shortage. Here we uncover the phenomenon of mineralocorticoid receptor (MR) phase separation, which exacerbates injury to the murine and human donor heart during cold storage and can be modulated with pharmacological inhibition to improve preservation quality. Interestingly, donor cardiomyocytes strongly expressed MR, which undergoes preservation-related phase separation. The phenomenon of macromolecular phase separation is not limited to the heart or MR during preservation. Cold preservation of the lung, liver and kidney also displays phase separation of other transcriptional regulators including histone deacetylase 1 (HDAC1), bromodomain-containing 4 (BRD4) and MR. Our results reveal an understudied area of preservation biology that may be further exploited to improve the preservation of multiple solid organs.

Metal-sensing properties of the disordered loop from the Arabidopsis metal transceptor IRT1

The plant iron-regulated transporter 1 (IRT1) iron transporter is a plasma membrane protein that takes up iron in the root under iron-limited conditions. Besides its primary metal substrate iron, IRT1 transports other divalent metals that overaccumulate in plants when soil iron is low and IRT1 is highly expressed. We previously reported that the intracellular regulatory loop between transmembrane helices TM4 and TM5 is involved in the post-translational regulation of IRT1 by its non-iron metal substrates. Upon excess of zinc, IRT1 undergoes phosphorylation by CIPK23 followed by its ubiquitination by IDF1 to target IRT1 for vacuolar degradation. This zinc-dependent down-regulation of IRT1 requires the presence of four histidine (H) residues in the IRT1 loop, which directly bind zinc. However, how selective metal binding is achieved and how this allows downstream regulation to take place is largely not known. Here, we characterized the metal-binding properties and structure of the IRT1 loop to better understand the molecular basis of non-iron metal sensing and signaling. Using a combination of circular dichroism and NMR, we reveal that zinc and manganese bind to the IRT1 loop with nanomolar range affinity and that metal binding does not trigger structuration of the loop. We validate that zinc and manganese binding is mediated by four H residues and identify aspartic acid (D) residue D173 as helping in metal co-ordination and participating to metal sensing and metal-dependent degradation of IRT1 in plants. Altogether, our data provide further understanding of how IRT1 regulatory loop senses high cytosolic divalent metal concentrations to regulate metal uptake in plants.

Stm1 regulates Ifh1 activity revealing crosstalk between ribosome biogenesis and ribosome dormancy

Nutrient abundance boosts ribosome biogenesis, whereas ribosome dormancy factors limit ribosome degradation upon starvation. The equilibrium between the two pathways governs cell growth. In this study, we identified suppressor of Tom1 (Stm1) as a molecular link between ribosome protection and biogenesis in Saccharomyces cerevisiae. While Stm1 was previously described as a dormancy factor, we show that it activates Ifh1, a transcriptional activator of ribosomal protein genes. Stm1 transiently localizes to the nucleolus, where it interacts with pre-ribosomes and directly binds RNA and Ifh1 through its C-terminal intrinsically disordered region (IDR). Although the IDR is dispensable for ribosome protection, its loss compromises cell growth. The IDR is phosphorylated upon nutrient starvation, which disrupts its interaction with Ifh1. Our findings reveal a molecular pathway sensing and adjusting ribosome abundance in response to nutrient availability, reinforcing the relevance of regulated ribosome homeostasis in physiology and disease.

Proximal relationships of moonlighting proteins in Escherichia coli: A mathematical genomics perspective

Moonlighting proteins in Escherichia coli (E.coli) perform multiple independent functions without altering their primary amino acid sequence, challenging the "one gene-one enzyme" hypothesis. Bacterial proteins serve various functions, including host cell adhesion, extracellular matrix interaction, and immune modulation, while also supporting essential physiological processes within the bacteria. Identifying these proteins in pathogens and tracking their genetic changes is crucial for understanding bacterial survival and virulence. A quantitative understanding of these proteins is pivotal as it enables the identification of specific patterns and relationships between amino acid composition, protein stability, and functional versatility. This study quantitatively analyzes 50 E. coli moonlighting proteins, revealing alanine as the most frequent residue (8.92 % median), while cysteine had the lowest (0.58 %). A preference for non-polar residues was observed (polar-to-non-polar ratio: 0.89). Quantitative features analyses identified seven distinct proximal sets, reflecting the pro- teins' spatial arrangements of amino acids, structural diversity, and functional roles in processes such as metabolism, stress response, and gene regulation. The highest percentage of disordered residues was 56.45 %, significantly lower than 100 % in human moonlighting proteins. These results deepen our understanding of the multifunctionality of E. coli moonlighting proteins, indicating their adaptability and implications for bacterial survival and pathogenicity.

Zooming into Gene Activation: Estrogen Receptor α Dimerization and DNA Binding Visualized by High-Speed Atomic Force Microscopy

Estrogen receptor α (ERα) is pivotal in gene regulation, particularly in estrogen-responsive cancers. However, the full-length molecular dynamic structure of ERα remains elusive. In this study, we employ high-speed atomic force microscopy (HS-AFM) to visualize ERα interactions with the estrogen response element (ERE) under both ligand-present and ligand-absent conditions. ERα binds to ERE even in the absence of estrogen, although the presence of the ligand significantly enhances binding precision and stability. Our real-time, high-resolution HS-AFM imaging captures ERα structural transitions from monomeric to dimeric forms, elucidating the molecular mechanisms by which estrogen modulates DNA-binding specificity. Based on these findings, we propose a ligand-induced dimerization (LID) model, wherein estrogen facilitates the optimal loading of ERα onto DNA. These insights deepen our understanding of hormone signaling in cancer and hold promise for the development of future therapeutic strategies targeting hormone-related malignancies.

Intrinsic Disorder and Phase Separation Coordinate Exocytosis, Motility, and Chromatin Remodeling in the Human Acrosomal Proteome

Intrinsic disorder refers to protein regions that lack a fixed three-dimensional structure under physiological conditions, enabling conformational plasticity. This flexibility allows for diverse functions, including transient interactions, signaling, and phase separation via disorder-to-order transitions upon binding. Our study focused on investigating the role of intrinsic disorder and liquid-liquid phase separation (LLPS) in the human acrosome, a sperm-specific organelle essential for fertilization. Using computational prediction models, network analysis, Structural Classification of Proteins (SCOP) functional assessments, and Gene Ontology, we analyzed 250 proteins within the acrosomal proteome. Our bioinformatic analysis yielded 97 proteins with high levels (>30%) of structural disorder. Further analysis of functional enrichment identified associations between disordered regions overlapping with SCOP domains and critical acrosomal processes, including vesicle trafficking, membrane fusion, and enzymatic activation. Examples of disordered SCOP domains include the PLC-like phosphodiesterase domain, the t-SNARE domain, and the P-domain of calnexin/calreticulin. Protein-protein interaction networks revealed acrosomal proteins as hubs in tightly interconnected systems, emphasizing their functional importance. LLPS propensity modeling determined that over 30% of these proteins are high-probability LLPS drivers (>60%), underscoring their role in dynamic compartmentalization. Proteins such as myristoylated alanine-rich C-kinase substrate and nuclear transition protein 2 exhibited both high LLPS propensities and high levels of structural disorder. A significant relationship (p < 0.0001, R² = 0.649) was observed between the level of intrinsic disorder and LLPS propensity, showing the role of disorder in facilitating phase separation. Overall, these findings provide insights into how intrinsic disorder and LLPS contribute to the structural adaptability and functional precision required for fertilization, with implications for understanding disorders associated with the human acrosome reaction.

