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At least 415 records · Page 23

Acetylcholinesterase: Structure, dynamics, and interactions with organophosphorus compounds

Acetylcholinesterase (AChE) is an enzyme that hydrolyzes the neurotransmitter acetylcholine (ACh), removing it from the synaptic cleft after the transmission of an electrical signal, making it an essential component of chemical neurotransmission. AChE is a serine hydrolase, containing a catalytic triad of Ser/His/Glu. AChE is a prime target for pharmaceuticals treating a variety of neurological disorders. It is also the target of synthetic organophosphorus (OP) compounds that have been used as pesticides and chemical warfare agents. OP compounds contain a potent leaving group, such as fluorine, and act by forming a covalent adduct with the catalytic serine of the AChE active site. A wealth of structural information is available for AChE, including over 300 structures, including a subset of structures in complex with drugs as well as OP compounds. This review will highlight the interactions between OP compounds and AChE from a structural and computational perspective, with a discussion of access to the active site, as well as side reactions that lead to dealkylation of the OP-catalytic serine adduct, a process known as aging. We conclude that while the majority of the conformational changes needed to accommodate the OP compounds are localized to the acyl loop in the crystal structures, molecular dynamics simulations highlight the potential for a far more dynamic enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance

Photosynthetic microorganisms rely on multiple pathways in central carbon metabolism to adapt to fluctuating light and energy availability across diel cycles. Mechanistic insight into the regulatory dynamics of this adaptation requires integrating processes spanning disparate timescales, from rapid redox-dependent post-translational modifications (PTMs) to slower changes in protein expression and metabolic pathway usage. To address this complexity beyond genome-based inference and traditional modeling, we develop a whole-cell four-dimensional (3D + time) model of the marine cyanobacterium Prochlorococcus marinus MED4 that explicitly represents the spatial organization of enzymatic and molecular processes in central carbon metabolism under light perturbation. We employ a perturbation-based research design to experimentally generate time-series, multi-omics measurements that provide molecular descriptors and cryo-ET derived 3D segmented volumes as constraints for this dynamic 4D framework. The integration of experiments and modeling across defined light regimes enables quantitative validation of system-level responses and forecasting under distinct light disturbances. We test the hypothesis that light-dependent redox PTMs regulating the structural assembly of a protein megacomplex, the “dark complex,” modulate metabolic flux at a conserved regulatory node of the Calvin–Benson cycle (CBC) in cyanobacteria. Our model shows that subcellular spatial organization buffers rapid light-induced changes in thylakoid reaction rates, which are followed by redox-PTM-mediated sequestration or release of CBC enzymes in the dark complex, ultimately impacting carbon fixation dynamics within carboxysomes. Comparison with an equivalently parameterized well-mixed stochastic model demonstrates that post-translational regulation not only buffers transcriptional noise and diffusion-driven fluctuations but also stabilizes phenotypic outcomes, underscoring the importance of spatial heterogeneity in phenotypic robustness. This ability to probe adaptive, spatiotemporally resolved mechanisms in photosynthetic machinery and central carbon metabolism addresses a critical gap in genotype-to-phenotype inference and expands modeling and design capabilities for understudied or genetically intractable autotrophs such as P. marinus MED4.

Johnson, Connah G.↗

De Novo Design of Proteins That Bind Naphthalenediimides, Powerful Photooxidants with Tunable Photophysical Properties

De novo protein design provides a framework to test our understanding of protein function and build proteins with cofactors and functions not found in nature. Here, we report the design of proteins designed to bind powerful photooxidants and the evaluation of the use of these proteins to generate diffusible small-molecule reactive species. Because excited-state dynamics are influenced by the dynamics and hydration of a photooxidant’s environment, it was important to not only design a binding site but also to evaluate its dynamic properties. Thus, we used computational design in conjunction with molecular dynamics (MD) simulations to design a protein, designated NBP (NDI Binding Protein), that held a naphthalenediimide (NDI), a powerful photooxidant, in a programmable molecular environment. Solution NMR confirmed the structure of the complex. We evaluated two NDI cofactors in this de novo protein using ultrafast pump–probe spectroscopy to evaluate light-triggered intra- and intermolecular electron transfer function. Moreover, we demonstrated the utility of this platform to activate multiple molecular probes for protein labeling.

