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Two-dimensional (2D) van der Waals heterostructures consist of different 2D crystals with diverse properties, constituting the cornerstone of the new generation of 2D electronic devices. Yet interfaces in heterostructures inevitably break bulk symmetry and structural continuity, resulting in delicate atomic rearrangements and novel electronic structures. In this paper, we predict that 2D interfaces undergo "spontaneous curvature", which means when two flat 2D layers approach each other, they inevitably experience out-of-plane curvature. Based on deep-learning-assisted large-scale molecular dynamics simulations, we observe significant out-of-plane displacements up to 3.8 Å in graphene/BN bilayers induced by curvature, producing a stable hexagonal moiré pattern, which agrees well with experimentally observations. Additionally, the out-of-plane flexibility of 2D crystals enables the propagation of curvature throughout the system, thereby influencing the mechanical properties of the heterostructure. These findings offer fundamental insights into the atomic structure in 2D van der Waals heterostructures and pave the way for their applications in devices. Lattice mismatch in 2D van der Waals heterostructures induces lattice reconstruction to optimize the stacking. Here, the authors show how this introduces curving of different heterobilayers from deep-learning-assisted molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

This document is a reply to a previous article by Brandani et al. regarding diffusion anomalies in nanopores. The authors of this reply provide a comprehensive response to the points raised by Brandani et al. They discuss the limitations of the dual-resistance model in decoupling surface barriers and intracrystalline diffusion based on theoretical analysis. The authors also present their own experimental results and calculations to support their findings. They acknowledge the challenges in comparing experimental results with molecular dynamics simulations and express gratitude for the funding and support received for their work. [Extracted from the article]

Structural information on channelrhodopsins' mechanism of light-gated ion conductance is scarce, limiting its engineering as optogenetic tools. Here, we use single-particle cryo-electron microscopy of peptidisc-incorporated protein samples to determine the structures of the slow-cycling mutant C110A of kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) in the dark and upon laser flash excitation. Upon photoisomerization of the retinal chromophore, the retinylidene Schiff base NH-bond reorients from the extracellular to the cytoplasmic side. This switch triggers a series of side chain reorientations and merges intramolecular cavities into a transmembrane K+ conduction pathway. Molecular dynamics simulations confirm K+ flux through the illuminated state but not through the resting state. The overall displacement between the closed and the open structure is small, involving mainly side chain rearrangements. Asp105 and Asp116 play a key role in K+ conductance. Structure-guided mutagenesis and patch-clamp analysis reveal the roles of the pathway-forming residues in channel gating and selectivity. Channelrhodopsins' mechanism of light-gated ion conductance could be engineered for use in optogenetic tools. Here, structures of the slow-cycling mutant of HcKCR1, including an open state structure, provide insight into channel gating and selectivity. [ABSTRACT FROM AUTHOR]

Hydrogen-transfer is the primary process responsible for elevating the degree of unsaturation of intermediates in zeolite-catalyzed methanol-to-hydrocarbon reactions, with olefins serving as the typical receptor and alkanes being produced as the by-product. Intriguingly, the introduction of CO was shown to suppress the selectivity of alkanes and enhance the production of aromatics, yet microscopic understanding of this phenomenon remains elusive. Here, based on ab initio molecular dynamics simulations and free energy sampling methods, we discover a non-olefin-induced hydrogen-transfer reaction in the presence of CO, with ketene/acetyl emerging as a more suitable hydrogen-transfer receptor than olefins. This predominant route enhances the degree of unsaturation of olefins without generating additional alkanes, and the produced dienes and acetaldehyde could further contribute to the formation of aromatics. Moreover, we construct a general mechanism applicable to a series of CO-coupled aromatics synthesis reactions, offering distinctive insights and strategies for the optimization of efficiency. The role of CO in zeolite-catalyzed methanol-to-hydrocarbon reactions remains unclear. Here, ab initio molecular dynamics and free energy sampling reveal a non-olefin-induced hydrogen transfer mediated by CO, with ketene/acetyl identified as a superior hydrogen-transfer receptor over olefins. [ABSTRACT FROM AUTHOR]

Gypsum (CaSO4·2H2O) plays a critical role in numerous natural and industrial processes. Nevertheless, the underlying mechanisms governing the formation of gypsum crystals on surfaces with diverse chemical properties remain poorly understood due to a lack of sufficient temporal-spatial resolution. Herein, we use in situ microscopy to investigate the real-time gypsum nucleation on self-assembled monolayers (SAMs) terminated with −CH3, −hybrid (a combination of NH2 and COOH), −COOH, −SO3, −NH3, and −OH functional groups. We report that the rate of gypsum formation is regulated by the surface functional groups and hydrophobicity, in the order of −CH3 > −hybrid > −COOH > −SO3 ≈ − NH3 > − OH. Results based on classical nucleation theory and molecular dynamics simulations reveal that nucleation pathways for hydrophilic surfaces involve surface-induced nucleation, with ion adsorption sites (i.e., functional groups) serving as anchors to facilitate the growth of vertically oriented clusters. Conversely, hydrophobic surfaces involve bulk nucleation with ions near the surface that coalesce into larger horizontal clusters. These findings provide new insights into the spatial and temporal characteristics of gypsum formation on various surfaces and highlight the significance of surface functional groups and hydrophobicity in governing gypsum formation mechanisms, while also acknowledging the possibility of alternative nucleation pathways due to the limitations of experimental techniques. This work demonstrates different gypsum nucleation pathways on hydrophilic and hydrophobic surfaces through in situ microscopy and molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

Sphingosine-1-phosphate (S1P) is a signaling lysolipid critical to heart development, immunity, and hearing. Accordingly, mutations in the S1P transporter SPNS2 are associated with reduced white cell count and hearing defects. SPNS2 also exports the S1P-mimicking FTY720-P (Fingolimod) and thereby is central to the pharmacokinetics of this drug when treating multiple sclerosis. Here, we use a combination of cryo-electron microscopy, immunofluorescence, in vitro binding and in vivo S1P export assays, and molecular dynamics simulations to probe SPNS2's substrate binding and transport. These results reveal the transporter's binding mode to its native substrate S1P, the therapeutic FTY720-P, and the reported SPNS2-targeting inhibitor 33p. Further capturing an inward-facing apo state, our structures illuminate the protein's mechanism for exchange between inward-facing and outward-facing conformations. Finally, using these structural, localization, and S1P transport results, we identify how pathogenic mutations ablate the protein's export activity and thereby lead to hearing loss. SPNS2 exports S1P and FTY720-P to control immune cell migration. Here, the authors use cryo-EM, immunofluorescence, in vitro binding and in vivo S1P export, and MD simulations to uncover the mechanisms of SPNS2's transport and inhibition. [ABSTRACT FROM AUTHOR]