Intrinsic disorder in protein interaction networks linking cancer with metabolic diseases

Complex diseases are usually driven by numerous proteins that operate as intricate network systems. Deciphering of their signals is required for more advanced level understanding of the cellular processes driven by protein interactions. Therefore, placing diseases into a framework, where they can be viewed together, represents an important and fruitful approach. The goal of this study was to assess the intrinsic disorder present in the proteins forming PPI networks linking cancer with different human diseases. To this end, we used a set of bioinformatics tools to explore intrinsic disorder and liquid-liquid phase separation predispositions of 340 proteins reported earlier by Hirsch et al. (Cancer Cell (2010) 17(4), 348-361; doi: 10.1016/j.ccr.2010.01.022) as differently expressed in common chronic diseases, such as cancer, obesity, diabetes, and cardiovascular diseases. We further examined selected proteins from this set for their interactability and intrinsic disorder-based functionality. Our analyses demonstrated that intrinsically disordered proteins and proteins with intrinsically disordered regions may act as active network promoters and operate as highly connected hubs, which further enables them to play key roles in the disease pathways. The study also indicated that differently expressed proteins involved in disease progression could be characterized by diverse degrees of intrinsic disorder and LLPS propensity. We hope that our findings in combination with the outputs of the proteomic and functional genomic analyses contain essential clues that can be used in further medical research leading to the design of better therapies.

Ebola virus nucleoprotein interaction with host protein phosphatase-1 regulates its dimerization and capsid formation

Ebola virus (EBOV) replication is regulated by the host protein phosphatases, PP1 and PP2A, which dephosphorylate the transcriptional cofactor of EBOV polymerase VP30. The PP1-targeting compound 1E7-03 induces VP30 phosphorylation and inhibits EBOV infection. Here, we investigate the broader role of PP1 in EBOV replication and transcription, including its interaction with nucleoprotein (NP). When EBOV-infected cells were continuously treated with 1E7-03, the NP E619K mutation was found and selected for further analysis. The NP E619K mutation moderately reduced the EBOV minigenome transcription, which was restored by the treatment with 1E7-03. Proteomics, immunoprecipitation, dimerization, split NanoBit, and colocalization analyses indicated that NP interacts with PP1 and that NP E619K mutations enhanced this binding. Treatment with 1E7-03 dissociated PP1-NP complex, but enhanced NP dimerization, which was more pronounced for NP E619K mutant. Mutation and deletion analyses pointed to several potential PP1-binding sites in NP that were located in the moderately disordered NP regions. When NP was co-expressed with VP24 and VP35, formation of EBOV capsids was impaired with NP E619K mutation. Treatment with 1E7-03 restored the capsid formation by the NP E619K mutant but inhibited capsids formed by WT NP. Our findings suggest that PP1 binds to NP and that this binding might regulate NP dimerization and capsid formation. Collectively, our results point to a new role for PP1 in EBOV replication, in which NP binding to PP1 may facilitate viral transcription by delaying capsid formation and EBOV replication.

Amino acid sequence-based IDR classification using ensemble machine learning and quantum neural networks

Biologically traditional methods, such as the Uversky plot, which rely on hydrophobicity and net charge, have inherent limitations in accurately distinguishing intrinsically disordered regions (IDRs) from ordered protein regions. To overcome these constraints, we propose a novel ensemble framework integrating Machine Learning (ML), Deep Neural Networks (DNN), and Quantum Neural Networks (QNN) to enhance IDR classification accuracy. Notably, this study is the first to employ QNNs for IDR classification, leveraging quantum entanglement to model intricate feature interactions. Amino acid sequences were analyzed to extract biophysical features, including charge distribution, hydrophobicity, and structural properties, which served as inputs for the predictive models. ML was utilized for independent feature learning, DNN for hierarchical interaction modeling, and QNN for capturing high-order dependencies. Our meta-model demonstrated an accuracy of 0.85, surpassing individual classifiers and highlighting the importance of buried amino acids and feature interactions between scaled hydrophobicity and large, buried, and charged residues. This study advances computational protein science by demonstrating the applicability of QNNs in bioinformatics and establishing a robust framework for IDR classification.

Prediction of interface between regions of varying degrees of order or disorderness in intrinsically disordered proteins from dihedral angles

Intrinsically disordered proteins (IDPs) are proteins that do not form uniquely defined three-dimensional (3-D) structures. Experimental research on IDPs is difficult since they go against the traditional protein structure-function paradigm. Although there are several predictors of disorder based on amino acid sequences, but very limited based on the 3-D structures of proteins. Dihedral angles have a significant role in predicting protein structure because they establish a protein's backbone, which, coupled with its side chain, establishes its overall shape. Here, we have carried out atomistic Molecular Dynamics (MD) simulations on four different proteins: one ordered protein (Monellin), two partially disordered proteins (p53-TAD and Amyloid beta (Aβ1-42) peptide), and one completely disordered protein (Histatin 5). The MD simulation trajectories for the corresponding four proteins were used to conduct dihedral angle (ϕ and ѱ) analysis. Then, the average dihedral angles for each of the residues were calculated and plotted against the residue index. We noticed steep rises or falls in the average ϕ value at certain locations in the plot. These sudden shifts in the average ϕ value reflect the interface between regions of varying degrees of order or disorderness in intrinsically disordered proteins. Using this method, the probable conformer of a protein with a higher degree of disorder can be found among the ensembles of structures sampled during the MD simulations. The results of our study offer new understandings on precisely identifying regions of various degrees of disorder in intrinsically disordered proteins.

Discovery of a Pyrazolopyridinone-Based MYC Inhibitor That Selectively Engages Intracellular c-MYC and Disrupts MYC-MAX Heterodimerization

c-MYC is an oncogenic transcription factor that plays a crucial role in the regulation of downstream targets involved in proliferation, apoptosis, differentiation, metabolism, signaling, and immune response processes whose deregulation leads to the progression of different pathologies. The development of selective and potent small-molecule inhibitors of c-MYC remains a grand challenge in chemical biology and medicine due to its undruggability, derived from extensive intrinsic disorder. In this study, we identified a novel dihydro pyrazolo pyridinone scaffold, MY05, that selectively targets c-MYC in cells and disrupts MYC-MAX interaction. MY05 engages intracellular c-MYC, modulates c-MYC thermal stability, reduces c-MYC transcriptional targets, and inhibits proliferation in cancer cells and tumor growth in mice. In summary, we identified a novel compound that directly interacts with c-MYC to disrupt the transcriptional program.

The conserved Spd-2/CEP192 domain adopts a unique protein fold to promote centrosome scaffold assembly

Centrosomes form when centrioles assemble pericentriolar material (PCM) around themselves. Spd-2/CEP192 proteins, defined by a conserved "Spd-2 domain" (SP2D) comprising two closely spaced AspM-Spd-2-Hydin (ASH) domains, play a critical role in centrosome assembly. Here, we show that the SP2D does not target Drosophila Spd-2 to centrosomes but rather promotes PCM scaffold assembly. Crystal structures of the human and honeybee SP2D reveal an unusual "extended cradle" structure mediated by a conserved interaction interface between the two ASH domains. Mutations predicted to perturb this interface, including a human mutation associated with male infertility and Mosaic Variegated Aneuploidy, disrupt PCM scaffold assembly in flies. The SP2D is monomeric in solution, but the Drosophila SP2D can form higher-order oligomers upon phosphorylation by PLK1 (Polo-like kinase 1). Crystal-packing interactions and AlphaFold predictions suggest how SP2Ds might self-assemble, and mutations associated with one such potential dimerization interface markedly perturb SP2D oligomerization in vitro and PCM scaffold assembly in vivo.

