Nuclear Transcription Factor-Y (NF-Y) is a transcription factor that binds CCAAT motifs to regulate gene expression, controlling cell proliferation, metabolism, and differentiation. NF-Y dysregulation contributes to diverse pathologies, including cancer, neurological disorders, cardiovascular disease, and tissue fibrosis. Using in silico molecular docking, we screened a library of eight million compounds to identify molecules targeting a pocket on the NF-YB/NF-YC dimer. We identified one compound, designated NFYi5, that was able to reduce the NF-Y activity. NFYi5 reduced mRNA levels of NF-Y target genes, while sparing housekeeping gene expression, and inhibiting cell proliferation. Mechanistic studies revealed that NFYi5 impaired NF-Y-DNA binding and accelerated NF-YA protein degradation, reducing its half-life from 16.5 ± 1.5 h to 8.5 ± 0.7 h. Together, these data establish NFYi5 as a small-molecule that can reduce NF-Y activity and is associated with antimitogenic properties. This proof-of-concept study demonstrates that NF-Y is pharmacologically tractable and highlights NFYi5 as a potential lead compound for therapeutic development in NF-Y-driven diseases.

Phosphorylation at serine 129 (pS129) is a dominant post-translational modification of α-synuclein (αSyn) and a widely used pathological marker in Parkinson’s disease, yet its mechanistic consequences remain debated across physiological and pathological contexts. Most studies rely on phosphomimetic substitutions such as S129D, which approximate net charge but do not reproduce the steric, geometric, or hydrogen-bonding properties of authentic phosphorylation. Here, we establish a robust bacterial coexpression platform that generates homogeneous, site-specifically phosphorylated αSyn using its native kinase, Polo-like kinase 2. Using this system, we show that authentic pS129 differs fundamentally from S129D: it induces local, NMR-detectable perturbations within the C-terminal conformational ensemble, exhibits distinct and context-dependent aggregation behavior, and elicits neuronal responses and modest, reproducible toxicity not reproduced by phosphomimetics. These data resolve inconsistencies in the literature and highlight the importance of chemically authentic post-translational modification. More broadly, this platform provides a generalizable and scalable route to chemically faithful phosphorylated proteins, enabling more accurate interrogation of post-translationally regulated protein function.

Abstract Designing redox proteins with predictable and tuneable electron transfer properties is a major goal in de novo bioenergetics. Here we show that replacing heme B with a series of structurally conservative non-natural metalloporphyrins enables broad modulation of redox potentials over 400 mV in the de novo designed monoheme m4D2 and diheme 4D2 T19D. The non-natural porphyrins bind with high affinity and do not compromise either the heme binding site or global protein structure, as evidenced by X-ray crystallography and NMR spectroscopy. We also report the native-like NMR structure of m4D2 loaded with the non-natural and symmetric iron 2,4-dimethyldeuteroporphyrin IX, confirming our modular approach to tetrahelical redox protein design. This work establishes a versatile platform for constructing tuneable electron carriers for engineered bioenergetic pathways and bioelectronic applications.

Preventing the aggregation of α-synuclein (αS) into toxic oligomers and conformers is a major therapeutic goal in conditions such as Parkinson's disease and Lewy body dementia. However, the large intracellular protein-protein interfaces within such aggregates make this a challenging target for small molecule approaches or biologics, which often lack cell permeability. Peptides occupy a suitable middle ground and are increasingly being explored as preventative treatments. We previously showed that the N-terminal lipid binding region (αS1-25) inhibits αS aggregation. Building on this, we designed a series of N- and C-terminal truncations to systematically reduce the peptide length, enabling a 56% downsizing (i.e., truncating 92% of the full-length αS protein), to identify the smallest functional unit capable of binding αS and potently blocking its aggregation and toxicity. We next introduced seven systematic i → i + 4 helix constraints to assess impact on (i) α-helicity, (ii) aggregation inhibition, (iii) serum stability, (iv) neuronal uptake, and (v) phenotypic rescue. This work maps key amphipathic features and identifies residues that are critical for αS engagement and inhibitory activity. The most effective helix-constrained peptide, αS2-12(L6), showed marked improvements across all metrics and represents a strong candidate for further therapeutic development.