carbonyls↗

Energy metric prediction for double insertion mutants via the RoseNet deep learning framework

Studying the structural and functional implications of protein mutations is an important task in computational biology and bioinformatics. We leverage our previously proposed RoseNet neural network architecture to predict energy metrics of proteins with double amino acid insertions or deletions (InDels). We train models on previously generated benchmark datasets containing the exhaustive double InDel mutations for three proteins, as well as an additional three proteins for which ∼145k random mutants, each with two InDels, have been generated. We expand on our previous work by evaluating three additional proteins and analyzing domain features that impact the prediction capabilities of RoseNet. These features include InDels into secondary structures and the solvent accessible surface area (SASA) scores of the residues. We uncover further evidence to support that RoseNet has a higher proficiency of generalizing to unseen residue combinations than unseen insertion positions. We also observe that RoseNet produces higher-quality predictions when inserting into a β-sheet over an α-helix. Additionally, when the insertions fall in an area of high SASA, RoseNet often displays better performance than inserting into areas of low SASA.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamic entity formed by protein and its hydration water

The interaction between protein and water plays a pivotal role in shaping the structure, dynamics, and function of biomacromolecules. A comprehensive understanding of this intricate interplay necessitates a systematic evaluation of interaction strength and its consequential impact on the dynamics of proteins and water across diverse protein systems. Despite numerous works on understanding the dynamics of water and proteins and the coupling between them, there are still unanswered questions. Here, we combine neutron scattering and isotope labeling to probe the dynamics of proteins and their hydration water in a variety of protein systems. We consider proteins of different structures and varying thermostability as well as proteins within living cells with distinct growth temperatures. Simultaneous characterization of protein and hydration water dynamics across diverse systems was achieved. Moreover, we performed water sorption isothermal measurements on three representative proteins to correlate the observed dynamics with the strength of the interaction energies governing each system. The experimental results underscore that proteins manifesting stronger attractive interactions with water display diffusionlike dynamics with higher flexibility upon hydration, concomitant with a reduced mobility in hydration water. Significantly, our findings suggest that, in fact, it is the interaction between protein and its hydration water that facilitates the transfer of mobility from water to protein, with stronger interactions correlating to greater protein flexibility and slower hydration water diffusion. Published by the American Physical Society 2024

Ye, Yongfeng (ORCID:0009000792374198)↗

Efficient analysis of small-angle scattering curves for large biomolecular assemblies using Monte Carlo methods

Structure elucidation from small-angle scattering curves of large biomolecular assemblies is notoriously challenging. This is because the simulation of high-resolution features in the structure of large macromolecular assemblies, such as de novo protein assemblies, is computationally demanding when it needs to cover a broad range of length scales. Conventional methods, such as the numerical approximation to the Debye equation or the use of spherical harmonics, do not scale well as the size of the assembly increases, which limits their application to small structures (e.g. individual proteins). This work explores the effectiveness of a Monte Carlo method to simulate and fit scattering curves for large biomolecular assemblies spanning over ranges covering atomic and molecular detail (e.g. spacing and orientation of proteins in an assembly) as well as large-scale (hundreds of nanometres) features. Owing to its speed and scalability, it can be combined with a fitting algorithm to extract structural features from experimental small-angle scattering curves in biomolecular assemblies that are otherwise intractable for interpretation. This work first demonstrates the effectiveness of the tool using experimental small-angle X-ray scattering (SAXS) data from tile-like proteins that assemble into 1D tube-like macromolecular structures. Here, the diameter distribution of tubes is extracted from SAXS fits, and this is quantitatively compared with distributions from electron microscopy. SAXS data are also obtained from 2D sheet-like protein assemblies, and the proposed method is used to quantify structural features such as the separation distance between protein building blocks and the flexing of the sheet. An open-source implementation of the methodology is provided for use in a broad range of biological systems involving multi-scale scattering analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Covalent labeling of the Arabidopsis plasma membrane H + ‐ ATPase reveals 3D conformational changes involving the C‐terminal regulatory domain