Conformational Analyses of the AHD1-UBAN Region of TNIP1 Highlight Key Amino Acids for Interaction with Ubiquitin

Tumor necrosis factor ɑ (TNFɑ)-induced protein 3 (TNFAIP3)-interacting protein 1 (TNIP1) is genetically and functionally linked to limiting auto-immune and inflammatory responses. We have shown that TNIP1 (alias A20-binding inhibitor of NF-κB 1, ABIN1), functioning as a hub location to coordinate other proteins in repressing inflammatory signaling, aligns with biophysical traits indicative of its being an intrinsically disordered protein (IDP). IDPs move through a repertoire of three-dimensional structures rather than being in one set conformation. Here we employed bioinformatic analysis and biophysical interventions via amino acid mutations to assess and alter, respectively, conformational flexibility along a crucial region of TNIP1, encompassing the ABIN homology domain 1 and ubiquitin-binding domain in ABIN proteins and NEMO (AHD1-UBAN), by purposeful replacement of key residues. In vitro secondary structure measurements were mostly in line with, but not necessarily to the same degree as, expected results from in silico assessments. Notably, changes in single amino acids outside of the ubiquitin-binding region for gain-of-order effects had consequences along the length of the AHD1-UBAN propagating to that region. This is evidenced by differences in recognition of the partner protein polyubiquitin ≥ 28 residues away, depending on the mutation site, from the previously identified key binding site. These findings serve to demonstrate the role of conformational flexibility in protein partner recognition by TNIP1, thus identifying key amino acids likely to impact the molecular dynamics involved in TNIP1 repression of inflammatory signaling at large.

Molecular genomic insights into melanoma associated proteins PRAME and BAP1

Melanoma, a globally prevalent skin cancer with over 325,000 new cases annually, necessitates a comprehensive under- standing of its molecular components. This study looks at the PRAME (cutaneous melanoma-associated antigen) and BAP1 (gene controlling gene-environment interactions) proteins. Both PRAME and BAP1 are associated with critical genomic alterations that significantly influence melanoma progression and patient outcomes. PRAME is overexpressed in various cancers, especially uveal melanoma (UM), where high levels correlate with poor prognosis and genomic instability linked to chromosome 8q12 alterations. Meanwhile, mutations in BAP1 contribute to increased genomic instability and a higher risk of metastasis in UM, highlighting its importance as a key prognostic marker in tumorigenesis. Established approaches along with features proposed in this work are used to investigate sequence conservation, polyglutamic acid presence, intrinsic disorder of proteins, polar-nonpolar residues arrangement PRAME and BAP1 conserved residues highlight their critical roles in protein function and interaction. Sequence invariance indicates the possibility of functional relevance and evolutionary conservation. PRAME has enhanced intrinsic disorder and flexibility, whereas BAP1 has changed disorder-promoting residue sequences. Polyglutamic acid strings are found in both proteins, emphasizing their modulatory involvement in protein interactions. The ratios and spatial arrangement of amino acids have a profound influence on interactions and gene dysregulation. This work contributes to a better knowledge of the two melanoma-associated proteins viz. PRAME and BAP1 by unraveling their structural and functional complexities.

IDP-EDL: enhancing intrinsically disordered protein prediction by combining protein language model and ensemble deep learning

Identification of intrinsically disordered regions (IDRs) in proteins is essential for understanding fundamental cellular processes. The IDRs can be divided into long disordered regions (LDRs) and short disordered regions (SDRs) according to their lengths. In previous studies, most computational methods ignored the differences between LDRs and SDRs, and therefore failed to capture the different patterns of LDRs and SDRs. In this study, we propose IDP-EDL, an ensemble of three predictors. The component predictors were first built based on pretrained protein language model and applied task-specific fine-tuning for short, long, and generic disordered regions. A meta predictor was then trained to integrate three task-specific predictors into the final predictor. The results of experiments show that task-specific supervised fine-tuning can capture the different features of LDRs and SDRs and IDP-EDL can achieve stable performance on datasets with different ratios of LDRs and SDRs. More importantly, IDP-EDL can reach or even surpass state-of-the-art performance than other existing predictors on independent test sets. IDP-EDL is available at https://github.com/joestarXjx/IDP-EDL.

Regulation of alternative splicing by CBF-mediated protein condensation in plant response to cold stress

Cold acclimation is critical for the survival of plants in temperate regions under low temperatures, and C-REPEAT BINDING FACTORs (CBFs) are well established as key transcriptional factors that regulate this adaptive process by controlling the expression of cold-responsive genes. Here we demonstrate that CBFs are involved in modulating alternative splicing during cold acclimation through their interaction with subunits of the spliceosome complex. Under cold stress, CBF proteins accumulate and directly interact with SKI-INTERACTING PROTEIN (SKIP), a key component of the spliceosome, which positively regulates acquired freezing tolerance. This interaction facilitates the formation of SKIP nuclear condensates, which enhances the association between SKIP and specific cold-responsive transcripts, thereby increasing their splicing efficiency. Our findings uncover a regulatory role of CBFs in alternative splicing and highlight their pivotal involvement in the full development of cold acclimation, bridging transcriptional and post-transcriptional regulatory mechanisms.

Critical functions and key interactions mediated by the RNase E scaffolding domain in Pseudomonas aeruginosa

The RNA degradosome is a bacterial multi-protein complex mediating mRNA processing and degradation. In Pseudomonadota, this complex assembles on the C-terminal domain (CTD) of RNase E through short linear motifs (SLiMs) that determine its composition and functionality. In the human pathogen Pseudomonas aeruginosa, the RNase E CTD exhibits limited similarity to that of model organisms, impeding our understanding of RNA metabolic processes in this bacterium. Our study systematically maps the interactions mediated by the P. aeruginosa RNase E CTD and highlights its critical role in transcript regulation and cellular functions. We identified the SLiMs crucial for membrane attachment, RNA binding and complex clustering, as well as for direct binding to the core components PNPase and RhlB. Transcriptome analyses of RNase E CTD mutants revealed altered expression of genes involved in quorum sensing, type III secretion, and amino acid metabolism. Additionally, we show that the mutants are impaired in cold adaptation, pH response, and virulence in an infection model. Overall, this work establishes the essential role of the RNA degradosome in driving bacterial adaptability and pathogenicity.

Covalent Destabilizing Degrader of AR and AR-V7 in Androgen-Independent Prostate Cancer Cells

Androgen-independent prostate cancers, correlated with heightened aggressiveness and poor prognosis, are caused by mutations or deletions in the androgen receptor (AR) or expression of truncated variants of AR that are constitutively activated. Currently, drugs and drug candidates against AR target the steroid-binding domain to antagonize or degrade AR. However, these compounds cannot therapeutically access largely intrinsically disordered truncated splice variants of AR, such as AR-V7, that only possess the DNA binding domain and are missing the ligand binding domain. Targeting intrinsically disordered regions within transcription factors has remained challenging and is considered "undruggable". Herein, we leveraged a cysteine-reactive covalent ligand library in a cellular screen to identify degraders of AR and AR-V7 in androgen-independent prostate cancer cells. We identified a covalent compound EN1441 that selectively degrades AR and AR-V7 in a proteasome-dependent manner through direct covalent targeting of an intrinsically disordered cysteine C125 in AR and AR-V7. EN1441 causes significant and selective destabilization of AR and AR-V7, leading to aggregation of AR/AR-V7 and subsequent proteasome-mediated degradation. Consistent with targeting both AR and AR-V7, we find that EN1441 completely inhibits total AR transcriptional activity in androgen-independent prostate cancer cells expressing both AR and AR-V7 compared to AR antagonists or degraders that only target the ligand binding domain of full-length AR, such as enzalutamide and ARV-110. Our results put forth a pathfinder molecule EN1441 that targets an intrinsically disordered cysteine within AR to destabilize, degrade, and inhibit both AR and AR-V7 in androgen-independent prostate cancer cells and highlights the utility of covalent ligand discovery approaches in directly targeting, destabilizing, inhibiting, and degrading classically undruggable transcription factor targets.