Cis -nonPro peptides, a very rare feature in protein structures, are of considerable importance for two opposite reasons. On one hand, their genuine occurrences are mostly found at sites critical to biological function, from the active sites of carbohydrate enzymes to rare adjacent-residue disulfide bonds. On the other hand, a cis -nonPro can easily be misfit into weak or ambiguous electron density, which has led to a high incidence of unjustified cis -nonPro over the last decade. This paper uses the greatly expanded crystallographic data and newly stringent quality-filtering to identify the genuine occurrences and survey both individual examples and broad patterns of their functionality. The accompanying paper describes the problem of cis -nonPro over-use, including its causes, validation, and correction.We explain the procedure developed to identify genuine cis -nonPro examples with almost no false positives, including the new observation that peptides with a glycine on one side or the other need extra care to avoid mis-assignment as cis -nonPro. We then survey a sample of the varied functional roles and structural contexts of cis -nonPro, emphasizing aspects not previously covered systematically: the preferred occurrence at β-strand ends in TIM barrel structures, the concentration of occurrence in proteins that process, bind, or contain carbohydrates, and the resulting complications in defining a simple occurrence frequency.

Bongkrekic acid is a potent respiratory toxin which inhibits the mitochondrial ATP/ADP carrier protein. The polyketide synthase that biosynthesises bongkrekic acid recruits a discrete cassette of β-branching enzymes (BonF-BonI) to install two distinct β-branches: an endo-β-methyl branch in module 1, and a carboxymethyl β-branch in module 11. Both β-branches contribute to specific interactions with bongkrekic acid's biological target. However, a critical component of the β-branching cassette, the donor acyl carrier protein (ACPD), has not been identified in previous studies. Furthermore for the module 11 carboxymethyl β-branch to be retained, conversion to an endo-β-methyl branch via the enoyl-coenzyme A hydratase (ECH), BonI, must be avoided. The mechanistic basis for these divergent β-branching pathways is poorly understood, both in the bongkrekic acid biosynthetic pathway and more generally where it arises in polyketide biosynthesis. Here, we confirm the roles of BonF-BonI by reconstituting β-branching in modules 1 and 11 in vitro and uncover the previously unannotated ACPD, BonN, to complete the β-branching cassette. We further demonstrate promiscuous BonI interactions with both module 1 and 11 ACPs that confounds simple ACP selectivity arguments for carboxymethyl β-branch versus endo-β-methyl branch installation, suggesting that this is instead regulated by a complex interplay between substrate and kinetic control.

Nature has evolved diverse electron transport proteins and multiprotein assemblies essential to the generation and transduction of biological energy. However, substantially modifying or adapting these proteins for user-defined applications or to gain fundamental mechanistic insight can be hindered by their inherent complexity. De novo protein design offers an attractive route to stripping away this confounding complexity, enabling us to probe the fundamental workings of these bioenergetic proteins and systems, while providing robust, modular platforms for constructing completely artificial electron-conducting circuitry. Here, we use a set of de novo designed mono-heme and di-heme soluble and membrane proteins to delineate the contributions of electrostatic micro-environments and dielectric properties of the surrounding protein medium on the inter-heme redox cooperativity that we have previously reported. Experimentally, we find that the two heme sites in both the water-soluble and membrane constructs have broadly equivalent redox potentials in isolation, in agreement with Poisson-Boltzmann Continuum Electrostatics calculations. BioDC, a Python program for the estimation of electron transfer energetics and kinetics within multiheme cytochromes, also predicts equivalent heme sites, and reports that burial within the low dielectric environment of the membrane strengthens heme-heme electrostatic coupling. We conclude that redox cooperativity in our diheme cytochromes is largely driven by heme electrostatic coupling and confirm that this effect is greatly strengthened by burial in the membrane. These results demonstrate that while our de novo proteins present minimalist, new-to-nature constructs, they enable the dissection and microscopic examination of processes fundamental to the function of vital, yet complex, bioenergetic assemblies.

