Proceedings of the National Academy of Sciences

Staphylococcus aureus is a species of Gram-positive bacteria that uses the accessory gene regulator (agr) quorum sensing system to regulate many aspects of cell behavior such as virulence and toxin production. Quorum sensing is activated in dense S. aureus populations by the extracellular accumulation of a signaling molecule called the autoinducing peptide (AIP). While the biosynthetic enzymes that produce AIP have been elucidated in certain subgroups of S. aureus, the mechanism of AIP secretion is unknown. Here, we show that the biosynthetic intermediate known as AgrD (1-32) thiolactone is actively exported into the surrounding environment in certain S. aureus subgroups. Using a high-throughput transposon mutagenesis screen, we identify the integral membrane transporters, AbcA and PmtCD, as being involved in the biosynthesis of certain AIPs. Subsequent genetic complementation and biochemical experiments reveal that these proteins actively transport AgrD (1-32) thiolactone out of the cell. This enables the production of AIP directly on the cell surface following the action of MroQ, an integral membrane protease demonstrated here to possess an active site facing the extracellular milieu. Furthermore, we show that media supplementation with catalytically-active MroQ nanodiscs rescues AIP production in an mroQ knockout strain. This observation suggests the possibility that some proportion of AgrD (1-32) thiolactone exported by one cell may travel to neighboring cell surfaces for further processing into the diffusive AIP molecule. Collectively, our studies shed light on a poorly understood step in the agr quorum sensing pathway with clear implications for the design of novel therapeutic strategies.

Molecular innovation and coevolution play major roles in the evolution of biological diversity, yet we have relatively few instances in which we understand the biological and molecular bases of coevolution. Rattlesnakes and other vipers have evolved resistance to their own novel venom metalloproteinase (MP) toxins through the invention and coevolution of serum-borne inhibitors (FETUAs) derived from the ancestral, non-inhibitory, serum glycoprotein Fetuin-A. However, how FETUAs acquired their function and their mechanism of action are unknown. Here, we use a combination of structure prediction, site-directed mutagenesis, functional analyses, and molecular dynamics to elucidate how the rattlesnake FETUA-3 protein evolved to inhibit three classes of venom MP toxins. We show that FETUA-3 uses a combination of structural motifs to bind multiple MPs with high-affinity and acts as a potent noncompetitive inhibitor by inserting its N-terminus into MP active sites and directly disrupting substrate cleavage. We also find strong selective constraints on key N-terminal residues that maintain FETUA-3 specificity for multiple MP targets. These results reveal that FETUA-3 evolved a unique mechanism of action distinct from other vertebrate metalloproteinase inhibitors and how a small number of FETUA proteins controls the activities of a large family of venom toxins.

In phototrophic organisms, pigment-protein membrane complexes are densely packed to form photosynthetic units (PSUs) that capture solar energy and convert it into chemical energy. Although the structures of many individual photosynthetic complexes have been resolved, how they are arranged and interact with others within photosynthetic membranes to enable efficient excitation energy transfer (EET) remains poorly understood. Here, we report cryo-electron microscopy structures of PSU supercomplex assemblies from the phototrophic a-proteobacterium Rhodovulum viride, including an RC-LH1 core associated with one or two peripheral LH2 complexes and a curved LH2 tetramer. These membrane-derived assemblies define the relative positions and orientations of neighboring photosynthetic complexes and place their pigment arrays in proximity across antenna-antenna and antenna-core interfaces. Structure-based simulations identify potential EET pathways within the PSU assemblies and reveal rapid energy transfer across both LH2-LH2 and LH2-LH1 interfaces. Collectively, these findings provide insights into the assembly and structural modularity of bacterial PSUs and elucidate how the lateral organization of membrane protein complexes facilitates efficient energy transfer. This work extends structural studies of bacterial photosynthesis from individual complexes to their native higher-order assembly, providing a framework for understanding how photosynthetic supercomplex organization shapes energy migration and for guiding the design of artificial photosynthesis.