Polêto M, Verli H, Almeida VM, Marana SR, Bender A, Godoi BF, Rodrigues VL, da S. Emery F, Trossini GHG. Fragment Screening Reveals Novel Scaffolds against Sirtuin-2-Related Protein 1 from Trypanosoma brucei

Sirtuin-2 (Sir2) is a histone deacetylase recognized as an antitrypanosomal target, yet there is limited knowledge regarding their potent inhibitors. This investigation employs the fragment-based drug discovery (FBDD) framework to identify novel inhibitors against Trypanosoma brucei Sir2-related protein 1. Initially, frequent residue-ligand interactions extracted from the crystallographic structures of human Sir2 and key features of human and parasitic Sir2 active sites were utilized to curate a targeted fragment library. Screening identified ten fragment hits, which introduced nine novel substructures compared to known Sir2 inhibitors. Among these, fragment 1 was the most potent, with an IC50 value of 17.8 μM and a ligand efficiency of 0.41. Further chemical space exploration of 30 compounds from the two most promising hits confirmed fragment 1 as the most potent. This study underscores the effectiveness of FBDD in discovering chemically distinct starting points with favorable ligand efficiency against protein targets in infectious diseases.

Protein kinase D1 mitigation against etoposide induced DNA damage in prostate cancer is associated with increased α-Catenin

BACKGROUND

The E-cadherin, α- and β-Catenin interaction at the cell adherens junction plays a key role in cell adhesion; alteration in the expression and function of these genes are associated with disease progression in several solid tumors including prostate cancer. The membranous β-Catenin is dynamically linked to the cellular cytoskeleton through interaction with α-Catenin at amino acid positions threonine 120 (T120) to 151 of β-Catenin. Nuclear presence of α-Catenin modulates the sensitivity of cells to DNA damage. The objective of this study is to determine the role of α-Catenin and protein kinase D1 (PrKD1) in DNA damage response.

METHODS

Prostate cancer cells; LNCaP, LNCaP (Sh-PrKD1; silenced PrKD1), C4-2 and C4-2 PrKD1 were used for various sets of experiments to determine the role of DNA damage in PrKD1 overexpression and silencing cells. These cells were treated with compound-10 (100 nM) and Etoposide (30 µM), total cell lysates, cytosolic and nuclear fractions were prepared to observe various protein expressions. We performed single cell gel electrophoresis (COMET assay) to determine the etoposide induce DNA damage in C4-2 and C4-2 PrKD1 cells. The animal experiments were carried out to determine the tolerability of compound-10 by mice and generate preliminary data on efficacy of compound-10 in modulating the α-Catenin and PrKD1 expressions in inhibiting tumor progression.

RESULTS

PrKD1, a novel serine threonine kinase, phosphorylates β-Catenin T120. In silico analysis, confirmed that T120 phosphorylation alters β- to α-Catenin binding. Forced expression of PrKD1 in prostate cancer cells increased β- and α-Catenin protein levels associated with reduced etoposide induced DNA damage. Downregulation of α-Catenin abrogates the PrKD1 mitigation of DNA damage. The in vitro results were corroborated in vivo using mouse prostate cancer patient derived xenograft model by inhibition of PrKD1 kinase activity with compound-10, a selective PrKD inhibitor, demonstrating decreased total β- and α-Catenin protein levels, and β-Catenin T120 phosphorylation.

CONCLUSIONS

Alteration in DNA damage response pathways play major role in prostate cancer progression. The study identifies a novel mechanism of α-Catenin dependent DNA damage mitigation role for PrKD1 in prostate cancer.

Studies of Protein Phase Separation Using Leishmania Kinetoplastid Membrane Protein-11

Despite the significant understanding of phase separation in proteins with intrinsically disordered regions, a considerable percentage of proteins without such regions also undergo phase separation, presenting an intriguing area for ongoing research across all kingdoms of life. Using a combination of spectroscopic and microscopic techniques, we report here for the first time that a low temperature and low pH can trigger the liquid-liquid phase separation (LLPS) of a parasitic protein, kinetoplastid membrane protein-11 (KMP-11). Electrostatic and hydrophobic forces are found to be essential for the formation and stability of phase-separated protein assemblies. We show further that the increase in the ionic strength beyond a threshold decreases the interchain electrostatic interactions acting between the alternate charged blocks, altering the propensity for phase separation. More interestingly, the addition of cholesterol inhibits LLPS by engaging the cholesterol recognition amino acid consensus (CRAC)-like domains present in the protein. This was further confirmed using a CRAC-deleted mutant with perturbed cholesterol binding, which did not undergo LLPS.

Evolutionary and Structural Insights into the RNA Polymerase I A34 Protein Family: A Focus on Intrinsic Disorder and Phase Separation

BACKGROUND

Eukaryotic RNA polymerase I consists of 12 or 11 core subunits and three dissociable subunits, Rrn3, A34, and A49. The A34 and A49 subunits exist as a heterodimer. In silico analysis of the A34 family of transcription factors demonstrates a commonly shared domain structure despite a lack of sequence conservation, as well as N-terminal and C-terminal disordered regions. The common structure of A34 has an N-terminal disordered region followed by a dimerization domain that, in conjunction with A49, contributes to a fold that resembles the TFIIF core. This in turn is followed by a short region that cryo-EM demonstrates resembles an arm and intimately interacts with the PolR1A, PolR1B, and PolR1C subunits of Pol I.

ANALYSES

This Pol I-binding domain is then followed by a region that is not resolved in cryo-EM and is predicted to be intrinsically disordered. Interestingly, the size/length of this disordered structure increases from yeast to humans, and is composed of repeats with unique sequence and biochemical features that also increase in number. Further analyses of the A34 CTD (carboxy-terminal domain) indicate that it has a high probability of undergoing liquid-liquid phase separation.

CONCLUSIONS

We suggest that this intrinsically disordered domain found in the A34 family of Pol I transcription factors serves a function similar to the CTD of the PolR2A subunit in coordinating transcription initiation and elongation and RNA processing. Lastly, we propose that dynamic acetylation of PAF49 may regulate interactions of the intrinsically disordered CTD and thereby specify liquid-liquid phase separations. Overall, we propose a new paradigm for a repeat-containing CTD in Pol I transcription.