Background: Deep vein thrombosis is a major cause of morbidity and mortality globally. While its pathophysiology is complex, increasing evidence suggests a more prominent role for platelets than previously suspected. Genetic deletion of Ral GTPases, RalA and RalB, conditionally in mouse platelets (RalAB double knockout [DKO]), results in a near complete defect in P-selectin externalization upon activation, while other platelet activation responses and arterial thrombosis are preserved. Objectives: Given the critical role of P-selectin in mediating platelet-neutrophil interaction and thromboinflammation, we sought to investigate whether platelet Rals would also play critical roles in venous thrombosis, a thromboinflammatory disease, using RalAB DKO mice. Methods: Deep vein thrombosis was induced by surgical partial ligation of the caudal (inferior) vena cava for 24 hours or 48 hours before venous thrombi were assessed by histology and immunofluorescence microscopy. Results: RalAB DKO mice showed a reduction in venous thrombus formation after 24 hours and near complete ablation of venous thrombosis by 48 hours post inferior vena cava ligation. Immunofluorescence microscopy revealed that cross-sections of thrombi from wild-type mice consisted of an organized scaffolded structure of platelets surrounding leukocytes/neutrophils producing neutrophil extracellular traps (NETs) to stabilize and propagate the thrombus. This organized structure was absent in plateletspecific conditional RalAB DKO thrombi. In vitro analysis of platelet-mediated NET formation was also significantly reduced when platelets lacked RalAB or when platelets were treated with the Ral inhibitor RBC8. Conclusion: We identify platelet Rals as novel, potentially critical regulators of venous thrombus stability through their ability to regulate neutrophil NET formation via platelet P-selectin.

Artificial intelligence-based protein structure prediction methods such as AlphaFold have revolutionized structural biology. The accuracies of these predictions vary, however, and they do not take into account ligands, covalent modifications or other environmental factors. Here, we evaluate how well AlphaFold predictions can be expected to describe the structure of a protein by comparing predictions directly with experimental crystallographic maps. In many cases, AlphaFold predictions matched experimental maps remarkably closely. In other cases, even very high-confidence predictions differed from experimental maps on a global scale through distortion and domain orientation, and on a local scale in backbone and side-chain conformation. We suggest considering AlphaFold predictions as exceptionally useful hypotheses. We further suggest that it is important to consider the confidence in prediction when interpreting AlphaFold predictions and to carry out experimental structure determination to verify structural details, particularly those that involve interactions not included in the prediction.

The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) a composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.

The leinamycin family of polyketides are promising antitumor antibiotics, yet several aspects of their biosynthesis remain elusive. All leinamycin family members bear a sulfur-containing moiety which is essential for the anticancer activity exhibited by leinamycin. The key building blocks required for the incorporation of these functionalities are introduced in the final module of the polyketide synthase (PKS), which elegantly combines β-branching and thiocysteine incorporation to generate a diverse library of sulfur-based molecular scaffolds. Two acyl carrier proteins (ACPs) form a key didomain component of this module, but their amino acid sequence divergence has brought into question the common notion of functional equivalence. Here, we provide unprecedented functional evidence that these tandem ACPs play distinct roles in the final module of polyketide assembly. Using the weishanmycin biosynthetic pathway as a template, the in vitro reconstitution of key polyketide chain extension and β-branching steps in this module has revealed strict functional selectivity for a single ACP. Furthermore, we propose a cryptic transacylation step must occur prior to polyketide off-loading and cyclization. Altogether, these mechanistic investigations suggest that an atypical in-series mechanism underpins sulfur incorporation in the leinamycin family, and provides significant progress towards delineating their late-stage assembly.

