Abstract Phosphatidylinositol 4-kinase alpha (PI4KA) is a lipid kinase that generates phosphatidylinositol 4-phosphate (PI4P) from phosphatidylinositol (PI) at the plasma membrane (PM). PI4P generated by PI4KA is essential for both plasma membrane identity and for PIP 2 and PIP 3 signalling driven by the PLC and PI3K family of enzymes. While the structure of PI4KA is known, the regulatory mechanisms that control its activity are undefined. Here, we discovered that PI4KA lipid kinase activity can be inhibited through tyrosine phosphorylation of the kα12 helix of the kinase domain (Y2090). This site can be phosphorylated by multiple tyrosine kinases. Structural studies using cryo-EM and HDX-MS defined the mechanism of how Y2090 phosphorylation inhibits activity, with this being driven through local conformational changes in the kα12 C-terminal helix of the PI4KA kinase domain. PI4KA activity is predominantly controlled through membrane recruitment by EFR3, with phosphorylation inhibiting the EFR3 tethered PI4KA complex. Phosphorylation of the kα12 C-terminal helix is found in multiple PI3Ks and PI4Ks, suggesting this may be an evolutionarily conserved regulatory mechanism for this family of phosphoinositide kinases. Overall, our work reveals novel molecular insight into inhibitory post-translational regulation of PI4KA.

The armadillo repeat protein ARMH3 regulates the activity and localization of the Golgi resident lipid kinase phosphatidylinositol 4 kinase IIIβ (PI4KB) and the Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 (GBF1) that activates Arf1. ARMH3 localizes to the trans-Golgi network (TGN) via the GTPase Arl5. We used hydrogen deuterium exchange mass spectrometry (HDX-MS) and AI-enabled modeling to define the interfaces of ARMH3 with its binding partners Arl5, PI4KB, and GBF1. The ARMH3-Arl5 interface was determined to consist of regions near the N and C termini of ARMH3, with Arl5 binding causing allosteric conformational changes in ARMH3 located at a shared PI4KB/GBF1 interface. ARMH3 binds to PI4KB and GBF1 at this shared competitive interface, with GBF1 binding to ARMH3 through a disordered loop we have named the ARMH3-binding region (ABR). Both GBF1 and PI4KB can form ternary complexes with ARMH3-Arl5. The ARMH3 interfaces in PI4KB and GBF1 contain phosphosites, with the phosphomimetic mutation of GBF1 blocking complex formation. These findings provide new insights into the role of ARMH3 as a master coordinator of GTPase and phosphoinositide signaling at the Golgi/TGN.

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an established technique that measures the exchange rate of amide hydrogens, with this exchange rate being a surrogate for protein conformational dynamics. Advances in instrumentation, automation, and data analysis have transformed HDX-MS into a high-throughput and highly reproducible method capable of probing complex biological systems and addressing key questions that have been challenging to study by other structural biology approaches. By enabling measurement of amide exchange rates and mapping of differential exchange between distinct conformational states, HDX-MS provides insight into both allosteric transitions and protein interaction interfaces. Recent advances in the capabilities of artificial intelligence (AI) have been rapidly adopted by structural biology, leading to an unprecedented expansion in the quantity and accessibility of structural predictions, underscoring the need for experimental methods to validate these predicted models and provide insight into both epitopes and allosteric conformational changes. This is particularly critical for non-evolutionarily driven interactions such as antibodies, nanobodies, and artificially designed proteins, where AI technologies can yield false positives. This review highlights how HDX-MS can be integrated synergistically into modern structural biology workflows (cryo-EM, X-ray crystallography, and AI-enabled modeling) and how combining these approaches can be powerful to advance our mechanistic understanding of complex biological processes.

Metastatic progression in aggressive breast cancer (BC) depends on a tightly controlled vesicular recycling network regulated by RAB11, a small guanosine triphosphate enzyme (GTPase). In a cohort of more than 1,000 patients with BC, we identified SH3BP5L as the most highly expressed guanine nucleotide exchange factor (GEF) for RAB11A. High SH3BP5L expression marked an advanced tumor stage, distant metastasis, and poor prognosis, with significant associations in human epidermal growth factor receptor 2-positive (HER2+) and triple-negative breast cancer (TNBC). Using Förster resonance energy transfer (FRET) sensors and artificial intelligence- (AI-assisted) microscopy, we showed that cargo delivery to the plasma membrane required SH3BP5L-dependent activation of RAB11A and assembly of a complex with the anterograde motor KIF5B. This trafficking governed key metastatic features of TNBC, including β1 integrin recycling and α3β1 integrin surface exposure. Inhibition of SH3BP5L or its GEF activity reduced cell spreading in zebrafish and lung metastasis in mouse models, revealing a previously unidentified driver of BC dissemination and a potential therapeutic vulnerability.

