A disulfide constrains the ToxR periplasmic domain structure, altering its interactions with ToxS and bile-salts
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99 GENERAL AND MISCELLANEOUS↗
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Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7
The genome of Escherichia coli O157:H7 bacteriophage vB_EcoM_CBA120 encodes four distinct tailspike proteins (TSPs). The four TSPs, TSP1-4, attach to the phage baseplate forming a branched structure. We report the 1.9 Å resolution crystal structure of TSP2 (ORF211), the TSP that confers phage specificity towards E. coli O157:H7. The structure shows that the N-terminal 168 residues involved in TSPs complex assembly are disordered in the absence of partner proteins. The ensuing head domain contains only the first of two fold modules seen in other phage vB_EcoM_CBA120 TSPs. The catalytic site resides in a cleft at the interface between adjacent trimer subunits, where Asp506, Glu568, and Asp571 are located in close proximity. Replacement of Asp506 and Asp571 for alanine residues abolishes enzyme activity, thus identifying the acid/base catalytic machinery. However, activity remains intact when Asp506 and Asp571 are mutated into asparagine residues. Analysis of additional site-directed mutants in the background of the D506N:D571N mutant suggests engagement of an alternative catalytic apparatus comprising Glu568 and Tyr623. Finally, we demonstrate the catalytic role of two interacting glutamate residues of TSP1, located in a cleft between two trimer subunits, Glu456 and Glu483, underscoring the diversity of the catalytic apparatus employed by phage vB_EcoM_CBA120 TSPs.
59 BASIC BIOLOGICAL SCIENCES↗
The mutualism effector MiSSP7 of Laccaria bicolor alters the interactions between the poplar JAZ6 protein and its associated proteins
Despite the pivotal role of jasmonic acid in the outcome of plant-microorganism interactions, JA-signaling components in roots of perennial trees like western balsam poplar (Populus trichocarpa) are poorly characterized. Here we decipher the poplar-root JA-perception complex centered on PtJAZ6, a co-repressor of JA-signaling targeted by the effector protein MiSSP7 from the ectomycorrhizal basidiomycete Laccaria bicolor during symbiotic development. Through protein–protein interaction studies in yeast we determined the poplar root proteins interacting with PtJAZ6. Moreover, we assessed via yeast triple-hybrid how the mutualistic effector MiSSP7 reshapes the association between PtJAZ6 and its partner proteins. In the absence of the symbiotic effector, PtJAZ6 interacts with the transcription factors PtMYC2s and PtJAM1.1. In addition, PtJAZ6 interacts with it-self and with other Populus JAZ proteins. Finally, MiSSP7 strengthens the binding of PtJAZ6 to PtMYC2.1 and antagonizes PtJAZ6 homo-/heterodimerization. We conclude that a symbiotic effector secreted by a mutualistic fungus may promote the symbiotic interaction through altered dynamics of a JA-signaling-associated protein–protein interaction network, maintaining the repression of PtMYC2.1-regulated genes.
59 BASIC BIOLOGICAL SCIENCES↗
GRB2 dimerization mediated by SH2 domain-swapping is critical for T cell signaling and cytokine production
GRB2 is an adaptor protein required for facilitating cytoplasmic signaling complexes from a wide array of binding partners. GRB2 has been reported to exist in either a monomeric or dimeric state in crystal and solution. GRB2 dimers are formed by the exchange of protein segments between domains, otherwise known as “domain-swapping”. Swapping has been described between SH2 and C-terminal SH3 domains in the full-length structure of GRB2 (SH2/C–SH3 domain-swapped dimer), as well as between α-helixes in isolated GRB2 SH2 domains (SH2/SH2 domain-swapped dimer). Interestingly, SH2/SH2 domain-swapping has not been observed within the full-length protein, nor have the functional influences of this novel oligomeric conformation been explored. We herein generated a model of full-length GRB2 dimer with an SH2/SH2 domain-swapped conformation supported by in-line SEC–MALS–SAXS analyses. This conformation is consistent with the previously reported truncated GRB2 SH2/SH2 domain-swapped dimer but different from the previously reported, full-length SH2/C-terminal SH3 (C–SH3) domain-swapped dimer. Our model is also validated by several novel full-length GRB2 mutants that favor either a monomeric or a dimeric state through mutations within the SH2 domain that abrogate or promote SH2/SH2 domain-swapping. GRB2 knockdown and re-expression of selected monomeric and dimeric mutants in a T cell lymphoma cell line led to notable defects in clustering of the adaptor protein LAT and IL-2 release in response to TCR stimulation. These results mirrored similarly-impaired IL-2 release in GRB2-deficient cells. These studies show that a novel dimeric GRB2 conformation with domain-swapping between SH2 domains and monomer/dimer transitions are critical for GRB2 to facilitate early signaling complexes in human T cells.