The delineation of the complex biosynthesis of the potent antibiotic mupirocin, which consists of a mixture of pseudomonic acids (PAs) isolated from Pseudomonas fluorescens NCIMB 10586, presents significant challenges, and the timing and mechanisms of several key transformations remain elusive. Particularly intriguing are the steps that process the linear backbone from the initial polyketide assembly phase to generate the first cyclic intermediate PA-B. These include epoxidation as well as incorporation of the tetrahydropyran (THP) ring and fatty acid side chain required for biological activity. Herein, we show that the mini-module MmpE performs a rare online (ACP-substrate) epoxidation and is integrated ('in-cis') into the polyketide synthase via a docking domain. A linear polyketide fragment with six asymmetric centres was synthesised using a convergent approach and used to demonstrate substrate flux via an atypical KS0 and a previously unannotated ACP (MmpE_ACP). MmpE_ACP-bound synthetic substrates were critical in demonstrating successful epoxidation in vitro by the purified MmpE oxidoreductase domain. Alongside feeding studies, these results confirm the timing as well as chain length dependence of this selective epoxidation. These mechanistic studies pinpoint the location and nature of the polyketide substrate prior to the key formation of the THP ring and esterification that generate PA-B.

With over 60 % of protein–protein interfaces featuring an α-helix, the use of α-helix mimetics as inhibitors of these interactions is a prevalent therapeutic strategy. However, methods to control the conformation of mimetics, thus enabling maximum efficacy, can be restrictive. Alternatively, conformation can be controlled through the introduction of destabilizing syn -pentane interactions. This tactic, which is often adopted by Nature, is not a common feature of lead optimization owing to the significant synthetic effort required. Through assembly-line synthesis with NMR and computational analysis, we have shown that alternating syn – anti configured contiguously substituted hydrocarbons, by avoiding syn -pentane interactions, adopt well-defined conformations that present functional groups in an arrangement that mimics the α-helix. The design of a p53 mimetic that binds to Mdm2 with moderate to good affinity, demonstrates the therapeutic promise of these scaffolds.

Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are modular megaenzymes that employ unusual catalytic domains to assemble diverse bioactive natural products. One such PKS is responsible for the biosynthesis of the oximidine anticancer agents, oxime-substituted benzolactone enamides that inhibit vacuolar H+ -ATPases. Here, we describe the identification of the oximidine gene cluster in Pseudomonas baetica and the characterization of four novel oximidine variants, including a structurally simpler intermediate that retains potent anticancer activity. Using a combination of in vivo, in vitro and computational approaches, we experimentally elucidate the oximidine biosynthetic pathway and reveal an unprecedented mechanism for O-methyloxime formation. We show that this process involves a specialized monooxygenase and methyltransferase domain and provide insight into their activity, mechanism and specificity. Our findings expand the catalytic capabilities of trans-AT PKSs and identify potential strategies for the production of novel oximidine analogues.

Experimental structure determination can be accelerated with AI-based structure prediction methods such as AlphaFold. Here we present an automatic procedure requiring only sequence information and crystallographic data that uses AlphaFold predictions to produce an electron density map and a structural model. Iterating through cycles of structure prediction is a key element of our procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. We applied this procedure to X-ray data for 215 structures released by the Protein Data Bank in a recent 6-month period. In 87% of cases our procedure yielded a model with at least 50% of C α atoms matching those in the deposited models within 2Å. Predictions from our iterative template-guided prediction procedure were more accurate than those obtained without templates. We suggest a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization.

AbstractMupirocin is a clinically important antibiotic produced by a trans‐AT Type I polyketide synthase (PKS) in Pseudomonas fluorescens. The major bioactive metabolite, pseudomonic acid A (PA−A), is assembled on a tetrasubstituted tetrahydropyran (THP) core incorporating a 6‐hydroxy group proposed to be introduced by α‐hydroxylation of the thioester of the acyl carrier protein (ACP) bound polyketide chain. Herein, we describe an in vitro approach combining purified enzyme components, chemical synthesis, isotopic labelling, mass spectrometry and NMR in conjunction with in vivo studies leading to the first characterisation of the α‐hydroxylation bimodule of the mupirocin biosynthetic pathway. These studies reveal the precise timing of hydroxylation by MupA, substrate specificity and the ACP dependency of the enzyme components that comprise this α‐hydroxylation bimodule. Furthermore, using purified enzyme, it is shown that the MmpA KS0 shows relaxed substrate specificity, suggesting precise spatiotemporal control of in trans MupA recruitment in the context of the PKS. Finally, the detection of multiple intermodular MupA/ACP interactions suggests these bimodules may integrate MupA into their assembly.