Dense, well-ordered material states of proteins form the amyloid fibers that are a hallmark of neurodegenerative disease in the brain. Beyond forming amyloid fibers, some of these proteins can also adopt other material states termed condensates which are initially liquid-like but evolve to a soft, glassy phase. Fiber growth requires a large supply of monomers and, thus, it is often speculated that fibers emerge from within a dense condensate as it ages and its microscopic dynamics slow into a glassy state. Here, we use the well-established model system Fused in Sarcoma (FUS) to directly observe, quantify and theoretically describe fiber growth and its interplay with condensates. We report the discovery that fibers grow overwhelmingly in the dilute phase surrounding the condensates while the condensates concurrently evolve to a glassy arrested solid. The resulting protein fibers and glassy condensates are both distinct solid-like phases that coexist but do not directly interconvert. Taken together, these findings reveal that there are two competitive aging pathways in FUS condensation that are linked through phase separation kinetics.

The core antenna of the photosystem I (PSI) complex of oxygenic photosynthesis operates at near perfect quantum efficiency, making it one of the most efficient energy conversation devices in nature. The presence of low energy or red chlorophylls (chls) is nearly universal in this core antenna, and these red chls are known to extend the light harvesting capacity and control the rate of energy migration in PSI. Surprisingly, the significance of the structural position of the red chls in PSI remains unknown. In this study, we introduced mutations that generate specific red sites in the PSI core antenna, consistent with those observed in natural species. Using CryoEM, we characterized the structural changes at these red sites. Using transient absorption spectroscopy, we measured the effects of red chlorophyll at specific sites on energy transfer and trapping in PSI to identify their functional significance. While one site funneled energy to the reaction center, the other slowed equilibration in the antenna. These opposing effects indicate different functions are associated with the different red chlorophyll location, reconciling previous seemingly incompatible suggestions as to their functional role.

Aerobic microbes use oxygen as a terminal electron acceptor to establish an electrochemical gradient across their cell membranes. While this membrane potential ({triangleup}{Psi}) is essential for multiple cellular processes, it is unknown if and how it is maintained in bacteria during shifts in oxygen availability. We find that bacteria hyperpolarize in response to drops in oxygen. Focusing on Bacillus subtilis and guided by modeling, we report that hyperpolarization magnitude scales with the degree of electron acceptor deprivation. We find that potassium efflux contributes to the response. Surveying mutants, we uncover genes involved in potassium homeostasis and oxygen stress that contribute to hyperpolarization. We show that hyperpolarization scales with faster growth rates resulting from nutrient type and colony spatial heterogeneity. Finally, we demonstrate that oxygen shift increases susceptibility to antibiotics. Our results demonstrate a conserved link between {triangleup}{Psi} and oxygen stress, suggesting a common mechanism for responding to shifting oxygen availability.

Herpes simplex virus 1 (HSV-1) establishes life-long latency in peripheral neurons following neuroinvasion, yet the early determinants governing latency versus productive infection remain poorly understood. Available in vitro models bypass the physiological route of infection by directly infecting neuronal cell bodies under antiviral suppression. Here, we established a compartmented axonal infection model that recapitulates HSV-1 neuroinvasion and latency establishment without pharmacological inhibitors. Using primary superior cervical ganglion (SCG) neurons, we demonstrated that low-dose axonal infection consistently establishes latency, whereas higher axonal doses or direct somatic infection led to productive replication. Latently infected neurons exhibit accumulation of the latency-associated transcript (LAT) and can be efficiently reactivated by UV-inactivated virus or VP16 expression. Remarkably, productive infection can be induced during low-dose axonal infection by simultaneous exposure of neuronal cell bodies, but not axons, to replication-deficient virions, implicating tegument delivery in soma overrides latency establishment. Conversely, excess replication-incompetent particles in axons suppress productive outcomes and subsequent reactivations, suggesting competition for retrograde transport. Together, these findings identify axonal entry and transport as critical regulatory checkpoints in HSV-1 latency establishment and suggest that interference with retrograde trafficking may represent a strategy to limit neuroinvasion and life-long reactivations.