Secondary organic aerosols (SOAs) significantly impact Earth's climate and human health. Although the oxidation of volatile organic compounds (VOCs) has been recognized as the major contributor to the atmospheric SOA budget, the mechanisms by which this process produces SOA-forming highly oxygenated organic molecules (HOMs) remain unclear. A major challenge is navigating the complex chemical landscape of these transformations, which traditional hypothesis-driven methods fail to thoroughly investigate. Here, we explore the oxidation of α-pinene, a critical atmospheric biogenic VOC, using a novel reaction discovery approach based on molecular dynamics and state-of-the-art enhanced sampling techniques. Our approach successfully identifies all established reaction pathways of α-pinene ozonolysis, as well as discovers multiple novel species and pathways without relying on a priori chemical knowledge. In particular, we unveil a key branching point that leads to the rapid formation of alkoxy radicals, whose high and diverse reactivity help to explain hitherto unexplained oxidation pathways suggested by mass spectral peaks observed in α-pinene ozonolysis experiments. This branching point is likely prevalent across a variety of atmospheric VOCs and could be crucial in establishing the missing link to SOA-forming HOMs. The ozonolysis of α-pinene is important in atmospheric secondary organic aerosols formation. Here, the authors use a molecular dynamics guided reaction discovery approach and identify endoperoxide-to-alkoxy isomerization as a key branching point in the mechanism. [ABSTRACT FROM AUTHOR]

The general control non-repressible 5 (GCN5)-related N-acetyltransferase (GNAT) SbzI, in the biosynthesis of the sulfonamide antibiotic altemicidin, catalyzes the transfer of the 2-sulfamoylacetyl (2-SA) moiety onto 6-azatetrahydroindane dinucleotide. While most GNAT superfamily utilize acyl-coenzyme A (acyl-CoA) as substrates, SbzI recognizes a carrier-protein (CP)-tethered 2-SA substrate. Moreover, SbzI is the only naturally occurring enzyme that catalyzes the direct incorporation of sulfonamide, a valuable pharmacophore in medicinal chemistry. Here, we present the structure-function analysis and structure-based engineering of SbzI. The crystal structure of SbzI in complex with the CP SbzG, along with cross-linking and isothermal titration calorimetry analyses of their variants, revealed the structural basis for CP recognition by the GNAT SbzI. Furthermore, docking simulation, molecular dynamics simulation, and mutagenesis studies indicated the intimate structural details of the unique reaction mechanism of SbzI, which does not utilize a general base residue in contrast to other typical GNATs. These findings facilitated rational engineering of the enzyme to expand the substrate range and to generate azaindane dinucleotide derivatives. This study uncovers the reaction mechanisms catalyzed by GNAT SbzI. The authors were able to detemine key structural features responsible for the recognition of carrier-protein SbzG through structure-function analysis, and structure-based enzyme engineering altered the substrate promiscuity to generate unnatural altemicidin derivatives. [ABSTRACT FROM AUTHOR]

Functional nanomaterials with enzyme-mimicking activities, termed as nanozymes, have found wide applications in various fields. However, the deviation between the working and optimal pHs of nanozymes has been limiting their practical applications. Here we develop a strategy to modulate the microenvironmental pHs of metal–organic framework (MOF) nanozymes by confining polyacids or polybases (serving as Brønsted acids or bases). The confinement of poly(acrylic acid) (PAA) into the channels of peroxidase-mimicking PCN-222-Fe (PCN = porous coordination network) nanozyme lowers its microenvironmental pH, enabling it to perform its best activity at pH 7.4 and to solve pH mismatch in cascade systems coupled with acid-denatured oxidases. Experimental investigations and molecular dynamics simulations reveal that PAA not only donates protons but also holds protons through the salt bridges between hydroniums and deprotonated carboxyl groups in neutral pH condition. Therefore, the confinement of poly(ethylene imine) increases the microenvironmental pH, leading to the enhanced hydrolase-mimicking activity of MOF nanozymes. This strategy is expected to pave a promising way for designing high-performance nanozymes and nanocatalysts for practical applications. NCOMMS-24-44031B Nanozymes have found wide applications in various fields, but the deviation between the working and optimal pHs of nanozymes limits their practical applications. Here, the authors report a strategy to modulate the microenvironmental pHs of metal–organic framework nanozymes, enabling them to exhibit optimal activity under neutral pH conditions. [ABSTRACT FROM AUTHOR]

The artificial engineering of an enzyme's structural conformation and dynamic properties to promote its catalytic activity and stability outside cellular environments is highly pursued in industrial biotechnology. Here, we describe an elegant strategy of combining the rationally designed liquid-solid hybrid microreactor with a tailor-made polyethylene glycol functional ionic liquid (PEG-IL) microenvironment to exercise a high level of control over the configuration of enzymes for practical continuous-flow biocatalysis. As exemplified by a lipase driven kinetic resolution reaction, the obtained system exhibits a 2.70 to 30.35-fold activity enhancement compared to their batch or traditional IL-based counterparts. Also, our results demonstrate that the thermal stability of encapsulated lipase can be significantly strengthened in the presence of PEG groups, showcasing a long-term continuous-flow stability even up to 1000 h at evaluated temperature of 60 oC. Through systematic experiment and molecular dynamics simulation studies, the conformational changes of the active site cavity in the modified lipases are correlated with enzymatic properties alteration, and the pronounced effects of PEG-groups in stabilizing enzyme's secondary structures by delaying unfolding at elevated temperatures are identified. We believe that this study will guide the design of high-performance enzymatic systems, promoting their utilization in real-world biocatalysis applications. The engineering of an enzyme's structural conformation and dynamic properties to promote its catalytic activity and stability outside cellular environments is challenging. Here, the authors combine the rationally designed liquid-solid hybrid microreactor with a tailor-made polyethylene glycol functional ionic liquid microenvironment to obtain a high level of control over the configuration of confined enzymes for practical continuous-flow biocatalysis. [ABSTRACT FROM AUTHOR]