The plasma membrane proton pump is the primary energy transducing, electrogenic ion pump of the plasma membrane in plants and fungi. Compared to its fungal counterpart, the plant plasma membrane proton pump's regulatory C‐terminal domain (CTD) contains an additional regulatory segment that links multiple sensory pathways regulating plant cell length through phosphorylation and recruitment of regulatory 14‐3‐3 proteins. However, a complete structural model of a plant proton pump is lacking. Here, we performed covalent labeling with mass spectrometric analysis (CL‐MS) on the Arabidopsis pump AHA2 to identify potential interactions between the CTD and the catalytic domains. Our results suggest that autoinhibition in the plant enzyme is much more structurally complex than in the fungal enzyme.

Blackburn, Matthew R. [Department of Biochemistry ↗

Computer Vision Pipeline for Image Analysis for Freeze‐Fracture Electron Microscopy: Rosette Cellulose Synthase Complexes Case

In materials science, plant biology, agriculture, and environmental research, the automated analysis of high-magnification, complex microscopy images, such as those generated by freeze-fracture electron microscopy (FF-TEM), remains a critical challenge that limits the scalability of data interpretation. We present a deep learning computer vision pipeline for high-throughput detection and morphological characterization analysis of cellulose synthase complexes (CSCs, or rosettes) in FF-TEM images. The pipeline integrates preprocessing, detection, human-in-the-loop verification, and semantic segmentation to quantify features such as rosette diameter and inter-lobe spacing. The approach was trained and tested on a curated dataset of high-resolution FF-TEM micrographs of Physcomitrium patens, expanded via strategic tiling and augmentation to over 650 images. We compare YOLOv8 and YOLOv9 architectures and demonstrate that YOLOv9 achieves superior performance in both localization accuracy (mAP50-95 = 0.854) and inference speed. The resulting distributions revealed biological variability consistent with prior manual studies, validating the approach for high-throughput applications. Our results show that the pipeline achieves human-expert level accuracy while dramatically reducing analysis time, enabling scalable, reproducible structural characterization of intramembrane protein complexes. The pipeline is broadly applicable to other domains requiring precise interpretation of complex microscopy data and establishes a foundation for future artificial intelligence (AI)-assisted workflows in biological imaging.

59 BASIC BIOLOGICAL SCIENCES↗

Crystallography Reveals Metal‐Triggered Restructuring of β‐Hairpins

Abstract Metal binding to β‐sheets occurs in many metalloproteins and is also implicated in the pathology of Alzheimer's disease. De novo designed metallo‐β‐sheets have been pursued as models and mimics of these proteins. However, no crystal structures of canonical β‐sheet metallopeptides have yet been obtained, in stark contrast to many examples for ɑ‐helical metallopeptides, leading to a poor understanding for their chemistry. To address this, we have engineered tryptophan zippers, stable 12‐residue β‐sheet peptides, to bind Cu(II) ions and obtained crystal structures through single crystal X‐ray diffraction (SC‐XRD). We find that metal binding triggers several unexpected supramolecular assemblies that demonstrate the range of higher‐order structures available to metallo‐β‐sheets. Overall, these findings underscore the importance of crystallography in elucidating the rich structural landscape of metallo‐β‐sheet peptides.