Accumulation of proteins such as amyloid beta (Abeta), hyperphosphorylated tau and alpha-synuclein within the brain alters neural information processing and causes neurodegeneration(1-3), but how toxic solutes are cleared from the brain remains highly controversial(4,5). Proposed exit routes include efflux across endothelial cells into the blood(6,7), and movement to the pial surface via vasomotion-induced pumping along spaces within arteriolar smooth muscle(8) or via outflow along the perivascular space of ascending venules promoted by water flux through astrocytes (the glymphatic system(9)). From the pial surface of the brain, drainage may continue to dural lymphatics, along the outer sheaths of exiting cranial nerves and across the cribriform plate(10-14). We now report the presence, in mice and humans, of 2 micron diameter conduits that remove fluorescently labelled tau and Abeta from the brain. These conduits form a spatially-organised mesh within the walls of penetrating arterioles and pial arteries, and around the surface of ascending venules and deep cerebral and pial veins. They course through the pial and arachnoid layers to span the CSF space, wrapping the brain and cranial nerves. They are formed of reticular fibroblasts, which label for VE-cadherin(15) and PDGFRalpha(16), the lymphatic markers(17) podoplanin, VEGFR3 and Prox1, and reticular fibroblast extracellular matrix components collagen I and VI(16,18-20). Parenchymal tau drains from the brain at a similar rate via arteriolar conduits and via conduits around venules, arguing against preferential removal by a glymphatic mechanism. In Alzheimer's disease model mice, Abeta is seen traversing these lymph node-like conduits. Modulation of molecular transfer via this route may accelerate or delay cognitive decline, and slowed transfer from arteriolar to pial-arachnoid conduits may initiate cerebral amyloid angiopathy.

Functional amyloid formation in Pseudomonas biofilms is coordinated by the six-gene Fap operon (fapA-fapF), which governs the production, secretion, and assembly of extracellular fibrils that reinforce the biofilm matrix. FapC, FapB, and FapE constitute the extracellular amyloid. FapC is the major fibrillar component, whereas FapB and FapE occur at lower abundance and other accessory Fap proteins regulate fibril composition, processing, and secretion. We recently determined the structure of FapC, a cross-b-solenoid major Pseudomonas extracellular fibril. The assembly mechanism and architecture of FapB, however, have remained undefined. Here, we elucidate the structural and mechanistic basis of FapB accessory amyloid, from an intrinsically disordered monomer to a cross-b-solenoid fibril. Using well-defined monomeric preparations, controlled fibrillation assays, NMR spectroscopy, cryo-EM, and structure prediction, we show that FapB efficiently self-assembles into structurally homogeneous helical fibrils. FapB fibrillation is highly sensitive to its initial oligomeric state and purity, as well as to environmental factors such as pH. Monomeric FapC does not measurably perturb the disordered conformational ensemble of FapB, whereas preformed FapB and FapC fibrils reciprocally cross-seed each other, revealing direct kinetic coupling between the two amyloid components. Finally, we present a 3.4A resolution cryo-EM structure of the FapB accessory fibril, revealing a compact cross-b-solenoid architecture closely related to that of FapC. Together, these findings establish FapB as an independently amyloidogenic, structurally defined component of the Fap system, provide structural basis for the first of accessory cross-b-solenoid fibril, and reveal a mechanistic framework for the post-secretion assembly of multicomponent extracellular functional amyloids in Pseudomonas biofilms.

Life runs on electron flow. Cells extract electrons from nutrients and transfer them through metabolism, coupling carbon use to energy conservation, biosynthesis and redox homeostasis. Yet how and even whether electron flow is organized at the system-level across metabolism remain unknown. Here we formalize the concept of the cellular electron economy: a quantitative, genome-wide, reaction-resolved representation of electron generation, transfer and disposal. This electron-centric perspective reveals a quantitative relationship governed by two distinct organizing factors: the carbon source sets the baseline and maximal rate of electron flow, whereas the capacity to dispose of electrons to terminal sinks determines where within this range the system operates. Carbon uptake can even increase as net electron flux falls. This system-level organization is shown to apply to five microorganisms with different intracellular electron routing pathways and predicts graded physiological responses to oxygen supply across carbon sources and respiratory architectures. The cellular electron economy thus links reaction-level redox chemistry to whole-cell metabolic organization and reveals how the same organizing principles govern electron flow across diverse metabolic architectures.