Hematite is a well-known catalyst for the oxygen evolution reaction on photoanodes in photoelectrochemical water-splitting cells. However, the knowledge of hematite-water interfaces and water oxidation mechanisms is still lacking, which limits improvements in photoelectrochemical water-splitting performance. Herein, we use the Fe-terminated hematite (0001) surface as a model and propose a comprehensive mechanism for the oxygen evolution reaction on both non-solvated and solvated surfaces. Key reaction intermediates are identified through ab initio molecular dynamics simulations at the density functional theory level with a Hubbard U correction. Several notable intermediates are proposed, and the effects of water solvent on these intermediates and the overall reaction mechanisms are suggested. The proposed mechanisms align well with experimental observations under photoelectrochemical water oxidation conditions. Additionally, we highlight the potential role of O2 desorption in the oxygen evolution reaction on hematite, as O2 adsorption may block reaction sites and increases surface hydrophobicity, leading to an unfavorable pathway for oxygen evolution. Hematite is a promising material for photoelectrochemical water splitting, but its mechanisms are not well understood. Here, the authors report a detailed mechanism, identifying key reaction intermediates and highlighting the influence of solvent water and oxygen desorption on the reaction pathways. [ABSTRACT FROM AUTHOR]

The phosphoethanolamine transferase EptA utilizes phosphatidylethanolamine (PE) in the bacterial cell membrane to modify the structure of lipopolysaccharide, thereby conferring antimicrobial resistance on Gram-negative pathogens. Previous studies have indicated that excessive consumption of PE can disrupt the cell membrane, leading to cell death. This implies the presence of a regulatory mechanism for EptA catalysis to maintain a balance between antimicrobial resistance and bacterial growth. Through microsecond-scale all-atom molecular dynamics simulations, we demonstrate that membrane lipid homeostasis modulates the conformational transition and catalytic activation of EptA. The conformation of EptA oscillates between closed and open states, ensuring the precise spatiotemporal sequence of substrates binding. Interestingly, the conformation of EptA is significantly influenced by its surrounding lipid microenvironment, particularly the PE proportion in the membrane. PE-rich membrane conditions initiate and stabilize the open conformation of EptA through both orthosteric and allosteric effects. Importantly, the reaction mediated by EptA gradually depletes PE in the membrane, ultimately hindering its conformational transition and catalytic activation. These findings collectively establish a self-promoted model, illustrating the regulatory mechanism of EptA during the development of antibiotic resistance. The phosphoethanolamine transferase modifies lipopolysaccharide structure and confers antibiotic resistance on Gram-negative bacteria. Here the authors reveal how the membrane lipid modulates the conformational transition of this important enzyme. [ABSTRACT FROM AUTHOR]

ABCB6 has been implicated in dyschromatosis universalis hereditaria, a condition characterized by hyperpigmented and hypopigmented skin macules. Dyschromatosis universalis hereditaria can also present with hearing loss. Dyschromatosis universalis hereditaria-associated mutations in ABCB6 have been reported, but the role of this protein in the inner ear has not been studied. Here we determine a high-resolution (2.93 Å) cryo-EM structure of ABCB6 and functionally characterized several dyschromatosis universalis hereditaria mutants. We find that the L356P mutant abolishes ABCB6 function, and affirm the underlying loss of ATP binding mechanism using molecular dynamics simulations based on our cryo-EM structure. To test the role of ABCB6 in the inner ear, we characterize Abcb6 (the ABCB6 homolog) in zebrafish. We show that Abcb6 suppression by morpholinos reduces inner ear and lateral line hair cell numbers. Morphants also lack the utricular otolith, which is associated with vestibular function. Co-injecting morpholinos with human ABCB6 mRNA partially rescues the morphant phenotype, suggesting that Abcb6 plays a developmental role in inner ear structures. Further, we show that Abcb6 knockout mice exhibit an increased auditory brainstem response threshold, resulting in reduced hearing sensitivity. Taken together, these data suggest ABCB6 plays a role in inner ear development and function. ABCB6 has been implicated in dyschromatosis universalis hereditaria, a condition that can present with hearing loss. Here, the authors use zebrafish and mice to perform experiments suggesting that ABCB6 plays a role in inner ear development. [ABSTRACT FROM AUTHOR]

The protein corona formed on nanoparticles (NPs) has potential as a valuable diagnostic tool for improving plasma proteome coverage. Here, we show that spiking small molecules, including metabolites, lipids, vitamins, and nutrients into plasma can induce diverse protein corona patterns on otherwise identical NPs, significantly enhancing the depth of plasma proteome profiling. The protein coronas on polystyrene NPs when exposed to plasma treated with an array of small molecules allows for the detection of 1793 proteins marking an 8.25-fold increase in the number of quantified proteins compared to plasma alone (218 proteins) and a 2.63-fold increase relative to the untreated protein corona (681 proteins). Furthermore, we discovered that adding 1000 µg/ml phosphatidylcholine could singularly enable the detection of 897 proteins. At this specific concentration, phosphatidylcholine selectively depletes the four most abundant plasma proteins, including albumin, thus reducing the dynamic range of plasma proteome and enabling the detection of proteins with lower abundance. Employing an optimized data-independent acquisition approach, the inclusion of phosphatidylcholine leads to the detection of 1436 proteins in a single plasma sample. Our molecular dynamics results reveal that phosphatidylcholine interacts with albumin via hydrophobic interactions, H-bonds, and water bridges. The addition of phosphatidylcholine also enables the detection of 337 additional proteoforms compared to untreated protein corona using a top-down proteomics approach. Given the critical role of plasma proteomics in biomarker discovery and disease monitoring, we anticipate the widespread adoption of this methodology for the identification and clinical translation of biomarkers. The protein corona on nanoparticles has potential for application in protein diagnostics. Here, the authors report on the use of small molecules to change the protein and proteoform patterns of protein corona on otherwise identical nanoparticles, which can be leveraged to significantly enhance the depth of plasma proteome profiling. [ABSTRACT FROM AUTHOR]

Vaccine development targeting rapidly evolving pathogens such as HIV-1 requires induction of broadly neutralizing antibodies (bnAbs) with conserved paratopes and mutations, and in some cases, the same Ig-heavy chains. The current trial-and-error search for immunogen modifications that improve selection for specific bnAb mutations is imprecise. Here, to precisely engineer bnAb boosting immunogens, we use molecular dynamics simulations to examine encounter states that form when antibodies collide with the HIV-1 Envelope (Env). By mapping how bnAbs use encounter states to find their bound states, we identify Env mutations predicted to select for specific antibody mutations in two HIV-1 bnAb B cell lineages. The Env mutations encode antibody affinity gains and select for desired antibody mutations in vivo. These results demonstrate proof-of-concept that Env immunogens can be designed to directly select for specific antibody mutations at residue-level precision by vaccination, thus demonstrating the feasibility of sequential bnAb-inducing HIV-1 vaccine design. In this work, researchers engineer HIV-1 immunogens using molecular dynamics simulations to enhance vaccine designs that select for specific antibody mutations. Their approach improved the selection of mutations crucial for broadly neutralizing antibody responses, offering a promising strategy for HIV vaccine development. [ABSTRACT FROM AUTHOR]