Thuc Dang, Viet↗

Understanding the stability of a plastic‐degrading Rieske iron oxidoreductase system

Abstract Rieske oxygenases (ROs) are a diverse metalloenzyme class with growing potential in bioconversion and synthetic applications. We postulated that ROs are nonetheless underutilized because they are unstable. Terephthalate dioxygenase (TPA DO PDB ID 7Q05 ) is a structurally characterized heterohexameric α 3 β 3 RO that, with its cognate reductase (TPA RED ), catalyzes the first intracellular step of bacterial polyethylene terephthalate plastic bioconversion. Here, we showed that the heterologously expressed TPA DO /TPA RED system exhibits only ~300 total turnovers at its optimal pH and temperature. We investigated the thermal stability of the system and the unfolding pathway of TPA DO through a combination of biochemical and biophysical approaches. The system's activity is thermally limited by a melting temperature ( T m ) of 39.9°C for the monomeric TPA RED , while the independent T m of TPA DO is 50.8°C. Differential scanning calorimetry revealed a two‐step thermal decomposition pathway for TPA DO with T m values of 47.6 and 58.0°C (Δ H = 210 and 509 kcal mol −1 , respectively) for each step. Temperature‐dependent small‐angle x‐ray scattering and dynamic light scattering both detected heat‐induced dissociation of TPA DO subunits at 53.8°C, followed by higher‐temperature loss of tertiary structure that coincided with protein aggregation. The computed enthalpies of dissociation for the monomer interfaces were most congruent with a decomposition pathway initiated by β‐β interface dissociation, a pattern predicted to be widespread in ROs. As a strategy for enhancing TPA DO stability, we propose prioritizing the re‐engineering of the β subunit interfaces, with subsequent targeted improvements of the subunits.

59 BASIC BIOLOGICAL SCIENCES↗

Selective Adsorption of Thiol-Containing Molecules on Copper Sulfide Surfaces via Molecule–Surface Disulfide Bridges

Recent results in the fields of nanoenhanced agriculture and expanding interest in prebiotic chemistry have placed increased emphasis on understanding the chemically selective interaction of small molecules with the surfaces of metal sulfides. Here, we present an integrated experimental and computational study of the interaction of thiol-containing molecules with copper sulfide (covellite) surfaces in aqueous media. In situ Fourier-transform infrared (FTIR) measurements and ex situ X-ray photoelectron spectroscopy (XPS) measurements show that molecules bearing free thiol groups, including glutathione and cysteine, bind strongly to CuS (covellite) nanoparticles and to CuS (001) single crystals, while control studies show that similar molecules lacking the free thiol group exhibit much less binding. Additional experiments show that these thiol-containing molecules interact transiently with CuO nanoparticle surfaces but are readily removed by rinsing. The FTIR and XPS experiments demonstrate that adsorption of molecular thiols to CuS surfaces occurs in a chemically selective manner. Further experimental studies and density functional calculations show that the preferred mode of binding is through the surface S atoms, forming a Solid–S–S–Molecule disulfide linkage. While the role of disulfide linkages in controlling structure and function of proteins and other biomolecules is widely known, the formation of surface disulfide linkages as a motif for covalent molecular binding at surfaces has not been established previously.

36 MATERIALS SCIENCE↗

Motion of Molecules in Supramolecular Scaffolds Enhances Bone Regeneration

The regeneration of human tissues is a great scientific challenge and a critical factor to achieve a long healthspan and prevent disabilities due to injury or disease. Materials chemistry can contribute to this goal with the development of bioactive supramolecular systems that can signal cells for regeneration. Recent work in our laboratory using in vivo models of spinal cord injury and cartilage regeneration has demonstrated that the motion of bioactive molecules in supramolecular scaffolds enhances receptor signaling. We report here on a novel molecular strategy to control supramolecular motion in filamentous assemblies using bone regeneration as a functional target. The supramolecular assemblies are composed of monomers that arrange, by design, with either parallel or antiparallel β-sheets, and some of them contain a terminal peptide sequence that binds BMP-2. We found that parallel β-sheet supramolecular assemblies promote greater osteogenic differentiation of progenitor cells in vitro relative to antiparallel assemblies, as well as superior quality of newly regenerated bone in a rat model of spinal fusion. Furthermore, these assemblies drastically reduce the dangerous supraphysiological dose of BMP-2 used clinically for spinal fusion. Here, we attribute the enhanced bioactivity to the weaker nature of hydrogen bonds in parallel relative to antiparallel β-sheet assemblies, which in turn allows greater supramolecular motion and cell signaling of the growth factor-binding molecules.