MR1 is a non-polymorphic, ubiquitously expressed, MHC class I-like antigen-presenting molecule that presents small-molecule metabolites to T cells. Studies have shown that MR1 plays a role in microbial infection, inflammation, and tumor immunity. The antigens it presents include metabolites of microbial and self-origin as well as small-molecule drugs and form stable complexes with MR1 that are displayed on the cell surface to activate T cells. However, unlike classical MHC I and II molecules, the fundamental biology of MR1 remains poorly understood, particularly the mechanisms governing antigen loading and intracellular trafficking. This knowledge gap is largely due to the lack of molecular tools available to precisely manipulate MR1 function. In this study, we describe a high-affinity (1.6 nM KD) anti-MR1 nanobody, MR1Nb1. We characterize the binding of this nanobody including affinity by ELISA and kinetics by BLI. Crucially, we map the binding epitope of MR1Nb1 on MR1 by HDX-MS, providing key insights into the mechanism through which it blocks MR1T cell activation. In functional assays MR1Nb1 effectively and specifically blocks MR1T cell activation by cells infected with M. tuberculosis or treated with M. smegmatis supernatant or the synthetic ligand deazalumazine. MR1Nb1 further stains MR1-ligand complexes on the cell surface in a flow cytometry assay. This nanobody represents a unique and versatile tool for the field, as it can be produced inexpensively and expressed intracellularly within antigen presenting cells. Hence, our study provides a powerful new molecular probe for dissecting the mechanistic underpinnings of MR1 biology and uncover its broader roles in immunity.

The SARS-CoV-2 nucleocapsid (N) protein is essential for viral RNA packaging, replication, and immune modulation. Despite its central role, the mechanistic contributions of its individual domains, the N-terminal domain (NTD), C-terminal domain (CTD), and the intrinsically flexible linker (LINK), remain poorly defined, largely due to the protein's structural complexity. In this study, we developed a panel of twelve alpaca-derived nanobodies (VHHs) targeting the NTD, CTD, and LINK regions of N. Using ELISA and biolayer interferometry, we characterized their binding affinities, and we mapped their epitopes via hydrogen-deuterium exchange-mass spectrometry (HDX-MS) and structural modeling. When expressed intracellularly, these VHHs inhibited SARS-CoV-2 infection. In vitro, they disrupted phase separation of the N protein, a critical step in viral replication. Strikingly, VHHs targeting each domain independently blocked both phase condensation and viral replication, underscoring the functional importance of all three regions. These findings establish domain-specific VHHs as versatile tools for dissecting N biology, with promising therapeutic potential.

The reasons why two multiprotein complexes – VPS34 complex I and VPS34 complex II – are activated by different Rab proteins are becoming clearer.

Bridge-like lipid transfer proteins (BLTPs) play fundamental roles in cellular lipid redistribution between organellar membranes. They comprise bridge domains spanning organelles at contact sites that allow lipids to transit through the cytosol between adjacent membranes. The assembly of BLTPs into complexes with adaptor proteins enables lipid transfer. To address the mechanisms underlying the assembly and regulation of BLTP complexes, we used cryo-EM to resolve the structure of one such BLTP, the Parkinson’s disease protein VPS13C, at near-atomic resolution. The structure identifies a lipid-transfer-nonpermissive conformation, in which the built-in C-terminal VAB adaptor module blocks the end of the lipid transfer bridge, interfering with lipid delivery. We also identify calmodulin (CaM), central to calcium signaling, as a constitutive VPS13C interactor. Calcium induces conformational changes in the VPS13C-CaM complex, suggesting calcium regulation of VPS13 function. Altogether, this structure of intact VPS13C serves as a starting point for understanding its regulation and that of other VPS13 proteins.