In chromatin replication, faithful recycling of histones from parental DNA to replicated strands is essential for maintaining epigenetic information across generations. A previous experiment has revealed that disrupting interactions between the N-terminal tail of Mcm2, a subunit in DNA replication machinery, and a histone H3/H4 tetramer perturb the recycling. However, the molecular pathways and the factors that regulate the ratio recycled to each strand and the destination location are yet to be revealed. Here, we performed molecular dynamics simulations of yeast DNA replication machinery, an H3/H4 tetramer, and replicated DNA strands. The simulations demonstrated that histones are recycled via Cdc45-mediated and unmediated pathways without histone chaperones, as our in vitro biochemical assays supported. Also, RPA binding regulated the ratio recycled to each strand, whereas DNA bending by Pol ε modulated the destination location. Together, the simulations provided testable hypotheses, which are vital for elucidating the molecular mechanisms of histone recycling. Parental histones are faithfully recycled in chromatin replication. Here the authors performed molecular dynamics simulations of replication machinery and proposed that histones are recycled via Cdc45-mediated and unmediated pathways. [ABSTRACT FROM AUTHOR]

Embedding of cell-surface receptors into a membrane defines their dynamics but also complicates experimental characterization of their signaling complexes. The hepatocyte growth factor receptor MET is a receptor tyrosine kinase involved in cellular processes such as proliferation, migration, and survival. It is also targeted by the pathogen Listeria monocytogenes, whose invasion protein, internalin B (InlB), binds to MET, forming a signaling dimer that triggers pathogen internalization. Here we use an integrative structural biology approach, combining molecular dynamics simulations and single-molecule Förster resonance energy transfer (smFRET) in cells, to investigate the early stages of MET activation. Our simulations show that InlB binding stabilizes MET in a conformation that promotes dimer formation. smFRET reveals that the in situ dimer structure closely resembles one of two previously published crystal structures, though with key differences. This study refines our understanding of MET activation and provides a methodological framework for studying other plasma membrane receptors. The hepatocyte growth factor receptor MET is a receptor tyrosine kinase involved in cellular processes such as proliferation, migration, and survival. Here the authors combine molecular dynamics simulations and smFRET in cells, to investigate the early stages of MET activation. [ABSTRACT FROM AUTHOR]

The intrinsically disordered carboxy-terminal domain (CTD) of the largest subunit of RNA Polymerase II (RNAPII) consists of multiple tandem repeats of the consensus heptapeptide Y1-S2-P3-T4-S5-P6-S7. The CTD promotes liquid-liquid phase-separation (LLPS) of RNAPII in vivo. However, understanding the role of the conserved heptad residues in LLPS is hampered by the lack of direct biochemical characterization of the CTD. Here, we generated a systematic array of CTD variants to unravel the sequence-encoded molecular grammar underlying the LLPS of the human CTD. Using in vitro experiments and molecular dynamics simulations, we report that the aromaticity of tyrosine and cis-trans isomerization of prolines govern CTD phase-separation. The cis conformation of prolines and β-turns in the SPXX motif contribute to a more compact CTD ensemble, enhancing interactions among CTD residues. We further demonstrate that prolines and tyrosine in the CTD consensus sequence are required for phosphorylation by Cyclin-dependent kinase 7 (CDK7). Under phase-separation conditions, CDK7 associates with the surface of the CTD droplets, drastically accelerating phosphorylation and promoting the release of hyperphosphorylated CTD from the droplets. Our results highlight the importance of conformationally restricted local structures within spacer regions, separating uniformly spaced tyrosine stickers of the CTD heptads, which are required for CTD phase-separation. The authors explore sequence-encoded molecular grammar underlying the liquid liquid phase-separation of the human RNA polymerase II C-terminal domain and demonstrate that phase-separation appears to accelerate on phosphorylation by CDK7. [ABSTRACT FROM AUTHOR]

Near-neutral HCO3– aqueous solution plays an essential role in respiratory, mineralization and catalysis, yet the interconversion between hydrated CO2, HCO3– and CO32– and the associated proton transfer under such proton-deficient conditions remain uncovered. Here we reveal that cation enables HCO3– to self-dissociate into OH– and CO2 through a pH-independent process, where CO2 hydration and subsequent proton transfer in acid-base reactions lead to the overall exchange of oxygen isotopes between HCO3– and H2O tracked by oxygen isotope-labeled Raman spectroscopy. Isolating HCO3– from cations with crown ether impedes HCO3– dissociation and the following reactions. Further molecular dynamics simulations demonstrate that the interplay between HCO3– and hydrated cations drives HCO3– dissociation. This study suggests a natural proton channel upon coupling HCO3– with cations. Unlike the traditional views that HCO3- anions transit to either CO2 or CO32- upon suffering pH changes. Here, the authors report that cation enables HCO3- to self-dissociate into OH- and CO2 through a pH independent process, leading to the formation of acid-base encounter pairs for proton transfer. [ABSTRACT FROM AUTHOR]

Sub-10 µm microplastics (MPs) in aquatic environments pose significant ecological and health risks due to their mobility and potential to carry harmful microcontaminants. Our effluent analysis from a Hong Kong Sewage Treatment Works shows that traditional treatment often fails to effectively remove these MPs. These small-sized MPs are commonly neglected due to challenges in accurate quantification, analysis, and removal. This study introduces a nanobubble-assisted flotation process that enhances the removal efficiency of both regular and irregular small-sized MPs from wastewater. The proposed process outperforms the traditional flotation process by fostering a more effective interaction between bubbles and MPs, increasing removal rates of MPs from 1 µm to 10 µm by up to 12% and providing a total efficiency boost of up to 17% for various particle sizes. Improvements are attributed to enhanced collision and adhesion probabilities, hydrophobic interactions, as well as better floc flotation. Supported by empirical evidence, mathematical models, and Molecular Dynamics simulations, this research elucidates the nanoscale mechanisms at play. The findings confirm the nanobubble-assisted flotation technique as an innovative and practical approach to removing sub-10 µm MPs in water treatment processes. Sub-10 µm microplastic pose severe environmental risks. Here, authors introduce an advanced nanobubble assisted flotation technique that enhances microplastic removal, providing a promising solution for effective water treatment. [ABSTRACT FROM AUTHOR]