59 BASIC BIOLOGICAL SCIENCES↗
AutoLabs: cognitive multi-agent systems with self-correction for autonomous chemical experimentation
The automation of chemical research through self-driving laboratories (SDLs) promises to accelerate scientific discovery, yet the reliability and granular performance of the underlying AI agents remain critical, under-examined challenges. In this work, we introduce AutoLabs, a self-correcting, multi-agent architecture designed to autonomously translate natural-language instructions into executable protocols for a high-throughput liquid handler. The system engages users in dialogue, decomposes experimental goals into discrete tasks for specialized agents, performs tool-assisted stoichiometric calculations, and iteratively self-corrects its output before generating a hardware-ready file. We present a comprehensive evaluation framework featuring five benchmark experiments of increasing complexity, from simple sample preparation to multi-plate timed syntheses. Through a systematic ablation study of 20 agent configurations, we assess the impact of reasoning capacity, architectural design (single- vs. multi-agent), tool use, and self-correction mechanisms. Our results demonstrate that agent reasoning capacity is the most critical factor for success, reducing quantitative errors in chemical amounts (nRMSE) by over 85% in complex tasks. When combined with a multi-agent architecture and iterative self-correction, AutoLabs approaches expert-authored reference procedures on the benchmark (F1-score > 0.89) on challenging multi-plate syntheses. These findings establish a clear blueprint for developing robust and trustworthy AI partners for autonomous laboratories, highlighting the synergistic effects of modular design, advanced reasoning, and self-correction to ensure both performance and reliability in high-stakes scientific applications. Code: https://github.com/pnnl/autolabs
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A
An aberrant fusion of the DNAJB1 and PRKACA genes generates a chimeric protein kinase (PKA-C DNAJB1 ) in which the J-domain of the heat shock protein 40 is fused to the catalytic α subunit of cAMP-dependent protein kinase A (PKA-C). Deceivingly, this chimeric construct appears to be fully functional, as it phosphorylates canonical substrates, forms holoenzymes, responds to cAMP activation, and recognizes the endogenous inhibitor PKI. Nonetheless, PKA-C DNAJB1 has been recognized as the primary driver of fibrolamellar hepatocellular carcinoma and is implicated in other neoplasms for which the molecular mechanisms remain elusive. Here we determined the chimera’s allosteric response to nucleotide and pseudo-substrate binding. We found that the fusion of the dynamic J-domain to PKA-C disrupts the internal allosteric network, causing dramatic attenuation of the nucleotide/PKI binding cooperativity. Our findings suggest that the reduced allosteric cooperativity exhibited by PKA-C DNAJB1 alters specific recognitions and interactions between substrates and regulatory partners contributing to dysregulation.
59 BASIC BIOLOGICAL SCIENCES↗
Staphylococcus aureus vWF-binding protein triggers a strong interaction between clumping factor A and host vWF
The Staphylococcus aureus cell wall-anchored adhesin ClfA binds to the very large blood circulating protein, von Willebrand factor (vWF) via vWF-binding protein (vWbp), a secreted protein that does not bind the cell wall covalently. Here we perform force spectroscopy studies on living bacteria to unravel the molecular mechanism of this interaction. We discover that the presence of all three binding partners leads to very high binding forces (2000 pN), largely outperforming other known ternary complexes involving adhesins. Strikingly, our experiments indicate that a direct interaction involving features of the dock, lock and latch mechanism must occur between ClfA and vWF to sustain the extreme tensile strength of the ternary complex. Our results support a previously undescribed mechanism whereby vWbp activates a direct, ultra-strong interaction between ClfA and vWF. This intriguing interaction represents a potential target for therapeutic interventions, including synthetic peptides inhibiting the ultra-strong interactions between ClfA and its ligands.