Extracellular matrix (ECM)-mediated cell adhesion and tension regulate development and disease through crosstalk with Receptor Tyrosine Kinases (RTKs). RTKs stimulate proliferation, survival, and metabolic reprogramming via Ras/ERK and PI3K/Akt signaling. Emerging evidence identify the biophysical and biochemical integration of integrin-mediated adhesions with RTK signaling, however, the molecular mechanisms regulating this phenotype remain poorly understood. Here, we demonstrate that ECM stiffness potentiates ligand-mediated epidermal growth factor receptor (EGFR) signaling at scales ranging from the single adaptor protein, Grb2 upward to multicellular spheroids and tissues. We show that ECM stiffness-driven RTK signaling is mediated by integrin adhesions that reshape the membrane to induce the formation of RTK signaling hotspots distributed globally across the cell membrane. A parsimonious computational model and biochemical membrane perturbations causally implicate membrane curvature and topography in tension-dependent integrin-EGFR crosstalk. The results demonstrate how the mechanical properties of the ECM direct molecular recruitment and confinement of signaling molecules to regulate growth factor-dependent RTK signaling. Given that many RTK-driven solid tumors develop a stiff stroma, the findings could explain why many therapeutic tyrosine kinase inhibitors develop clinical resistance. The findings suggest clarifying how tension regulates transmembrane receptor signaling could identify unique force-dependent molecular regulators towards which new antitumor therapies could be applied.

Enzymes are central to biological function, catalyzing the chemical transformations that sustain metabolism, signalling, molecular transport, and cellular regulation. Understanding their catalytic activity requires connecting molecular structure and conformational dynamics to measurable reaction kinetics. Classical Michaelis--Menten kinetics describes turnover through a dominant catalytic pathway approaching a single saturation limit, whereas conformational-selection, induced-fit, allosteric, and dynamic-disorder models account for additional complexity arising from conformational exchange and heterogeneous catalytic states. Experimental studies further reveal concentration-dependent changes in pathway usage, cooperative or sigmoidal responses, transitions between distinct turnover regimes, and intermittent single-molecule activity. These behaviours are typically treated within separate kinetic descriptions, leaving their mechanistic relationship within a common physical picture incompletely resolved. Here, we formulate a minimal conformational free-energy landscape with interconverting enzyme states and competing catalytic routes to examine whether these apparently distinct kinetic signatures can arise from a shared physical mechanism. In this framework, substrate availability and conformational barriers redistribute catalytic flux between slower and faster pathways, thereby altering both pathway occupancy and turnover times. Stochastic Gillespie simulations together with deterministic mean-first-passage-time analysis show that different parameter regimes generate low- and high-turnover states, concentration-dependent kinetic crossovers, burst--halt intermittency consistent with single-molecule observations, and effectively Michaelis--Menten-like or sigmoidal allosteric-like responses. The same underlying landscape can therefore produce qualitatively different kinetic behaviours depending on how conformational exchange and substrate capture partition catalytic flux. It also explains how finite substrate windows can mask underlying bimodal behaviour. These results provide a physically interpretable framework linking conformational dynamics, pathway selection, and experimentally observed enzyme kinetics.

Learning and memory require neural representations that are simultaneously robust and adaptable. How do neural systems reconcile these opposing demands of stability and flexibility? Here, we use hippocampal granule cells, which transform spatially diffuse entorhinal inputs into sparse sharply-tuned spatial representations, to address this fundamental question using emergence, stabilization, remapping, and suppression of place-fields as ideal systems to study stability-flexibility balance. Employing an unbiased population-based approach involving different strengths of plasticity in several components, we show that sharply tuned place-cell firing does not arise from a unique plasticity mechanism. We employed a population of heterogeneous, experimentally constrained biophysical models of dentate gyrus granule cells receiving cortical grid-field and contextual inputs to demonstrate that spatially restricted synaptic potentiation is insufficient to selectively route spatial information. Instead, each of the four distinct target transitions, namely reliable emergence, stabilization, remapping, and suppression of place-fields, were achievable by coordinated plasticity spanning excitatory synapses and several intrinsic ion channels. Across each of these four transitions, we identify numerous mechanistically distinct plasticity combinations that generate equivalent functional outcomes. These solutions are non-random and highly diverse, exhibiting weak dependence among individual plasticity components despite converging onto constrained functional states, through a combination of targeted amplification and global suppression of spatial firing. Our findings reveal extensive plasticity degeneracy in hippocampal spatial coding and suggest that flexible neural representations emerge not from unique plasticity rules involving one single component, but from a repertoire of alternative plasticity routes that are capable of implementing the same computation.