Rlip76 in ageing and Alzheimer's disease: Focus on oxidative stress and mitochondrial mechanisms

RLIP76 (Rlip), a stress-responsive protein, plays a multifaceted role in cellular function. This protein acts primarily as a glutathione-electrophile conjugate (GS-E) transporter, crucial for detoxifying hazardous compounds and converting them into mercapturic acids. RLIP76 also modulates cytoskeletal motility and membrane plasticity through its role in the Ral-signaling pathway, interacting with RalA and RalB, key small GTPases involved in growth and metastasis. Beyond its ATP-dependent transport functions in various tissues, RLIP76 also demonstrates GTPase Activating Protein (GAP) activity towards Rac1 and Cdc42, with a preference for Ral-GTP over Ral-GDP. Its functions span critical physiological processes including membrane dynamics, oxidative stress response, and mitochondrial dynamics. The protein's widespread expression and evolutionary conservation underscore its significance. Our lab discovered that Rlip interacts with Alzheimer's disease (AD) proteins, amyloid beta and phosphorylated and induce oxidative stress, mitochondrial dysfnction and synaptic damage in AD. Our in vitro studies revealed that overexpression of Rlip reduces mitochondrial abnormalities. Further, our in vivo studies (Rlip+/- mice) revealed that a partial reduction of Rlip in mice (Rlip+/-), leads to mitochondrial abnormalities, elevated oxidative stress, and cognitive deficits resembling late-onset AD, emphasizing the protein's crucial role in neuronal health and disease. Finally, we discuss the experimental cross-breedings of overexpression of mice Rlip TG/TG or Rlip + /- mice with Alzheimer's disease models - earlyonset 5XFAD, late-onset APPKI and Tau transgenic mice, providing new insights into RLIP76's role in AD progression and development. This review summarizes RLIP76's structure, function, and cellular pathways, highlighting its implications in AD and its potential as a therapeutic target.

Effects of the Amyotrophic Lateral Sclerosis-related Q108P Mutation on the Structural Ensemble Characteristics of CHCHD10

INTRODUCTION

The Q108P pathological variant of the mitochondrial Coiled-Coil-Helix-- Coiled-Coil-Helix Domain-Containing Protein 10 (CHCHD10) has been implicated in amyotrophic lateral sclerosis (ALS). Both the wild-type and CHCHD10Q108P proteins exhibit intrinsically disordered regions, posing challenges for structural studies with conventional experimental tools.

METHODS

This study presents the foundational characterization of the structural features of CHCHD10Q108P and compares them with those of the wild-type counterpart. We conducted multiple run molecular dynamics simulations and bioinformatics analyses.

RESULTS

Our findings reveal distinct differences in structural properties, free energy surfaces, and the outputs of principal component analysis between these two proteins. These results contribute significantly to the comprehension of CHCHD10 and its Q108P variant in terms of pathology, biochemistry, and structural biology.

CONCLUSION

The reported structural properties hold promise for informing the development of more effective treatments for ALS.

Ageing drop by drop: Disturbance of the membrane-less organelle biogenesis as an aging hallmark

Despite extensive research, the features associated with the aging phenotype are not all-inclusive and need to be updated on a regular basis to incorporate new findings. We propose to include the dysfunction of membrane-less organelle (MLO) as a new aging hallmark. Special scaffold proteins with a high degree of intrinsic disorder drive the formation of MLOs via the liquid-liquid phase separation (LLPS) process. Aberrant behavior of MLOs was shown to be associated with the pathogenesis of many neurodegenerative diseases. In this work, we challenge the aging through bidirectional bioinformatics analysis of human proteins found in Granulome consisting of 7264 protein and Ageome containing 1624 aging-related proteins. The analysis indicates the interconnectivity of MLOs and aging. Approximately 67 % of the Ageome are presented in Granulome thereby constituting the Intersectome that include 1084 proteins showing an enrichment significantly higher than for the random datasets of the same size. Furthermore, for proteins in 10 representative MLOs, we analyzed in detail molecular functions, association with the already known aging hallmarks, and the roles in MLO formation (scaffold, client, or regulator). Cumulatively, our results strengthen the hypothesis that the dysfunction of MLOs can serve as a potent new aging hallmark.

RNA-dependent RNA polymerase of predominant human norovirus forms liquid-liquid phase condensates as viral replication factories

Many viral proteins form biomolecular condensates via liquid-liquid phase separation (LLPS) to support viral replication and evade host antiviral responses, and thus, they are potential targets for designing antivirals. In the case of nonenveloped positive-sense RNA viruses, forming such condensates for viral replication is unclear and less understood. Human noroviruses (HuNoVs) are positive-sense RNA viruses that cause epidemic and sporadic gastroenteritis worldwide. Here, we show that the RNA-dependent RNA polymerase (RdRp) of pandemic GII.4 HuNoV forms distinct condensates that exhibit all the signature properties of LLPS with sustained polymerase activity and the capability of recruiting components essential for viral replication. We show that such condensates are formed in HuNoV-infected human intestinal enteroid cultures and are the sites for genome replication. Our studies demonstrate the formation of phase-separated condensates as replication factories in a positive-sense RNA virus, which plausibly is an effective mechanism to dynamically isolate RdRp replicating the genomic RNA from interfering with the ribosomal translation of the same RNA.

The strand exchange domain of tumor suppressor PALB2 is intrinsically disordered and promotes oligomerization-dependent DNA compaction

The partner and localizer of BRCA2 (PALB2) is a scaffold protein linking BRCA1 with BRCA2 and RAD51 during homologous recombination (HR). PALB2 interaction with DNA strongly enhances HR in cells, while the PALB2 DNA-binding domain (PALB2-DBD) supports DNA strand exchange in vitro. We determined that PALB2-DBD is intrinsically disordered beyond a single N-terminal α-helix. Coiled-coil mediated dimerization is stabilized by interaction between intrinsically disordered regions (IDRs) leading to a 2-fold structural compaction. Single-stranded (ss)DNA binding promotes additional structural compaction and protein tetramerization. Using confocal single-molecule FRET, we observed bimodal and oligomerization-dependent compaction of ssDNA bound to PALB2-DBD, suggesting a novel strand exchange mechanism. Bioinformatics analysis and preliminary observations indicate that PALB2 forms protein-nucleic acids condensates. Intrinsically disordered DBDs are prevalent in the human proteome. PALB2-DBD and similar IDRs may use a chaperone-like mechanism to aid formation and resolution of DNA and RNA multichain intermediates during DNA replication, repair and recombination.

Decoding the biogenesis of HIV-induced CPSF6 puncta and their fusion with the nuclear speckle

Viruses rely on host cellular machinery for replication. After entering the nucleus, the HIV genome accumulates in nuclear niches where it undergoes reverse transcription and integrates into neighboring chromatin, promoting high transcription rates and new virus progeny. Despite anti-retroviral treatment, viral genomes can persist in these nuclear niches and reactivate if treatment is interrupted, likely contributing to the formation of viral reservoirs. The post-nuclear entry dynamics of HIV remain unclear, and understanding these steps is critical for revealing how viral reservoirs are established. In this study, we elucidate the formation of HIV-induced CPSF6 puncta and the domains of CPSF6 essential for this process. We also explore the roles of nuclear speckle scaffold factors, SON and SRRM2, in the biogenesis of these puncta. Through genetic manipulation and depletion experiments, we demonstrate the key role of the intrinsically disordered region of SRRM2 in enlarging nuclear speckles in the presence of the HIV capsid. We identify the FG domain of CPSF6 as essential for both puncta formation and binding to the viral core, which serves as the scaffold for CPSF6 puncta. While the low-complexity regions (LCRs) modulate CPSF6 binding to the viral capsid, they do not contribute to puncta formation, nor do the disordered mixed charge domains (MCDs) of CPSF6. These results demonstrate how HIV evolved to hijack host nuclear factors, enabling its persistence in the host. Of note, this study provides new insights into the underlying interactions between host factors and viral components, advancing our understanding of HIV nuclear dynamics and offering potential therapeutic targets for preventing viral persistence.