Carboxylesterases serve as potent biocatalysts in the enantioselective synthesis of chiral carboxylic acids and esters. However, naturally occurring carboxylesterases exhibit limited enantioselectivity, particularly toward ethyl 3-cyclohexene-1-carboxylate (CHCE, S1), due to its nearly symmetric structure. While machine learning effectively expedites directed evolution, the lack of models for predicting the enantioselectivity for carboxylesterases has hindered progress, primarily due to challenges in obtaining high-quality training datasets. In this study, we devise a high-throughput method by coupling alcohol dehydrogenase to determine the apparent enantioselectivity of the carboxylesterase AcEst1 from Acinetobacter sp. JNU9335, generating a high-quality dataset. Leveraging seven features derived from biochemical considerations, we quantitively describe the steric, hydrophobic, hydrophilic, electrostatic, hydrogen bonding, and π-π interaction effects of residues within AcEst1. A robust gradient boosting regression tree model is trained to facilitate stereodivergent evolution, resulting in the enhanced enantioselectivity of AcEst1 toward S1. Through this approach, we successfully obtain two stereocomplementary variants, DR3 and DS6, demonstrating significantly increased and reversed enantioselectivity. Notably, DR3 and DS6 exhibit utility in the enantioselective hydrolysis of various symmetric esters. Comprehensive kinetic parameter analysis, molecular dynamics simulations, and QM/MM calculations offer insights into the kinetic and thermodynamic features underlying the manipulated enantioselectivity of DR3 and DS6. Carboxylesterases catalyze the enantioselective synthesis of chiral carboxylic acids and esters but exhibit limited enantioselectivity, particularly toward ethyl 3-cyclohexene-1- carboxylate (CHCE). Here, the authors establish a high-throughput method to generate a high-quality dataset for carboxylesterase AcEst1 from Acinetobacter sp. JNU9335 using CHCE as the substrate, use it to train a machine learning predictor and design two stereocomplementary mutants to synthesize both enantiomers of chiral CHCE. [ABSTRACT FROM AUTHOR]

α7 nicotinic acetylcholine receptors (nAChRs) are homopentameric ligand-gated ion channels with critical roles in the nervous system. Recent studies have resolved and functionally annotated closed, open, and desensitized states of these receptors, providing insight into ion permeation and lipid binding. However, the process by which α7 nAChRs transition between states remains unclear. To understand gating and lipid modulation, we generated two ensembles of molecular dynamics simulations of apo α7 nAChRs, with or without cholesterol. Using symmetry-adapted Markov state modeling, we developed a five-state gating model. Free energies recapitulated functional behavior, with the closed state dominating in absence of agonist. Open-to-nonconducting transition rates corresponded to experimental open durations. Cholesterol relatively stabilized the desensitized state, and reduced open-desensitized barriers. These results establish plausible asymmetric transition pathways between states, define lipid modulation effects on the α7 nAChR conformational cycle, and provide an ensemble of structural models applicable to rational design of lipidic pharmaceuticals. The α7 nicotinic acetylcholine receptor plays important roles in the human nervous system. Here, authors use molecular simulations to develop a gating model and reveal cholesterol effects, offering insights applicable to drug design. [ABSTRACT FROM AUTHOR]

Intermetallic nanoparticles (NPs) possess significant potentials for catalytic applications, yet their production presents challenges as achieving the disorder-to-order transition during the atom ordering process involves overcoming a kinetic energy barrier. Here, we demonstrate a robust approach utilizing atomic gas-migration for the in-situ synthesis of stable and homogeneous intermetallic alloys for propane dehydrogenation (PDH). This approach relies on the physical mixture of two separately supported metal species in one reactor. The synthesized platinum-zinc intermetallic catalysts demonstrate exceptional stability for 1300 h in continuous propane dehydrogenation under industrially relevant industrial conditions, with extending 95% propylene selectivity and propane conversions approaching thermodynamic equilibrium values at 550–600 oC. In situ characterizations and density functional theory/molecular dynamics simulation reveal Zn atoms adsorb on the particle surface and then diffuse inward, aiding in the formation of ultrasmall and highly ordered intermetallic alloys. This in-situ gas-migration strategy is applicable to a wide range of intermetallic systems. Intermetallic alloys (IMAs) hold significant potential for catalysis. Here, the authors present a robust gas-migration method for synthesizing stable and uniform IMAs, which exhibit exceptional stability over 1300 h in propane dehydrogenation. [ABSTRACT FROM AUTHOR]

The multi-phase oxidation of S(IV) plays a crucial role in the atmosphere, leading to the formation of haze and severe pollution episodes. We here contribute to its understanding on a molecular level by reporting experimentally determined pKa values of the various S(IV) tautomers and reaction barriers for SO2 formation pathways. Complementary state-of-the-art molecular-dynamics simulations reveal a depletion of bisulfite at low pH at the liquid-vapor interface, resulting in a different tautomer ratio at the interface compared to the bulk. On a molecular-scale level, we explain this with the formation of a stable contact ion pair between sulfonate and hydronium ions, and with the higher energetic barrier for the dehydration of sulfonic acid at the liquid-vapor interface. Our findings highlight the contrasting physicochemical behavior of interfacial versus bulk environments, where the pH dependence of the tautomer ratio reported here has a significant impact on both SO2 uptake kinetics and reactions involving NOx and H2O2 at aqueous aerosol interfaces. The complex equilibria of sulfur compounds at the liquid-vapor interface play key roles in atmospheric processes. Here, using X-ray photoelectron spectroscopy, Raman spectroscopy, and molecular dynamics simulations the authors determining pKa values and tautomer ratios at the air-vapor interface in a liquid microjet. [ABSTRACT FROM AUTHOR]

Poly(ADP-ribose) (PAR), a non-canonical nucleic acid, is essential for DNA/RNA metabolism and protein condensation, and its dysregulation is linked to cancer and neurodegeneration. However, key structural insights into PAR's functions remain largely uncharacterized, hindered by the challenges in synthesizing and characterizing PAR, which are attributed to its length heterogeneity. A central issue is how PAR, comprised solely of ADP-ribose units, attains specificity in its binding and condensing proteins based on chain length. Here, we integrate molecular dynamics simulations with small-angle X-ray scattering to analyze PAR structures. We identify diverse structural ensembles of PAR that fall into distinct subclasses and reveal distinct compaction of two different lengths of PAR upon the addition of small amounts of Mg2+ ions. Unlike PAR15, PAR22 forms ADP-ribose bundles via local intramolecular coil-to-globule transitions. Understanding these length-dependent structural changes could be central to deciphering the specific biological functions of PAR. This study reveals the 3D structures of poly(ADP-ribose) (PAR) using small-angle X-ray scattering and molecular dynamics simulations. It demonstrates how cation concentration and polymer length influence PAR's structure, providing insights into how a homopolymer can have specific functional roles. [ABSTRACT FROM AUTHOR]