Biofilms are structured microbial communities whose extracellular matrix is widely regarded as a basis of their protection against antimicrobial compounds. Yet how matrix production by individual bacteria gives rise to collective architecture and antimicrobial protection remains poorly understood. Here, we systematically varied expression of the master biofilm regulator csgD in Salmonella enterica and found that increasing matrix production reorganizes biofilms from dense, isotropic packings into sparse, nematically aligned communities by altering cell-cell interactions. By combining experimentally measured biofilm architectures with reaction-diffusion modeling, we show that these structural changes produce distinct patterns of antimicrobial killing, ranging from preferential killing near the liquid-biofilm interface to more uniform killing throughout the community. Consequently, increasing matrix production unexpectedly reduces antimicrobial survival by shifting the biofilm into different transport regimes, while strain-specific physiological differences further modulate antimicrobial depletion. Rather than acting as a passive barrier, EPS therefore shapes antimicrobial susceptibility by reorganizing biofilm architecture and its transport properties. EPS thus provides a physical link between molecular regulation, collective architecture and antimicrobial survival, providing a quantitative framework for understanding how cellular matrix production generates emergent biofilm function.

Viral entry requires remodeling the host membrane with a short fusion peptide (FP) that anchors and deforms the target lipid bilayer. However, the contribution of the FP throughout the full fusion pathway remains unknown. Here, all-atom molecular dynamics simulations define the membrane- deformation mechanisms associated with two distinct insertion configurations of membrane-bound human parainfluenza virus type 3 (HPIV3) FP. Molecular simulations quantifying the linear response of curvature to the peptide are complemented with analyses of lipid organization and FP-lipid interactions to define the underlying membrane-deformation mechanisms. The surface-parallel FP configuration generates positive membrane curvature through deformation of the proximal leaflet, consistent with the classical hydrophobic insertion (wedging) mechanism. In contrast, the transmembrane FP configuration generates curvature through localized deformation of the distal leaflet, a distinct mechanism that would strongly influence later stages of fusion. Cryo-electron tomography shows that target membrane curvature at virus-host contact sites is consistent with the molecular dynamics prediction. In the absence of F-protein activation and FP insertion, the cryo-ET-determined curvature distribution shifts toward negative values, thereby isolating the role of the fusion protein in inducing early-stage curvature that enables the host and virus membranes to approach one another. Modeling key mutational changes isolates how aromatic and electrostatic interactions act together to promote curvature generation. Taken together, these findings establish FP insertion configuration as a determinant of productive membrane curvature across the full fusion pathway.

Neural response latency measures when stimulus-evoked activity becomes detectable, but it does not reveal when the brain assigns the causal contribution of that activity to events in the external world. We define this temporal adjustment as projected delay and measure it in the macaque inferotemporal cortex using optogenetic stimulation and behavior. Two rhesus macaques performed a cortical perturbation detection task in which a visual masker appeared at different times relative to stimulation. Detection was selectively impaired when the masker began 200 ms before stimulation. We then tested this timing using Perceptography, a method that optimizes image perturbations to mimic stimulation-evoked visual events. Image perturbations presented 200 ms before stimulation elicited higher false-alarm rates than perturbations presented at stimulation onset. Here, we show that stimulation-evoked visual events in inferotemporal cortex depend preferentially on visual information originating approximately 200 ms before the cortical perturbation. This projected delay exceeds typical inferotemporal response latencies and suggests temporally extended readout mechanisms relevant to causal models of visual perception and the timing of cortical visual prostheses.