Anatomy↗

Mesoporous peptide frameworks engineered from crystallizable collagen-mimetic peptide amphiphiles

The rational design of porous frameworks with tunable pore dimensions and chemical functionalities is a critical step toward their implementation in diverse applications. While traditional porous materials are typically constructed from abiotic components, there is increasing interest in employing biologically derived building blocks (e.g., peptides and proteins) that offer unmatched structural and functional diversity. Here, we report the construction of crystalline mesoporous frameworks that are self-assembled from amphiphilic collagen-mimetic peptides. Comprehensive structural characterization via microscopy, spectroscopy, and computational techniques provides insights into the assembly packing model, in which hexagonally packed channels are interconnected by antiparallel-aligned collagen triple helices via hydrophobic and electrostatic interactions. Lastly, we demonstrate the functional potential of aCMP frameworks through the encapsulation of various molecular guests, including doxorubicin, an anti-cancer drug. Overall, this work establishes a class of mesoporous frameworks, derived from synthetically engineerable peptide conjugates, marking a significant step forward in broadening the architectural scope and application potential of peptide-based materials.

Perez, Anthony R↗

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.

Fiamenghi, Mateus B↗

Mediation of Colloidal Encounter Dynamics by Surface Roughness

Rigorous understanding on the self-assembly of colloidal nanocrystals is crucial to develop tailored nanostructured materials for energy storage, sensing, and optical fields. Despite extensive studies on the self-assembly, a mechanistic understanding of self-assembly under an external field still remains an ongoing challenge. Here, in this work, we used optical tweezers that impose an external attractive force field, resulting in the self-assembly of alpha-phase sodium yttrium fluoride nanocrystals. The dynamic force that is strongly dependent on the surface roughness of the nanocrystals is shown to be a decisive factor for a direct contact between the nanocrystals, manifested by the roughness-dependent hydrodynamic resistivity and Langevin dynamic simulations. Our study provides direct evidence that the role of dynamics is equally important in understanding the self-assembly, which has been rarely observed in the self-assembly in contrast with many studies on the equilibrium forces. These results may have further impact in other fields, such as having explanatory power for the probability of nonclassical crystal growth or the structure of viral spike proteins that affect the probability of viruses binding with cells.

Felsted, Robert G. [Univ. of Washington, Seattle, ↗

ProteinTuneRL

ProteinTuneRL is a framework designed to harness the power of reinforcement learning for advanced protein design. The project enables fine-tuning of generative models to explore and optimize protein sequences with tailored structural and functional properties.

Landajuela Larma, Mikel [Lawrence Livermore Nation↗

What Makes a Bifurcase? Insights from a NADH-Dependent Reduced Ferredoxin: NADP+ Oxidoreductase (Nfn) and Homologs