59 BASIC BIOLOGICAL SCIENCES↗
Widespread bacterial diversity within the bacteriome of fungi
Abstract Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number and diversity of examinations have increased, but current knowledge is predominantly limited to a small number of fungal taxa and bacterial partners. Here, we screened for potential bacterial associates in over 700 phylogenetically diverse fungal isolates, representing 366 genera, or a tenfold increase compared with previously examined fungal genera, including isolates from several previously unexplored phyla. Both a 16 S rDNA-based exploration of fungal isolates from four distinct culture collections spanning North America, South America and Europe, and a bioinformatic screen for bacterial-specific sequences within fungal genome sequencing projects, revealed that a surprisingly diverse array of bacterial associates are frequently found in otherwise axenic fungal cultures. We demonstrate that bacterial associations with diverse fungal hosts appear to be the rule, rather than the exception, and deserve increased consideration in microbiome studies and in examinations of microbial interactions.
59 BASIC BIOLOGICAL SCIENCES↗
Dynamic interactions at the mineral–organic matter interface
Minerals are widely assumed to protect organic matter (OM) from degradation in the environment, promoting the persistence of carbon in soil and sediments. In this Review, we describe the mechanisms and processes operating at the mineral–organic interface as they relate to OM transformation dynamics. A broad set of interactions occur, with minerals adsorbing organic compounds to their surfaces and/or acting as catalysts for organic reactions. Minerals can serve as redox partners for OM through direct electron transfer or by generating reactive oxygen species, which then oxidize OM. Finally, the compartmentalization of soil and sediment by minerals creates unique microsites that host diverse microbial communities. Acknowledgement of this multiplicity of interactions suggests that the general assumption that the mineral matrix provides a protective function for OM is overly simplistic. Future work must recognize adsorption as a condition for further reactions instead of as a final destination for organic adsorbates, and should consider the spatial and functional complexity that is characteristic of the environments where mineral–OM interactions are observed.
54 ENVIRONMENTAL SCIENCES↗
Emerging investigator series: ion diffusivities in nanoconfined interfacial water films contribute to mineral carbonation thresholds
The dynamics and reactivity of nanoconfined fluids play critical roles across a wide range of environmental and technological systems, though reaction mechanisms and kinetics are not well understood. Here, the carbonation kinetics of forsterite (Mg 2 SiO 4 ) exposed to 90 atm supercritical carbon dioxide at 35–65 °C and 85–100% relative humidity (RH) was monitored with in situ X-ray diffraction, and partner molecular dynamics simulations were used to describe the free energy landscape of Mg 2+ adsorption and diffusion on forsterite surfaces covered in water films 3–10 monolayers thick. The collective findings reveal how decreasing the water film thickness by ~1.4 monolayers, from ~0.92 to ~0.64 nm, inhibited reaction rates by up to 97%, promoted anhydrous Mg-carbonate (magnesite, MgCO 3 ) precipitation, and more than doubled the apparent activation energy of carbonation. The transport simulations suggest that four monolayers are required to enable sufficiently facile Mg 2+ diffusion, helping explain previously observed water film thickness-dependent reactivity thresholds.