Hsp90 is a molecular chaperone of central importance for protein homeostasis in the cytosol of eukaryotic cells, with key functional and structural traits conserved from yeast to man. During evolution, Hsp90 has gained additional functional importance, leading to an increased number of interacting co-chaperones and client proteins. Here, we show that the overall conformational transitions coupled to the ATPase cycle of Hsp90 are conserved from yeast to humans, but cycle timing as well as the dynamics are significantly altered. In contrast to yeast Hsp90, the human Hsp90 is characterized by broad ensembles of conformational states, irrespective of the absence or presence of ATP. The differences in the ATPase rate and conformational transitions between yeast and human Hsp90 are based on two residues in otherwise conserved structural elements that are involved in triggering structural changes in response to ATP binding. The exchange of these two mutations allows swapping of the ATPase rate and of the conformational transitions between human and yeast Hsp90. Our combined results show that Hsp90 evolved to a protein with increased conformational dynamics that populates ensembles of different states with strong preferences for the N-terminally open, client-accepting states. Hsp90 is a molecular chaperone important for protein homeostasis. Here, the authors show that the conformational transitions during the Hsp90 ATPase cycle are conserved from yeast to humans, but a few mutations alter cycle timing and dynamics. [ABSTRACT FROM AUTHOR]

The potent neurotoxic venom of the black widow spider contains a cocktail of seven phylum-specific latrotoxins (LTXs), but only one, α-LTX, targets vertebrates. This 130 kDa toxin binds to receptors at presynaptic nerve terminals and triggers a massive release of neurotransmitters. It is widely accepted that LTXs tetramerize and insert into the presynaptic membrane, thereby forming Ca2+-conductive pores, but the underlying mechanism remains poorly understood. LTXs are homologous and consist of an N-terminal region with three distinct domains, along with a C-terminal domain containing up to 22 consecutive ankyrin repeats. Here we report cryoEM structures of the vertebrate-specific α-LTX tetramer in its prepore and pore state. Our structures, in combination with AlphaFold2-based structural modeling and molecular dynamics simulations, reveal dramatic conformational changes in the N-terminal region of the complex. Four distinct helical bundles rearrange and together form a highly stable, 15 nm long, cation-impermeable coiled-coil stalk. This stalk, in turn, positions an N-terminal pair of helices within the membrane, thereby enabling the assembly of a cation-permeable channel. Taken together, these data give insight into a unique mechanism for membrane insertion and channel formation, characteristic of the LTX family, and provide the necessary framework for advancing novel therapeutics and biotechnological applications. Black widow spider venom contains seven structurally related toxins acting at presynaptic nerve terminals. Here, the authors provide cryo-EM structures of vertebrate-specific αLTX in two states and decipher how the toxin forms cation-selective pores. [ABSTRACT FROM AUTHOR]

The immiscibility of hydrogen-helium mixture under the temperature and pressure conditions of planetary interiors is crucial for understanding the structures of gas giant planets (e.g., Jupiter and Saturn). While the experimental probe at such extreme conditions is challenging, theoretical simulation is heavily relied in an effort to unravel the mixing behavior of hydrogen and helium. Here we develop a method via a machine learning accelerated molecular dynamics simulation to quantify the physical separation of hydrogen and helium under the conditions of planetary interiors. The immiscibility line achieved with the developed method yields substantially higher demixing temperatures at pressure above 1.5 Mbar than earlier theoretical data, but matches better to the experimental estimate. Our results suggest a possibility that H-He demixing takes place in a large fraction of the interior radii of Jupiter and Saturn, i.e., 27.5% in Jupiter and 48.3% in Saturn. This indication of an H-He immiscible layer hints at the formation of helium rain and offers a potential explanation for the decrease of helium in the atmospheres of Jupiter and Saturn. The immiscibility of H-He mixtures in gas giants remains poorly understood. Here the authors use large scale machine learning accelerated molecular dynamics simulations to suggest that H-He demixing may occur within large interior radii of Jupiter and Saturn. [ABSTRACT FROM AUTHOR]

The interaction of condensed phase systems with external electric fields is of major importance in a myriad of processes in nature and technology, ranging from the field-directed motion of cells (galvanotaxis), to geochemistry and the formation of ice phases on planets, to field-directed chemical catalysis and energy storage and conversion systems including supercapacitors, batteries and solar cells. Molecular simulation in the presence of electric fields would give important atomistic insight into these processes but applications of the most accurate methods such as ab-initio molecular dynamics (AIMD) are limited in scope by their computational expense. Here we introduce Perturbed Neural Network Potential Molecular Dynamics (PNNP MD) to push back the accessible time and length scales of such simulations. We demonstrate that important dielectric properties of liquid water including the field-induced relaxation dynamics, the dielectric constant and the field-dependent IR spectrum can be machine learned up to surprisingly high field strengths of about 0.2 V Å−1 without loss in accuracy when compared to ab-initio molecular dynamics. This is remarkable because, in contrast to most previous approaches, the two neural networks on which PNNP MD is based are exclusively trained on molecular configurations sampled from zero-field MD simulations, demonstrating that the networks not only interpolate but also reliably extrapolate the field response. PNNP MD is based on rigorous theory yet it is simple, general, modular, and systematically improvable allowing us to obtain atomistic insight into the interaction of a wide range of condensed phase systems with external electric fields. External electric fields are pivotal in modifying chemical reactivity for energy applications. Here the authors introduce a modular approach to include them in machine learning molecular dynamics simulations of condensed phase systems. [ABSTRACT FROM AUTHOR]

Allosteric drugs offer a new avenue for modern drug design. However, the identification of cryptic allosteric sites presents a formidable challenge. Following the allostery nature of residue-driven conformation transition, we propose a state-of-the-art computational pipeline by developing a residue-intuitive hybrid machine learning (RHML) model coupled with molecular dynamics (MD) simulation, through which we can efficiently identify the allosteric site and allosteric modulator as well as reveal their regulation mechanism. For the clinical target β2-adrenoceptor (β2AR), we discover an additional allosteric site located around residues D792.50, F2826.44, N3187.45 and S3197.46 and one putative allosteric modulator ZINC5042. Using Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and protein structure network (PSN), the allosteric potency and regulation mechanism are probed to further improve identification accuracy. Benefiting from sufficient computational evidence, the experimental assays then validate our predicted allosteric site, negative allosteric potency and regulation pathway, showcasing the effectiveness of the identification pipeline in practice. We expect that it will be applicable to other target proteins. The identification of cryptic allosteric sites presents a formidable challenge. Here, the authors develop a residue-intuitive hybrid ML model coupled with MD simulation to successfully identify a novel allosteric site of β2AR and a negative allosteric modulator. [ABSTRACT FROM AUTHOR]