Next-generation antibodies include a growing number of bispecific and multispecific antibodies that are commonly used to redirect the immune system to fight cancer. Herein, we assessed the depth and breadth of epitope coverage as a proxy for functional diversity in human immune repertoires produced by two complementary in vivo platforms utilizing a common light chain, in a chicken (OmniClicTM) or rat (OmniFlic®) host species. We adopted NKp46 as a model to target antigen due to its use in emerging natural killer (NK) immune engagers that are being explored clinically as potentially safer alternatives to traditional CD3-based T cell engagers. To probe the epitope diversity of our antibody repertoires, we performed a detailed high throughput epitope binning study using surface plasmon resonance and corroborated our binning assignments with epitope mapping data deduced from hydrogen deuterium exchange mass spectrometry. Our results revealed broad epitope coverage and nuanced diversity both within and across repertoires, with few epitopes shared, suggesting that the complementary use of OmniClicTM and OmniFlic® produces more comprehensive coverage than either alone. Furthermore, our epitope binning assignments aligned with our complementarity-determining region-based sequence lineage assignments, enabling a direct comparison of sequence diversity across Clic and Flic repertoires despite their use of different scaffolds, a single functionally rearranged V(D)J scaffold versus multiple combinatorially assembled V(D)J scaffolds, respectively. The rich epitope diversity of both OmniClicTM and OmniFlic® yielded multiple candidates for functional NK activators, as determined in an antibody-dependent cellular cytotoxicity assay, demonstrating their value as building blocks in constructing optimized immune engagers.

The nonstructural protein 1 (NS1) of influenza A virus performs a broad variety of proviral activities in the infected cell, primarily mediating evasion from the host innate immune response by being the main viral interferon antagonist. However, there are several interactions whose biological relevance remains obscure, such as the ability of NS1 to bind and activate class IA phosphoinositide 3-kinases (PI3Ks). PI3Ks are highly regulated lipid kinases that act as critical nodes in multiple cell signaling networks and are also important proto-oncogenes. This activation is mediated by NS1 binding specifically to the p85β subunit. To better understand the consequences of this interaction, we developed a bimolecular fluorescence complementation (BiFC) assay to selectively track the different PI3K heterodimers and, using this system, we found that NS1 induces an isoform-specific relocation and activation of the different PI3K heterodimers. We found that clinically relevant oncogenic mutations in both catalytic and regulatory subunits of PI3K could mimic the effect caused by NS1, and partially rescue the loss of viral fitness in a recombinant virus encoding a p85β-binding deficient NS1.

The Tec kinases are a family of five paralogous mammalian genes that play crucial roles in cell growth, proliferation and differentiation, particularly in immune cells. The recruitment and activation of the Tec kinases depends on the generation of the lipid second messenger, PIP3, in the plasma membrane. However, the mechanisms by which PIP3 activates the Tec kinases are not well understood. In order to elucidate the mechanism by which all Tec kinases are regulated by PIP3, we studied an ancestral Tec kinase from the choanoflagellate Monosiga brevicollis. Here, we demonstrate that PIP3relieves autoinhibition of MbTec by displacing its PH domain from an inhibitory interaction with its kinase domain. Unexpectedly, we found that a conserved polyproline motif within MbTec promotes its activation in a kinase-intrinsic mechanism. Finally, we show that the PH domain is sufficient to restore autoinhibition in a constitutively active mutant of MbTec. Our findings reveal that PIP3 is necessary, but not sufficient for MbTec activation and that the coincident detection of multiple membrane-localized signals is required to switch MbTec on. ### Competing Interest Statement The authors have declared no competing interest. FWF Austrian Science Fund, https://ror.org/013tf3c58, P28135, P30584, P33066, P36212 Cancer Research Society, https://ror.org/00t38a349, 1052949

The Src homology 2 (SH2) domain-containing inositol polyphosphate 5-phosphatase 1 (SHIP1) is an immune cell-specific enzyme that regulates phosphatidylinositol-(3,4,5)-trisphosphate signaling at the plasma membrane following receptor activation. SHIP1 plays an important role in processes, such as directed cell migration, endocytosis, and cortical membrane oscillations. Alterations in SHIP1 expression have been shown to perturb myeloid cell chemotaxis and differentiation. In the brain, SHIP1 regulates microglial cell behaviors, which have been linked to Alzheimer's disease. Understanding the structural and functional relationships of SHIP1 is critical for developing ways to modulate SHIP1 membrane localization and lipid phosphatase activity during immune cell signaling. Recently, we discovered that the N-terminal SH2 domain of SHIP1 suppresses lipid phosphatase activity. SHIP1 autoinhibition can be relieved through interactions with receptor-derived phosphotyrosine peptides presented on membranes or in solution. Using hydrogen-deuterium exchange mass spectrometry, we identified intramolecular contacts between the N-terminal SH2 domain and the CBL1 motif of the C2 domain that limit SHIP1 membrane localization and activity. Single-molecule measurements of purified SHIP1 on supported lipid bilayers and in neutrophil-like cells support a model in which the SH2 domain blocks membrane binding of the central catalytic module. Mutations that disrupt autoinhibition enhance the membrane binding frequency and increase the catalytic efficiency of SHIP1. Although dimerization of SHIP1 enhances membrane localization and the apparent phosphatase activity, it is not required for SHIP1 autoinhibition. Overall, our results provide new insight concerning SHIP1's structural organization, membrane binding dynamics, and the mechanism of autoinhibition.