54 ENVIRONMENTAL SCIENCES↗
Nanobodies against the metal binding domains of ATP7B as tools to study copper transport in the cell
Abstract Nanobodies are genetically engineered single domain antibodies derived from the unusual heavy-chain only antibodies found in llamas and camels. The small size of the nanobodies and flexible selection schemes make them uniquely versatile tools for protein biochemistry and cell biology. We have developed a panel of nanobodies against the metal binding domains of the human copper transporter ATP7B, a multidomain membrane protein with a complex regulation of enzymatic activity and intracellular localization. To enable the use of the nanobodies as tools to investigate copper transport in the cell, we characterized their binding sites and affinity by isothermal titration calorimetry and NMR. We have identified nanobodies against each of the first four metal binding domains of ATP7B, with a wide affinity range, as evidenced by dissociation constants from below 10−9 to 10−6 M. We found both the inhibitory and activating nanobodies among those tested. The diverse properties of the nanobodies make the panel useful for the structural studies of ATP7B, immunoaffinity purification of the protein, modulation of its activity in the cell, protein dynamics studies, and as mimics of copper chaperone ATOX1, the natural interaction partner of ATP7B.
Uhlemann, Eva-Maria E.↗
Characterizing electronic and atomic structures for amorphous and molecular metal oxide catalysts at functional interfaces by combining soft X-ray spectroscopy and high-energy X-ray scattering
Amorphous thin film materials and heterogenized molecular catalysts supported on electrode and other functional interfaces are widely investigated as promising catalyst formats for applications in solar and electrochemical fuels catalysis. However the amorphous character of these catalysts and the complexity of the interfacial architectures that merge charge transport properties of electrode and semiconductor supports with discrete sites for multi-step catalysis poses challenges for probing mechanisms that activate and tune sites for catalysis. This minireview discusses advances in soft X-ray spectroscopy and high-energy X-ray scattering that provide opportunities to resolve interfacial electronic and atomic structures, respectively, that are linked to catalysis. This review discusses how these techniques can be partnered with advances in nanostructured interface synthesis for combined soft X-ray spectroscopy and high-energy X-ray scattering analyses of thin film and heterogenized molecular catalysts. Further, these combined approaches enable opportunities for the characterization of both electronic and atomic structures underlying fundamental catalytic function, and that can be applied under conditions relevant to device applications.
14 SOLAR ENERGY↗
Aqueous-soluble bipyridine cobalt($\tiny{II}$/$\tiny{III}$) complexes act as direct redox mediators in photosystem I-based biophotovoltaic devices
Sustainable energy production is critical for meeting growing worldwide energy demands. Due to its stability and reduction potential, photosystem I (PSI) is attractive as the photosensitizer in biophotovoltaic devices. Herein, we characterize aqueous and organic solvent soluble synthetic bipyridine-based cobalt complexes as redox mediators for PSI-based biophotovoltaics applications. Cobalt-based complexes are not destructive to protein and have appropriate midpoint potentials for electron donation to PSI. We report on PSI stability in organic solvents commonly used in biophotovoltaics. We also show the effects of a mixed organic solvent phase on PSI reduction kinetics, slowing reduction rates approximately 8–38 fold as compared to fully aqueous systems, with implications for dye regeneration rates in PSI-based biophotovoltaics. Further, we show evidence of direct electron transfer from cobalt complexes to PSI. Finally, we report on photocurrent generation from Co mediator-PSI biophotovoltaic devices. Taken together, we discuss the development of novel Co complexes and our ability to fine-tune their characteristics via functional groups and counteranion choice to drive interaction with a biological electron acceptor on multiple levels from redox midpoints, spectral overlap, and solvent requirements, among others. This work suggests that fine-tuning of redox active species for interaction with a biological partner is possible for the creation and improvement of low cost, carbon-neutral energy production in the future.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Inelastic scattering in isotopologues of O 2 –Ar: the effects of mass, symmetry, and density of states