Recent advances in engineering synthetic biomolecular condensates

Biomolecular condensates are intriguing entities found within living cells. These structures possess the ability to selectively concentrate specific components through phase separation, thereby playing a crucial role in the spatiotemporal regulation of a wide range of cellular processes and metabolic activities. To date, extensive studies have been dedicated to unraveling the intricate connections between molecular features, physical properties, and cellular functions of condensates. This collective effort has paved the way for deliberate engineering of tailor-made condensates with specific applications. In this review, we comprehensively examine the underpinnings governing condensate formation. Next, we summarize the material states of condensates and delve into the design of synthetic intrinsically disordered proteins with tunable phase behaviors and physical properties. Subsequently, we review the diverse biological functions demonstrated by synthetic biomolecular condensates, encompassing gene regulation, cellular behaviors, modulation of biochemical reactions, and manipulation of endogenous protein activities. Lastly, we discuss future challenges and opportunities in constructing synthetic condensates with tunable physical properties and customized cellular functions, which may shed light on the development of new types of sophisticated condensate systems with distinct functions applicable to various scenarios.

The landscape of intrinsically disordered proteins in Leishmania parasite: Implications for drug discovery

Proteins that lack three-dimensional structures are known as Intrinsically disordered proteins (IDPs). In this study, we aimed to identify intrinsically disordered proteins in the Leishmania donovani proteome using various predictors that can identify IDPs based on amino acid residues and charge hydropathy. Top identified IDPs are analyzed using STRING, PSP-Hunter, Deep Loc-2.0, and Alpha fold to understand the protein-protein interaction, phase separation, localization, and structural assessment of those proteins. From this study, we found that >50 % of Leishmania donovani proteome has proteins or regions of proteins that are intrinsically disordered with VSL2 score >0.5; most proteins interact with many other proteins with PPI enrichment p-value <1.0e-16. Few proteins, such as Protein phosphatase inhibitor, UMSBP, and Zinc knuckle, have redox-sensitive regions. Functional disorder profiles of identified IDPs showed MoRFs and predicted protein domains. HASPB, UTP11, Nucleolar protein 12, and UMSBP have a high probability of undergoing phase separation. Localization studies showed that most of these proteins are in the cytoplasm and nucleus. Our present study of identifying IDPs in Leishmania proteome yields significant information on druggable targets and can serve as a basis for further studies to identify unexplored pathways.

Survey of the Aβ-peptide structural diversity: molecular dynamics approaches

The review deals with the application of Molecular Dynamics (MD) to the structure modeling of beta-amyloids (Aβ), currently classified as intrinsically disordered proteins (IDPs). In this review, we strive to relate the main advances in this area but specifically focus on the approaches and methodology. All relevant papers on the Aβ modeling are cited in the Tables in Supplementary Data, including a concise description of the applied approaches, sorted according to the types of the studied systems: modeling of the monomeric Aβ and Aβ aggregates. Similar sections focused according to the type of modeled object are present in the review. In the final part of the review, novel methods of general IDP modeling not confined to Aβ are described.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-024-01253-y.

Perturbing TET2 condensation promotes aberrant genome-wide DNA methylation and curtails leukaemia cell growth

The ten-eleven translocation (TET) family of dioxygenases maintain stable local DNA demethylation during cell division and lineage specification. As the major catalytic product of TET enzymes, 5-hydroxymethylcytosine is selectively enriched at specific genomic regions, such as enhancers, in a tissue-dependent manner. However, the mechanisms underlying this selectivity remain unresolved. Here we unveil a low-complexity insert domain within TET2 that facilitates its biomolecular condensation with epigenetic modulators, such as UTX and MLL4. This co-condensation fosters a permissive chromatin environment for precise DNA demethylation. Disrupting low-complexity insert-mediated condensation alters the genomic binding of TET2 to cause promiscuous DNA demethylation and genome reorganization. These changes influence the expression of key genes implicated in leukaemogenesis to curtail leukaemia cell proliferation. Collectively, this study establishes the pivotal role of TET2 condensation in orchestrating precise DNA demethylation and gene transcription to support tumour cell growth.

Key genes and pathways in the molecular landscape of pancreatic ductal adenocarcinoma: A bioinformatics and machine learning study

Pancreatic ductal adenocarcinoma (PDAC) is recognized for its aggressive nature, dismal prognosis, and a notably low five-year survival rate, underscoring the critical need for early detection methods and more effective therapeutic approaches. This research rigorously investigates the molecular mechanisms underlying PDAC, with a focus on the identification of pivotal genes and pathways that may hold therapeutic relevance and prognostic value. Through the construction of a protein-protein interaction (PPI) network and the examination of differentially expressed genes (DEGs), the study uncovers key hub genes such as CDK1, KIF11, and BUB1, demonstrating their substantial role in the pathogenesis of PDAC. Notably, the dysregulation of these genes is consistent across a spectrum of cancers, positing them as potential targets for wide-ranging cancer therapeutics. This study also brings to the fore significant genes encoding intrinsically disordered proteins, in particular GPRC5A and KRT7, unveiling promising new pathways for therapeutic intervention. Advanced machine learning techniques were harnessed to classify PDAC patients with high accuracy, utilizing the key genetic markers as a dataset. The Support Vector Machine (SVM) model leveraged the hub genes to achieve a sensitivity of 91 % and a specificity of 85 %, while the RandomForest model notched a sensitivity of 91 % and specificity of 92.5 %. Crucially, when the identified genes were cross-referenced with TCGA-PAAD clinical datasets, a tangible correlation with patient survival rates was discovered, reinforcing the potential of these genes as prognostic biomarkers and their viability as targets for therapeutic intervention. This study's findings serve as a potent testament to the value of molecular analysis in enhancing the understanding of PDAC and in advancing the pursuit for more effective diagnostic and treatment strategies.

Implications of intrinsic disorder and functional proteomics in the merkel cell polyomavirus life cycle

Infection with merkel cell polyomavirus (MCPyV) is implicated in the development of merkel cell carcinoma (MCC), a rare but aggressive skin cancer. MCC has a mortality rate near 50%, and incidence has been rapidly increasing in recent decades, making development of improved treatment strategies critical to addressing its growing social burden. The parallel increasing necessity for novel research to better understand MCPyV pathogenesis has prompted numerous studies in recent years, yet the role of intrinsic disorder in MCPyV proteins remains unexplored. This study carries out computational characterization of intrinsic disorder within the MCPyV proteome and suggests mechanisms that may contribute to the oncogenicity of the virus to invade and hijack host immune systems. Our analysis finds that significant levels of intrinsic disorder are present in proteins LT, ALTO, 57kT, and VP1, and suggests that regions of sT may also contain large, disordered regions. The investigation further shows correlation of disorder propensity with the outputs for functional predictors of eukaryotic linear motifs (ELMs), molecular recognition features (MoRFs), and propensity for liquid-liquid phase separation (LLPS). Our findings indicate that MCPyV may use disorder and phase condensation to alter viral function that may accentuate or provide the basis for oncogenic activities. It is intended that this study will inform future experimental validation efforts around the phase separation capacity of MCPyV and its host protein-protein interactions. Furthermore, we hope to inform other investigators on the potential role of disorder in the MCPyV life cycle toward ultimately progressing the development of novel therapeutic agents.

Intrinsically disordered proteins and liquid-liquid phase separation in SARS-CoV-2 interactomes

This paper discusses the properties of proteins and their relations in the interactomes of the selected subsets of SARS-CoV-2 proteome-the membrane protein, nonstructural proteins, and, finally, full proteome. Protein disorder according to several measures, liquid-liquid phase separation probabilities, and protein node degrees in the interaction networks were singled out as the features of interest. Additionally, viral interactomes were combined with the interactome of human lung tissue so as to examine if the new connections in the resulting viral-host interactome are linked to protein disorder. Correlation analysis shows that there is no clear relationship between raw features of interest, whereas there is a positive correlation between the protein disorder and its neighborhood mean disorder. There are also indications that highly connected viral hubs tend to be on average more ordered than proteins with a small number of connections. This is in contrast to previous similar studies conducted on eukaryotic interactomes and possibly raises new questions in research on viral interactomes.