Phospholipase C gamma (PLCγ) enzymes are key components of intracellular signal transduction processes and are involved in disease development, including immune dysregulation, specific cancer types and neurodegeneration. Although recognised as important targets for intervention, validated pharmacological tools are lacking. Here, we demonstrate that inhibitory nucleotides bind directly to an allosteric site at the interface between the PLC-core and regulatory-array unique for PLCγ, underlying their specificity for the PLCγ family. This binding site overlaps with the PLCγ autoinhibitory interface, suggesting that the inhibitory impact of nucleotides involves stabilisation of autoinhibition. We have also analysed disease-linked variants of PLCγ1 and PLCγ2 to show that multiple mechanisms could underpin their gain-of-function phenotype. While the sensitivity of these variants to physiological nucleotide inhibition is reduced, we identified artificial nucleotide compounds that can inhibit such variants not only in vitro but also in cell-based assays. Therefore, our findings suggest a route for development of isozyme specific PLCγ inhibitors allowing further studies of their roles in health and disease.

Transcription factor ubiquitination is a decisive regulator of growth and development. The DET1-DDB1-DDA1 (DDD) complex associates with the Cullin-4 ubiquitin ligase (CRL4) and a second ubiquitin ligase, COP1, to control ubiquitination of transcription factors involved in neurological, metabolic, and immune cell development. Here, we report the structure of the human DDD complex, revealing a specific segment of DET1 that can recruit ubiquitin-conjugating (E2) enzymes. Structural variability analysis, mass spectrometry, and mutagenesis based on AlphaFold predictions suggest that dynamic closure of DET1, stabilized by DDA1, underlies coordinated recruitment of E2 enzymes and COP1. Biochemical assays suggest that the E2 acts as a recruitment factor to bring COP1 to DET1 for more effective substrate ubiquitination, which parallels a catalytically inactive E2 enzyme (COP10) in plant DDD complexes. This work provides a clear architecture for regulation and cooperative CRL4DET1-COP1 complex assembly, which can affect degradation of diverse targets by COP1 complexes.

Protein kinases are master regulators of myriad processes in eukaryotic cells playing critical roles in growth, metabolism, cellular differentiation, and motility. A subclass of protein kinases is regulated by their ability to be localized and activated by the phosphoinositide phosphatidylinositol (3,4,5)-trisphosphate (PIP3). This includes multiple members of the AGC and TEC family kinases, which contain PIP3 binding pleckstrin homology (PH) domains. It has been postulated that they can be activated by PIP3-mediated disruption of autoinhibitory interactions between their kinase domains and PH domains. There has been considerable controversy based on differing molecular models for how these kinases are regulated by lipid binding and post-translational modifications. This review focuses on understanding the molecular underpinnings for how the PH domains of these enzymes regulate kinase activity and what role PIP3 plays in pathway activation. A specific focus is on the integration of experimental data derived from X-ray crystallography, cryo-electron microscopy, and hydrogen deuterium exchange mass spectrometry along with recent advances in artifical intelligence enabled protein modeling. The main lipid-binding enzymes described are the AGC protein kinases 3-phosphoinositide-dependent kinase (PDK1) and Akt, and the TEC family kinase, Bruton's agammaglobulinemia tyrosine kinase (BTK).