Electron transfer between proteins is mediated by transient complexes that sample many binding orientations, only a subset productive. Protein electron carriers (PECs) form such complexes with diverse enzymes across central metabolism, yet no general framework predicts which PEC-enzyme pairs will function. A representative case is IspG, the iron-sulfur enzyme catalyzing the penultimate methylerythritol phosphate pathway reaction, whose [4Fe-4S] cluster must be reduced after each turnover by the Escherichia coli flavodoxin FldA. It is not known whether FldA engages the open (substrate-free) or closed (substrate-bound) conformation of IspG, or how the cofactor redox states shape their interaction. Using atomistic molecular dynamics with custom cofactor parameters, we find that FldA preferentially engages the open conformation, implying that reduction precedes substrate binding. A positively charged arginine patch anchors FldA, and a single residue, Tyr58, provides a short tunneling bridge to the cluster. Electron transfer then weakens this interface, driving the complex toward dissociation -- pointing to an intrinsic mechanism by which a PEC binds its targets transiently yet productively: conformational selection recruits the partner, and electron transfer releases it.

Cells employ dense networks of transient protein-protein interactions mediated by modular peptide-binding domains and unstructured peptidic motifs for high-fidelity information processing. How these networks physically execute computations through protein interactions governed by complex intra- and intermolecular mechanisms remains indiscernible from current, sparse and non-quantitative, maps of the human interactome. Here, we introduce a quantitative statistical mechanical modeling (QSM) approach for machine learning domain-peptide affinities with experimental-level accuracy. Leveraging a new, principled algorithm for data harmonization and a biophysically informed neural network architecture, QSM learns to predict dissociation constants directly from amino acid sequences with calibrated confidence. We use QSM to construct the first quantitative drafts of human signaling networks and study these networks across three physical scales--recognition mechanisms of modular binding domains, combinatorial logic of multi-dentate proteins, and pathways inferred from de novo inference of protein interaction networks. We find that (i) modular domains, based on their binding preferences, selectivities, and strengths, fall into a limited number of biophysical equivalence groups, (ii) those domains, along with peptidic motifs, are "syntactically" combined within proteins to yield multivalent recognition mechanisms, and (iii) the organization of cellular function can be traced back to algorithmically detectable modules induced by domain-mediated interactions. In aggregate, these analyses instantiate a tractable roadmap towards a comprehensive, mechanistic, and simulatable articulation of the systems biology of signaling.

TAMs (Tyro3, Axl, and MerTK) are receptor tyrosine kinases with primary roles in apoptotic clearance and immune suppression. In apoptosis, bridging complexes form between TAM receptors on phagocytic cells and TAM ligand bound to phosphatidylserine exposed on the surface of dying cells, but how these complexes form or why lipid is required for receptor activation is poorly understood. We present the first structures of a complete TAM receptor (Axl) and ligand (Gas6) 2:2 bridging complex with and without lipid, which suggest that the lipid functions to stabilize and promote active complexes. We also observe a stable 1:1 complex, presumed to be inactive, and provide evidence that these complexes are conversely able to form higher-order oligomers. We propose a mechanism for how lipids promote TAM receptor activation, providing a structural and biochemical basis for developing therapies that selectively target the lipid-dependent, immunosuppressive arm of TAM signaling exploited by tumors.

Many protein kinases, ubiquitous signal transducers across all kingdoms of life, are activated by phosphorylation of one or more conserved residues in their activation loops. This reaction is widely considered to be intermolecular (trans) in nature, dependent on the transient dimerization of two kinase domains. However, since the substrate, product and reaction chemistry are identical, bulk solution kinase assays cannot distinguish between intra- and inter-molecular reactions. Discriminating between these two mechanisms is crucial because they impose different requirements on the cell for acute, high-fidelity signal transduction. Using single-molecule reaction chambers fabricated from DNA origami, we show that the paradigmatic insulin receptor kinase (IRK) undergoes intramolecular (cis) autophosphorylation with kinetics indistinguishable from those in free solution. Furthermore, we demonstrate that the bacterial serine/threonine kinase protein kinase B (PknB) undergoes intramolecular autophosphorylation, allosterically stimulated by intermolecular (trans) interactions. Our findings establish that intramolecular activation loop autophosphorylation is not only possible, but likely an ancient and conserved feature of protein kinase signaling. More broadly, our work provides new tools for single-molecule enzymology.