Unveiling the potential of Hamigeran-B from marine sponges as a probable inhibitor of Nipah virus RDRP through molecular modelling and dynamics simulation studies

The Nipah virus (NiV) is an emerging pathogenic paramyxovirus that causes severe viral infection with a high mortality rate. This study aimed to model the effectual binding of marine sponge-derived natural compounds (MSdNCs) towards RNA-directed RNA polymerase (RdRp) of NiV. Based on the functional relevance, RdRp of NiV was selected as the prospective molecular target and 3D-structure, not available in its native form, was modelled. The effectual binding of selected MSdNCs that fulfilled the pharmacokinetics properties were docked against RdRp and the binding energy (BE) of the interaction was compared with the BE of the interaction between standard antiviral compound Remdesivir and RdRp. The stability of the best-docked pose was further confirmed by molecular dynamics (MD) simulation and binding free energy calculations. The current study revealed that the hypothetical RdRp model showed ideal stereochemical features. Molecular docking, dynamic and energy calculations suggested that Hamigeran-B (1R,3aR,9bR)-7- bromo-6-hydroxy-3a,8-dimethyl-1-propan-2-yl-1,2,3,9b-tetrahydrocyclopenta[a]naphthalene-4,5-dione) is a potent binder (BE: -6.35 kcal/mol) to RdRp when compared with the BE of Remdesivir and RdRp (-4.98 kcal/mol). This study suggests that marine sponge-derived Hamigeran-B is a potential binder to NiV-RdRp and that the present in silico model provides insight for future drug discovery against NiV infections.

A tetramer of BCL11A is required for stable protein production and fetal hemoglobin silencing

Down-regulation of BCL11A protein reverses the fetal (HbF, α2γ2) to adult (HbA, α2β2) hemoglobin switch and is exploited in gene-based therapy for hemoglobin disorders. Because of reliance on ex vivo cell manipulation and marrow transplant, such therapies cannot lessen disease burden. To develop new small-molecule approaches, we investigated the state of BCL11A protein in erythroid cells. We report that tetramer formation mediated by a single zinc finger (ZnF0) is required for production of steady-state protein. Beyond its role in protein stability, the tetramer state is necessary for γ-globin gene repression, because an engineered monomer fails to engage a critical co-repressor complex. These aspects of BCL11A protein production identify tetramer formation as a vulnerability for HbF silencing and provide opportunities for drug discovery.

The kinase NEK6 positively regulates LSD1 activity and accumulation in local chromatin sub-compartments

LSD1 plays a crucial role in mammalian biology, regulated through interactions with coregulators and post-translational modifications. Here we show that the kinase NEK6 stimulates LSD1 activity in cells and observe a strong colocalization of NEK6 and LSD1 at distinct chromatin sub-compartments (CSCs). We demonstrate that LSD1 is a substrate for NEK6 phosphorylation at the N-terminal intrinsically disordered region (IDR) of LSD1, which shows phase separation behavior in vitro and in cells. The LSD1-IDR is important for LSD1 activity and functions to co-compartmentalize NEK6, histone peptides and DNA. The subsequent phosphorylation of LSD1 by NEK6 supports the concentration of LSD1 at these distinct CSCs, which is imperative for dynamic control of transcription. This suggest that phase separation is crucial for the regulatory function of LSD1 and our findings highlight the role of NEK6 in modulating LSD1 activity and phase separation, expanding our understanding of LSD1 regulation and its implications in cellular processes.

Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases

DNA methylation is an important epigenetic mechanism essential for transposon silencing and genome integrity. Across evolution, the substrates of DNA methylation have diversified between kingdoms. In plants, chromomethylase3 (CMT3) and CMT2 mediate CHG and CHH methylation, respectively. However, how these two methyltransferases diverge on substrate specificities during evolution remains unknown. Here, we reveal that CMT2 originates from a duplication of an evolutionarily ancient CMT3 in flowering plants. Lacking a key arginine residue recognizing CHG in CMT2 impairs its CHG methylation activity in most flowering plants. An engineered V1200R mutation empowers CMT2 to restore CHG and CHH methylations in Arabidopsis cmt2cmt3 mutant, testifying a loss-of-function effect for CMT2 during evolution. CMT2 has evolved a long and unstructured amino terminus critical for protein stability, especially under heat stress, and is plastic to tolerate various natural mutations. Together, this study reveals the mechanism of chromomethylase divergence for context-specific DNA methylation in plants and sheds important lights on DNA methylation evolution and function.

Structural study of the intrinsically disordered tardigrade damage suppressor protein (Dsup) and its complex with DNA

Studies of proteins, found in one of the most stress-resistant animals tardigrade Ramazzottius varieornatus, aim to reveal molecular principles of extreme tolerance to various types of stress and developing applications based on them for medicine, biotechnology, pharmacy, and space research. Tardigrade DNA/RNA-binding damage suppressor protein (Dsup) reduces DNA damage caused by reactive oxygen spices (ROS) produced upon irradiation and oxidative stresses in Dsup-expressing transgenic organisms. This work is focused on the determination of structural features of Dsup protein and Dsup-DNA complex, which refines details of protective mechanism. For the first time, intrinsically disordered nature of Dsup protein with highly flexible structure was experimentally proven and characterized by the combination of small angle X-ray scattering (SAXS) technique, circular dichroism spectroscopy, and computational methods. Low resolution models of Dsup protein and an ensemble of conformations were presented. In addition, we have shown that Dsup forms fuzzy complex with DNA.

Computational insights into intrinsically disordered regions in protein-nucleic acid complexes

We study transitions in intrinsically disordered regions (IDRs) upon complex formation, utilizing X-ray-solved structural dataset of protein-DNA and protein-RNA complexes, along with their available unbound protein forms. The identified IDRs are categorized into three classes: Disordered-to-Ordered (D-O), Disordered-to-Partial Ordered (D-PO) and Disordered-to-Disordered (D-D) after comparing them in unbound and complex forms. In the D-O class, IDRs form secondary structures like coils, helices, and strands upon binding to nucleic acids. Though a majority of these IDRs are present at the surface of the complexes, a significant number of IDRs are also observed at the interfaces and are involved in polar interactions. The hydrogen bonds made by the interface IDRs (B_IDRs) with phosphates and bases of nucleic acids are comparatively more than those formed with sugars. B_IDRs form more H-bonds with the ribose in protein-RNA than with the deoxyribose in protein-DNA. Among the B_IDRs, Arg and Lys prefer to interact with the major and minor grooves of DNA and RNA, respectively. Ser, however, prefers the minor groove in both the nucleic acids. Interestingly, we report 61 and 48 IDRs in 31 protein-DNA and 22 protein-RNA complexes, respectively, suggesting nucleic acid binding to proteins may also result in ordered-to-disordered transitions.