Poly(ADP-ribose) (PAR), a non-canonical nucleic acid, is essential for DNA/RNA metabolism and protein condensation, and its dysregulation is linked to cancer and neurodegeneration. However, key structural insights into PAR's functions remain largely uncharacterized, hindered by the challenges in synthesizing and characterizing PAR, which are attributed to its length heterogeneity. A central issue is how PAR, comprised solely of ADP-ribose units, attains specificity in its binding and condensing proteins based on chain length. Here, we integrate molecular dynamics simulations with small-angle X-ray scattering to analyze PAR structures. We identify diverse structural ensembles of PAR that fall into distinct subclasses and reveal distinct compaction of two different lengths of PAR upon the addition of small amounts of Mg2+ ions. Unlike PAR15, PAR22 forms ADP-ribose bundles via local intramolecular coil-to-globule transitions. Understanding these length-dependent structural changes could be central to deciphering the specific biological functions of PAR. This study reveals the 3D structures of poly(ADP-ribose) (PAR) using small-angle X-ray scattering and molecular dynamics simulations. It demonstrates how cation concentration and polymer length influence PAR's structure, providing insights into how a homopolymer can have specific functional roles. [ABSTRACT FROM AUTHOR]

Glucose is the primary source of energy for many organisms and is efficiently taken up by bacteria through a dedicated transport system that exhibits high specificity. In Escherichia coli, the glucose-specific transporter IICBGlc serves as the major glucose transporter and functions as a component of the phosphoenolpyruvate-dependent phosphotransferase system. Here, we report cryo-electron microscopy (cryo-EM) structures of the glucose-bound IICBGlc protein. The dimeric transporter embedded in lipid nanodiscs was captured in the occluded, inward- and occluded, outward-facing conformations. Together with biochemical and biophysical analyses, and molecular dynamics (MD) simulations, we provide insights into the molecular basis and dynamics for substrate recognition and binding, including the gates regulating the binding sites and their accessibility. By combination of these findings, we present a mechanism for glucose transport across the plasma membrane. Overall, this work provides molecular insights into the structure, dynamics, and mechanism of the IICBGlc transporter in a native-like lipid environment. Glucose is a key energy source for many organisms, efficiently transported in bacteria by specific systems. Here, the authors reveal cryo-EM structures of the glucose transporter IICB from E. coli, providing insights into its mechanism and dynamics. [ABSTRACT FROM AUTHOR]

The simulation of chemical reactions and mechanical properties including failure from atoms to the micrometer scale remains a longstanding challenge in chemistry and materials science. Bottlenecks include computational feasibility, reliability, and cost. We introduce a method for reactive molecular dynamics simulations using a clean replacement of non-reactive classical harmonic bond potentials with reactive, energy-conserving Morse potentials, called the Reactive INTERFACE Force Field (IFF-R). IFF-R is compatible with force fields for organic and inorganic compounds such as IFF, CHARMM, PCFF, OPLS-AA, and AMBER. Bond dissociation is enabled by three interpretable Morse parameters per bond type and zero energy upon disconnect. Use cases for bond breaking in molecules, failure of polymers, carbon nanostructures, proteins, composite materials, and metals are shown. The simulation of bond forming reactions is included via template-based methods. IFF-R maintains the accuracy of the corresponding non-reactive force fields and is about 30 times faster than prior reactive simulation methods. Molecular dynamics is a common tool to study microscopic physicochemical systems, however, it is limited by the inhability to form and break chemical bonds. Here the authors present a method to modify traditional force-fields implementing bond dissociation and bond forming. [ABSTRACT FROM AUTHOR]

Poly(ADP-ribose) (PAR), a non-canonical nucleic acid, is essential for DNA/RNA metabolism and protein condensation, and its dysregulation is linked to cancer and neurodegeneration. However, key structural insights into PAR's functions remain largely uncharacterized, hindered by the challenges in synthesizing and characterizing PAR, which are attributed to its length heterogeneity. A central issue is how PAR, comprised solely of ADP-ribose units, attains specificity in its binding and condensing proteins based on chain length. Here, we integrate molecular dynamics simulations with small-angle X-ray scattering to analyze PAR structures. We identify diverse structural ensembles of PAR that fall into distinct subclasses and reveal distinct compaction of two different lengths of PAR upon the addition of small amounts of Mg2+ ions. Unlike PAR15, PAR22 forms ADP-ribose bundles via local intramolecular coil-to-globule transitions. Understanding these length-dependent structural changes could be central to deciphering the specific biological functions of PAR. This study reveals the 3D structures of poly(ADP-ribose) (PAR) using small-angle X-ray scattering and molecular dynamics simulations. It demonstrates how cation concentration and polymer length influence PAR's structure, providing insights into how a homopolymer can have specific functional roles. [ABSTRACT FROM AUTHOR]

ρ-type γ-aminobutyric acid-A (GABAA) receptors are widely distributed in the retina and brain, and are potential drug targets for the treatment of visual, sleep and cognitive disorders. Endogenous neuroactive steroids including β-estradiol and pregnenolone sulfate negatively modulate the function of ρ1 GABAA receptors, but their inhibitory mechanisms are not clear. By combining five cryo-EM structures with electrophysiology and molecular dynamics simulations, we characterize binding sites and negative modulation mechanisms of β-estradiol and pregnenolone sulfate at the human ρ1 GABAA receptor. β-estradiol binds in a pocket at the interface between extracellular and transmembrane domains, apparently specific to the ρ subfamily, and disturbs allosteric conformational transitions linking GABA binding to pore opening. In contrast, pregnenolone sulfate binds inside the pore to block ion permeation, with a preference for activated structures. These results illuminate contrasting mechanisms of ρ1 inhibition by two different neuroactive steroids, with potential implications for subtype-specific gating and pharmacological design. Neurological processes from vision to cognition rely on precise control of ion channels, particularly GABAA receptors. Here, the authors report structures of a ρ1 GABAA receptor with naturally occurring steroids, revealing their specific interactions and suggesting approaches to understand and develop drugs. [ABSTRACT FROM AUTHOR]