The class I phosphoinositide 3-kinase pathway (PI3K) is a master regulator of cellular growth, and plays essential roles in controlling immune cell function, metabolism, chemotaxis and proliferation. Activation of class I PI3Ks generates the signalling lipid PIP3 that activates multiple pro-growth signalling pathways. Class I PI3Ks can be activated by multiple plasma membrane stimuli, including G-protein coupled receptors, Ras superfamily GTPases, and receptor tyrosine kinases. The dysregulation of class I PI3Ks is critical in the progression of many human diseases, including cancers, immunodeficiencies, and developmental disorders. Highlighting this is frequent oncogenic mutations (2nd most frequently mutated gene in all human cancers) in PIK3CA encoding the p110α catalytic subunit of class IA PI3K. The class I PI3Ks are obligate heterodimers composed of a catalytic and regulatory subunit, split into two subclasses, class IA and class IB. Recent elucidation of the structures of class I PI3Ks bound to activating stimuli, with activating disease-linked mutations and bound to allosteric conformational selective inhibitors/activators, has revealed extensive insight into the molecular basis of class I PI3K regulation. This review will summarize our current molecular knowledge of class I PI3K regulation, as well as how this information is being used to generate both small molecules and biologics that can either inhibit or activate kinase activity as potential therapeutic agents and biochemical tools.

Class IA phosophoinositide kinases (PI3Ks) are master regulators of growth, metabolism, and immunity. The class IA PI3Ks are a heterodimer composed of a p110 catalytic subunit and one of five possible regulatory subunits (p85α, p85β, p55γ, p55α, p50α). The regulatory subunit plays critical roles in stability, inhibition, and activation of the p110 catalytic subunit. The p110α catalytic subunit frequently contains activating mutations in human cancer, with many of these mutations altering the interaction between catalytic and regulatory subunits. It has been found that different regulatory subunits play unique roles in human disease, but it is unknown how these different subunits regulate p110α. Here, using a synergy of biochemical assays and hydrogen deuterium exchange mass spectrometry (HDX-MS) we examined how the five different regulatory subunits inhibit, activate, and interact with the p110α catalytic subunit. We find that there are no significant differences in lipid kinase activity or in membrane recruitment between the different heterodimer complexes. HDX-MS in the presence and absence of an activating phosphopeptide also showed only minor conformational differences between different regulatory subunit complexes. Overall, our work reveals that the different regulatory subunits interact with and inhibit p110α in a similar fashion at a molecular level.

Phosphatidylinositol 4 kinase IIIα (PI4KIIIα/PI4KA) is an essential lipid kinase that plays a critical role in regulating plasma membrane identity. PI4KA is primarily recruited to the plasma membrane through the targeted recruitment by the proteins, EFR3A and EFR3B, which bind to the PI4KA accessory proteins TTC7 (TTC7A/B) and FAM126 (FAM126A/B). Here we characterised how both EFR3 isoforms interact with all possible TTC7-FAM126 combinations and developed a nanobody that specifically blocked EFR3-mediated PI4KA recruitment in TTC7B containing complexes. Most EFR3-TTC7-FAM126 combinations show similar binding affinities, with the exception of EFR3A-TTC7B-FAM126A, which binds with a ∼10-fold higher affinity. Moreover, we showed that EFR3B phosphorylation markedly decreased binding to TTC7-FAM126. Using a yeast display approach, we isolated a TTC7B selective nanobody that blocked EFR3 binding. Cryo-electron microscopy and hydrogen deuterium exchange mass spectrometry showed an extended interface with both PI4KA and TTC7B that sterically blocks EFR3 binding. The nanobody caused decreased membrane recruitment both on lipid bilayers and in cells, with decreased PM production of PI4P. Collectively, these findings provide new insights into PI4KA regulation and provide a tool for manipulating PI4KA complexes, that may be valuable for therapeutic targeting.

The heterodimeric Rab3GAP complex is a guanine nucleotide exchange factor (GEF) for the Rab18 GTPase that regulates lipid droplet metabolism, ER-to-Golgi trafficking, secretion, and autophagy. Why both subunits of Rab3GAP are required for Rab18 GEF activity and the molecular basis of how Rab3GAP engages and activates its cognate substrate are unknown. Here we show that human Rab3GAP is conformationally flexible and potentially autoinhibited by the C-terminal domain of its Rab3GAP2 subunit. Our high-resolution structure of the catalytic core of Rab3GAP, determined by cryo-EM, shows that the Rab3GAP2 N-terminal domain binds Rab3GAP1 via an extensive interface. AlphaFold3 modelling analysis together with targeted mutagenesis and in vitro activity assay reveal that Rab3GAP likely engages its substrate Rab18 through an interface away from the switch and interswitch regions. Lastly, we find that three Warburg Micro Syndrome-associated missense mutations do not affect the overall architecture of Rab3GAP but instead likely interfere with substrate binding.