Chaperone BiP controls ER stress sensor Ire1 through interactions with its oligomers

The complex multistep activation cascade of Ire1 involves changes in the Ire1 conformation and oligomeric state. Ire1 activation enhances ER folding capacity, in part by overexpressing the ER Hsp70 molecular chaperone BiP; in turn, BiP provides tight negative control of Ire1 activation. This study demonstrates that BiP regulates Ire1 activation through a direct interaction with Ire1 oligomers. Particularly, we demonstrated that the binding of Ire1 luminal domain (LD) to unfolded protein substrates not only trigger conformational changes in Ire1-LD that favour the formation of Ire1-LD oligomers but also exposes BiP binding motifs, enabling the molecular chaperone BiP to directly bind to Ire1-LD in an ATP-dependent manner. These transient interactions between BiP and two short motifs in the disordered region of Ire1-LD are reminiscent of interactions between clathrin and another Hsp70, cytoplasmic Hsc70. BiP binding to substrate-bound Ire1-LD oligomers enables unfolded protein substrates and BiP to synergistically and dynamically control Ire1-LD oligomerisation, helping to return Ire1 to its deactivated state when an ER stress response is no longer required.

Intrinsic disorder and salt-dependent conformational changes of the N-terminal region of TFIP11 splicing factor

Tuftelin Interacting Protein 11 (TFIP11) was identified as a critical human spliceosome assembly regulator, interacting with multiple proteins and localising in membrane-less organelles. However, a lack of structural information on TFIP11 limits the rationalisation of its biological role. TFIP11 is predicted as an intrinsically disordered protein (IDP), and more specifically concerning its N-terminal (N-TER) region. IDPs lack a defined tertiary structure, existing as a dynamic conformational ensemble, favouring protein-protein and protein-RNA interactions. IDPs are involved in liquid-liquid phase separation (LLPS), driving the formation of subnuclear compartments. Combining disorder prediction, molecular dynamics, and spectroscopy methods, this contribution shows the first evidence TFIP11 N-TER is a polyampholytic IDP, exhibiting a structural duality with the coexistence of ordered and disordered assemblies, depending on the ionic strength. Increasing the salt concentration enhances the protein conformational flexibility, presenting a more globule-like shape, and a fuzzier unstructured arrangement that could favour LLPS and protein-RNA interaction. The most charged and hydrophilic regions are the most impacted, including the G-Patch domain essential to TFIP11 function. This study gives a better understanding of the salt-dependent conformational behaviour of the N-TER TFIP11, supporting the hypothesis of the formation of different types of protein assembly, in line with its multiple biological roles.

Transcription factor condensates, 3D clustering, and gene expression enhancement of the MET regulon

Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the functions of these TF condensates in 3-Dimentional (3D) genome organization and gene regulation remain elusive. In response to methionine (met) starvation, budding yeast TF Met4 and a few co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro. In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes is clustered in 3D in a Met4-dependent manner. A MET3pr-GFP reporter inserted near several native Met4-binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4-binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to methionine depletion.

RNA-dependent RNA polymerase of predominant human norovirus forms liquid-liquid phase condensates as viral replication factories

Many viral proteins form biomolecular condensates via liquid-liquid phase separation (LLPS) to support viral replication and evade host antiviral responses, and thus, they are potential targets for designing antivirals. In the case of non-enveloped positive-sense RNA viruses, forming such condensates for viral replication is unclear and less understood. Human noroviruses (HuNoV) are positive-sense RNA viruses that cause epidemic and sporadic gastroenteritis worldwide. Here, we show that the RNA-dependent-RNA polymerase (RdRp) of pandemic GII.4 HuNoV forms distinct condensates that exhibit all the signature properties of LLPS with sustained polymerase activity and the capability of recruiting components essential for viral replication. We show that such condensates are formed in HuNoV-infected human intestinal enteroid cultures and are the sites for genome replication. Our studies demonstrate the formation of phase separated condensates as replication factories in a positive-sense RNA virus, which plausibly is an effective mechanism to dynamically isolate RdRp replicating the genomic RNA from interfering with the ribosomal translation of the same RNA.

Reversible Disulfide Bond Cross-Links as Tunable Levers of Phase Separation in Designer Biomolecular Condensates

Biomolecular condensates (BCs) are membraneless hubs enriched with proteins and nucleic acids that have emerged as important players in many cellular functions. Uncovering the sequence determinants of proteins for phase separation is essential in understanding the biophysical and biochemical properties of BCs. Despite significant discoveries in the past decade, the role of cysteine residues in BC formation and dissolution has remained unknown. Here, to uncover the involvement of disulfide cross-links and their redox sensitivity in BCs, we designed a "stickers and spacers" model of phase-separating peptides interspersed with cysteines. Through biophysical investigations, we learned that cysteines promote liquid-liquid phase separation in oxidizing conditions and perpetuate liquid condensates through disulfide cross-links, which can be reversibly tuned with redox chemistry. By varying the composition of cysteines, subtle but distinct changes in the viscoelastic behavior of the condensates were observed. Empirically, we conclude that cysteines function neither as stickers nor spacers but as covalent nodes to lower the effective concentrations for sticker interactions and inhibit system-spanning percolation networks. Together, we unmask the possible role of cysteines in the formation of biomolecular condensates and their potential use as tunable covalent cross-linkers in developing redox-sensitive viscoelastic materials.

Regulation of the structural dynamics, aggregation, and pathogenicity of polyQ-expanded Huntingtin by osmolytes

Huntington Disease is an autosomal dominant neurodegenerative disease caused by expansion of the polymorphic trinucleotide CAG repeat of the HTT gene to code for an expanded glutamine track of the mutant Huntingtin protein (mHTT). Like other neurodegenerative diseases, symptomatic presentation of Huntington Disease is age-dependent or age-related. This age-dependent manifestation of an autosomal dominant disease trait underscores important and possibly priming role of age-related changes in cellular physiology that are conducive to disease presentation. Herein, we present studies on the effects of osmolytes on mHTT structuring and aggregation, vis-a-vis pathogenicity. We show that stabilizing polyol osmolytes, by their generic activity in promoting protein structuring and compaction, drive aggregation of the disordered mHTT protein and simultaneously inhibit their binding to and sequestration of key transcription factors for improved homeostasis and cell survival under stress. These and related observations in the literature give strong support to the notion that lower molecular weight and structurally dynamic forms of mHTT contribute importantly to disease pathogenesis. Aging is associated with important changes in the cell environment-disease protein accumulation, reduced hydration, and macromolecular crowding as examples. These changes have significant consequences on the structuring and pathogenicity of the disordered mHTT protein. A crowded and less hydrated aging cell environment is conducive to mHTT binding to and inhibition of cell regulatory protein function on the one hand, and in promoting mHTT aggregation on the other hand, to culminate in Huntington disease presentation.

Sequestration of DBR1 to stress granules promotes lariat intronic RNAs accumulation for heat-stress tolerance

Heat stress (HS) poses a significant challenge to plant survival, necessitating sophisticated molecular mechanisms to maintain cellular homeostasis. Here, we identify SICKLE (SIC) as a key modulator of HS responses in Arabidopsis (Arabidopsis thaliana). SIC is required for the sequestration of RNA DEBRANCHING ENZYME 1 (DBR1), a rate-limiting enzyme of lariat intronic RNA (lariRNA) decay, into stress granules (SGs). The sequestration of DBR1 by SIC enhances the accumulation of lariRNAs, branched circular RNAs derived from excised introns during pre-mRNA splicing, which in turn promote the transcription of their parental genes. Our findings further demonstrate that SIC-mediated DBR1 sequestration in SGs is crucial for plant HS tolerance, as deletion of the N-terminus of SIC (SIC1-244) impairs DBR1 sequestration and compromises plant response to HS. Overall, our study unveils a mechanism of transcriptional regulation in the HS response, where lariRNAs are enriched through DBR1 sequestration, ultimately promoting the transcription of heat stress tolerance genes.