NADH-dependent ferredoxin:NADP+ oxidoreductases (Nfn) is an enzyme family that engage in flavin-based electron bifurcation (FBEB), a mode of energy conservation utilized by life. The protein comprises one large (NfnL) and one small (NfnS) subunits. Thermoanaerobacterium sacchaloryticum (Tsac) is an anaerobic thermophilic bacterium that - with known involvement of Tsac Nfn - can produce ethanol in high, commercially viable concentrations. We sought to investigate the activity and energetic landscape of Tsac Nfn to determine how the enzyme effectuates FBEB. Tsac NfnS, NfnL, and the partner ferredoxin (Tsac Fd) were recombinantly expressed, purified, and reconstituted with iron-sulfur cluster and FAD cofactors. Electron paramagnetic resonance (EPR) was utilized for all proteins. Spectroelectrochemistry was performed with NfnL. Square-wave voltammetry was conducted on NfnL and Fd. Spectrophotometric activity was assayed for NfnL with or without NfnS. Our group continues to investigate the Nfn from Pyrococcus furiosus (Pf Nfn). Unlike Pf NfnS, Tsac NfnS can be stably expressed, purified, and reconstituted in the absence of its partner NfnL, allowing for this subunit to be characterized separately. The energetic profile of FBEB in Tsac Nfn is overall similar to that of Pf NfnL, with some differences: (1) the proximal cluster is at a lower potential (-780 mV vs -711), (2) the bifurcating FAD is at a higher potential (-406 mV vs -436 mV), and (3) Tsac Fd has two [4Fe-4S] clusters at -550 and -410 mV, unlike Pf Fd with a single cluster at approximately 400 mV. Activity assays indicate that the two enzymes perform FBEB in a similar way. Our work continues to build upon the new field of FBEB by demonstrating that the energetic landscape between distantly related archael (Pf) and bacterial (Tsac Nfn) are largely similar. This equips us to understand design principles for FBEB, allowing us to modulate the process in vivo for specific metabolic outcomes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Catalytic Bias of NADH-Dependent Reduced Ferredoxin: NADP+ Oxidoreductase (Nfn) and its Relevance to Ethanol Production in Thermoanaerobacterium Saccharolyticum

NADH-dependent reduced ferredoxin: NADP+ oxidoreductase (Nfn) enzyme catalyzes an energy-conserving flavin-based electron bifurcation (FBEB) reaction. In microbial metabolism, Nfn links redox pools of three electron carriers - ferredoxin (Fd), NAD(H), and NADP(H) - through the following FBEB reaction: 2 NADPH + NAD+ + 2 Fdox 2 NADP+ + NADH + 2 Fdred + H+ The forward reaction is termed electron bifurcation, and the reverse reaction is electron confurcation. Catalytic bias describes an enzyme's tendency to favor one direction of a reversible reaction over the other and is expressed as the ratio of activities in the two directions. Thermoanaerobacterium saccharolyticum (Tsac) is a thermophilic, ethanologenic bacterium that ferments hemicellulose to ethanol at yields above 90%. Its Nfn enzyme is known to support ethanol production, presumably by operating in the confurcating direction to balance cellular cofactors, but this has not previously been demonstrated. To investigate the Tsac Nfn further, we heterologously expressed, purified, and reconstituted the proteins NfnS (NfnA), NfnL (NfnB), and the putative partner Fd with iron-sulfur cluster and/or FAD cofactors. Activity assays monitoring the oxidation or reduction of Fd showed that, across pH 5-10, Tsac Nfn is catalytically biased towards the confurcating direction, favoring NADPH generation over NADPH oxidation by at least fivefold. Using protein electrochemistry, we also determined the reduction potentials of the cofactors in NfnL and Fd. These results indicate that the energetic landscape of FBEB in Tsac Nfn is similar to that in an ortholog. However, Tsac Fd has redox properties distinct from previously assayed Fds, suggesting that the identity and redox properties of Fd may help determine the catalytic bias of Nfn. Additionally, we confirmed the standalone ferredoxin: NADP+ oxidoreductase (FNOR) activity of NfnL but found it to be low and likely insignificant for in vivo redox conversion. We also show how the catalytic bias of Nfn integrates with the hydrogen cycling mechanism proposed in Tsac to better explain cofactor balancing for ethanol production. Our work advances the understanding of electron transfer processes within metabolic networks for the generation of valuable bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