Background: Patients with COVID-19 are at increased risk of thrombosis, which is associated with altered platelet function and coagulopathy, contributing to excess mortality.Objectives: To characterize the mechanism of altered platelet function in COVID-19 patients.Methods: The platelet proteome, platelet functional responses, and platelet-neutrophil aggregates were compared between patients hospitalized with COVID-19 and healthy control subjects using tandem mass tag proteomic analysis, Western blotting, and flow cytometry.Results: COVID-19 patients showed a different profile of platelet protein expression (858 altered of the 5773 quantified). Levels of COVID-19 plasma markers were enhanced in the platelets of COVID-19 patients. Gene ontology pathway analysis demonstrated that the levels of granule secretory proteins were raised, whereas those of platelet activation proteins, such as the thrombopoietin receptor and protein kinase C & alpha;, were lowered. Basally, platelets of COVID-19 patients showed enhanced phosphatidylserine exposure, with unaltered integrin & alpha;IIb & beta;3 activation and P-selectin expression. Agonist-stimulated integrin & alpha;IIb & beta;3 activation and phosphatidylserine exposure, but not P-selectin expression, were decreased in COVID-19 patients. COVID-19 patients had high levels of platelet-neutrophil aggregates, even under basal conditions, compared to controls. This association was disrupted by blocking P-selectin, demonstrating that platelet P-selectin is critical for the interaction.Conclusions: Overall, our data suggest the presence of 2 platelet populations in patients with COVID-19: one of circulating platelets with an altered proteome and reduced functional responses and another of P-selectin-expressing neutrophil-associated platelets. Platelet-driven thromboinflammation may therefore be one of the key factors enhancing the risk of thrombosis in COVID-19 patients.

Platelets, small hemostatic blood cells, are derived from megakaryocytes. Both bone marrow and lung are principal sites of thrombopoiesis although underlying mechanisms remain unclear. Outside the body, however, our ability to generate large number of functional platelets is poor. Here we show that perfusion of megakaryocytes ex vivo through the mouse lung vasculature generates substantial platelet numbers, up to 3000 per megakaryocyte. Despite their large size, megakaryocytes are able repeatedly to passage through the lung vasculature, leading to enucleation and subsequent platelet generation intravascularly. Using ex vivo lung and an in vitro microfluidic chamber we determine how oxygenation, ventilation, healthy pulmonary endothelium and the microvascular structure support thrombopoiesis. We also show a critical role for the actin regulator Tropomyosin 4 in the final steps of platelet formation in lung vasculature. This work reveals the mechanisms of thrombopoiesis in lung vasculature and informs approaches to large-scale generation of platelets.

Misfolding and aggregation of alpha-synuclein (aS) into toxic conformations is involved in numerous neurodegenerative diseases. In Parkinson's disease (PD), this occurs within dopaminergic neurons, causing cell death and disease symptoms. During aS aggregation, many protein-protein interactions (PPIs) form over broad and flat protein surfaces, limiting potential for small-molecule intervention. Peptides, however, harbor great therapeutic promise since they can selectively engage with and modulate the large surface areas involved yet are small enough to function as druggable agents if suitably structured. Here, we explore the first 25 residues of aS (aS1-25) as a template for peptide-based aS aggregation antagonists. We report that aS1-2 5 inhibits lipid-induced aS aggregation in a dose dependent manner. aS1-25 functions by binding to lipids to prevent aS binding, with both aS and peptide requiring lipid for inhibition to occur. These findings present a potential mechanistic route for the treatment or prevention of PD.