The two species considered here, O 2 (oxygen molecule) and Ar (argon-atom), are both abundant components of Earth's atmosphere and hence familiar collision partners in this medium. O 2 is quite reactive and extensively involved in atmospheric chemistry, including Chapman's cycle of the formation and destruction of ozone; while Ar, like N 2 , typically plays the nevertheless crucial role of inert collider. Inert species can provide stabilization to metastable encounter-complexes through the energy transfer associated with inelastic collisions. The interplay of collision frequency and energy transfer efficiency, with state lifetimes and species concentrations, contributes to the rich and varied chemistry and dynamics found in diverse environments ranging from planetary atmospheres to the interstellar and circumstellar media. The nature and density of bound and resonance states, coupled electronic states, symmetry, and nuclear spin-statistics can all play a role. Here, we systematically investigate some of those factors by looking at the O 2 –Ar system, comparing rigorous quantum-scattering calculations for the 16 O 16 O– 40 Ar, 18 O 16 O– 40 Ar, and 18 O 18 O– 40 Ar isotope combinations. A new accurate potential energy surface was constructed for this purpose holding the O 2 bond distance at its vibrationally averaged distance.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Spiers Memorial Lecture: Next generation chalcogenide-based absorbers for thin-film solar cells
Inorganic-based thin-film photovoltaics (TFPV) represents an important component of the growing low-carbon energy market and plays a vital role in the drive toward lower cost and increased penetration of solar energy. Yet, commercialized thin-film absorber technologies suffer from some non-ideal characteristics, such as toxic or non-abundant element use (e.g., CdTe and Cu(In,Ga)(S,Se) 2 , which bring into question their suitability for terawatt deployment. Numerous promising chalcogenide, halide, pnictide and oxide semiconductors are being pursued to bridge these concerns for TFPV and several promising paths have emerged, both as prospective replacements for the entrenched technologies, and to serve as partner (i.e., higher bandgap) absorbers for tandem junction devices—e.g., to be used with a lower bandgap Si bottom cell. The current perspective will primarily focus on emerging chalcogenide-based technologies and provide both an overview of absorber candidates that have been of recent interest and a deeper dive into an exemplary Cu 2 BaSnS 4 -related family. Altogether, considering the combined needs of high-performance, low-cost, and operational stability, as well as the experiences gained from existing commercialized thin-film absorber technologies, chalcogenide-based semiconductors represent a promising direction for future PV development and also serve to highlight common themes and needs among the broader TFPV materials family.
14 SOLAR ENERGY↗
Photodoping of graphene with long-lived electrons by interfacing with Janus WSSe
The performance of semiconductor optoelectronic devices depends on efficient photodoping of active materials, where optical excitation generates photocarriers. Despite more than two decades of research, efficient photodoping in graphene remains elusive due to the formation of neutral excitons with ultrashort lifetimes. Here, by interfacing graphene with a Janus WSSe monolayer, we achieve unipolar photodoping of graphene with long-lived carriers. The Janus monolayer was synthesized via selenium implantation of WS 2 monolayers grown by chemical vapor deposition. We fabricated the heterostructure by transferring a mechanically exfoliated graphene monolayer onto the Se-terminated side of WSSe. Through photoluminescence and transient absorption spectroscopy, we demonstrate that photoexcited electrons in WSSe transfer efficiently to graphene, while a portion of the photoexcited holes remains confined in WSSe due to its built-in electric field. This charge separation leads to a net electron population in graphene. These electrons exhibit extended lifetimes due to spatial separation from their recombination partners, offering a promising route to enhancing the performance of graphene-based optoelectronic devices.
Zheng, Ting [Southeast Univ., Nanjing (China); Uni↗
Exploring the roles of microbes in facilitating plant adaptation to climate change
Plants benefit from their close association with soil microbes which assist in their response to abiotic and biotic stressors. Yet much of what we know about plant stress responses is based on studies where the microbial partners were uncontrolled and unknown. Under climate change, the soil microbial community will also be sensitive to and respond to abiotic and biotic stressors. Thus, facilitating plant adaptation to climate change will require a systems-based approach that accounts for the multi-dimensional nature of plant–microbe–environment interactions. In this perspective, we highlight some of the key factors influencing plant–microbe interactions under stress as well as new tools to facilitate the controlled study of their molecular complexity, such as fabricated ecosystems and synthetic communities. When paired with genomic and biochemical methods, these tools provide researchers with more precision, reproducibility, and manipulability for exploring plant–microbe–environment interactions under a changing climate.
59 BASIC BIOLOGICAL SCIENCES↗