Small-molecule compounds that elicit mRNA-selective translation repression have attracted interest due to their potential for expansion of druggable space. However, only a limited number of examples have been reported to date. Here, we show that desmethyl desamino pateamine A (DMDA-PatA) represses translation in an mRNA-selective manner by clamping eIF4A, a DEAD-box RNA-binding protein, onto GNG motifs. By systematically comparing multiple eIF4A inhibitors by ribosome profiling, we found that DMDA-PatA has unique mRNA selectivity for translation repression. Unbiased Bind-n-Seq reveals that DMDA-PatA-targeted eIF4A exhibits a preference for GNG motifs in an ATP-independent manner. This unusual RNA binding sterically hinders scanning by 40S ribosomes. A combination of classical molecular dynamics simulations and quantum chemical calculations, and the subsequent development of an inactive DMDA-PatA derivative reveals that the positive charge of the tertiary amine on the trienyl arm induces G selectivity. Moreover, we identified that DDX3, another DEAD-box protein, is an alternative DMDA-PatA target with the same effects on eIF4A. Our results provide an example of the sequence-selective anchoring of RNA-binding proteins and the mRNA-selective inhibition of protein synthesis by small-molecule compounds. Here the authors report that DMDA-PatA, an anti-tumor compound, functions as a mRNA-selective translational inhibitor. This drug clamps the target eIF4A and DDX3 RNA-binding proteins on the GNG RNA motif, providing steric hindrance for scanning ribosomes. [ABSTRACT FROM AUTHOR]

The article discusses the phenomenon of diffusion in nanoporous materials and its potential impact on matter upgrading and productivity. The authors highlight the occurrence of ultra-fast diffusion in one-dimensional channels of a zeolite based on molecular simulations and uptake rate measurements. However, a re-analysis of the uptake data suggests that experimental validation of ultra-fast diffusion is yet to be confirmed. The article also explores previous research on enhanced diffusion in nanoporous materials and the challenges faced by experimentalists in observing diffusion anomalies. The authors emphasize the need for good experimental practice and the development of guidelines for measuring and reporting diffusion properties in nanoporous materials. [Extracted from the article]

Microbial ion-pumping rhodopsins (MRs) are extensively studied retinal-binding membrane proteins. However, their biogenesis, including oligomerisation and retinal incorporation, remains poorly understood. The bacterial green-light absorbing proton pump proteorhodopsin (GPR) has emerged as a model protein for MRs and is used here to address these open questions using cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulations. Specifically, conflicting studies regarding GPR stoichiometry reported pentamer and hexamer mixtures without providing possible assembly mechanisms. We report the pentameric and hexameric cryo-EM structures of a GPR mutant, uncovering the role of the unprocessed N-terminal signal peptide in the assembly of hexameric GPR. Furthermore, certain proteorhodopsin-expressing bacteria lack retinal biosynthesis pathways, suggesting that they scavenge the cofactor from their environment. We shed light on this hypothesis by solving the cryo-EM structure of retinal-free proteoopsin, which together with mass spectrometry and MD simulations suggests that decanoate serves as a temporary placeholder for retinal in the chromophore binding pocket. Further MD simulations elucidate possible pathways for the exchange of decanoate and retinal, offering a mechanism for retinal scavenging. Collectively, our findings provide insights into the biogenesis of MRs, including their oligomeric assembly, variations in protomer stoichiometry and retinal incorporation through a potential cofactor scavenging mechanism. Microbial rhodopsins are prevalent retinal-binding membrane proteins. Here, authors reveal the roles of the N-terminal signal peptide in oligomerization and of decanoate as a retinal placeholder, providing proteorhodopsin structures and retinal incorporation mechanisms. [ABSTRACT FROM AUTHOR]

Microbial ion-pumping rhodopsins (MRs) are extensively studied retinal-binding membrane proteins. However, their biogenesis, including oligomerisation and retinal incorporation, remains poorly understood. The bacterial green-light absorbing proton pump proteorhodopsin (GPR) has emerged as a model protein for MRs and is used here to address these open questions using cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulations. Specifically, conflicting studies regarding GPR stoichiometry reported pentamer and hexamer mixtures without providing possible assembly mechanisms. We report the pentameric and hexameric cryo-EM structures of a GPR mutant, uncovering the role of the unprocessed N-terminal signal peptide in the assembly of hexameric GPR. Furthermore, certain proteorhodopsin-expressing bacteria lack retinal biosynthesis pathways, suggesting that they scavenge the cofactor from their environment. We shed light on this hypothesis by solving the cryo-EM structure of retinal-free proteoopsin, which together with mass spectrometry and MD simulations suggests that decanoate serves as a temporary placeholder for retinal in the chromophore binding pocket. Further MD simulations elucidate possible pathways for the exchange of decanoate and retinal, offering a mechanism for retinal scavenging. Collectively, our findings provide insights into the biogenesis of MRs, including their oligomeric assembly, variations in protomer stoichiometry and retinal incorporation through a potential cofactor scavenging mechanism. Microbial rhodopsins are prevalent retinal-binding membrane proteins. Here, authors reveal the roles of the N-terminal signal peptide in oligomerization and of decanoate as a retinal placeholder, providing proteorhodopsin structures and retinal incorporation mechanisms. [ABSTRACT FROM AUTHOR]

Simulating electronic behavior in materials and devices with realistic large system sizes remains a formidable task within the ab initio framework due to its computational intensity. Here we show DeePTB, an efficient deep learning-based tight-binding approach with ab initio accuracy to address this issue. By training on structural data and corresponding ab initio eigenvalues, the DeePTB model can efficiently predict tight-binding Hamiltonians for unseen structures, enabling efficient simulations of large-size systems under external perturbations such as finite temperatures and strain. This capability is vital for semiconductor band gap engineering and materials design. When combined with molecular dynamics, DeePTB facilitates efficient and accurate finite-temperature simulations of both atomic and electronic behavior simultaneously. This is demonstrated by computing the temperature-dependent electronic properties of a gallium phosphide system with 106 atoms. The availability of DeePTB bridges the gap between accuracy and scalability in electronic simulations, potentially advancing materials science and related fields by enabling large-scale electronic structure calculations. Electronic simulations of large systems are computationally demanding. Here, authors develop DeePTB, a deep learning approach for efficient tight-binding calculations with ab initio accuracy, enabling million-atom simulations at finite temperatures. [ABSTRACT FROM AUTHOR]

Low-molecular-weight heparin (LMWH), derived from unfractionated heparin (UFH), has enhanced anticoagulant efficacy, long duration of action, and extended half-life. Patients receiving LMWH for preventive therapies would strongly benefit from its long-term effects, however, achieving this is challenging. Here, we design and evaluate a nanoengineered LMWH and octadecylamine conjugate (LMHO) that can act for a long time while maintaining close to 97 ± 3% of LMWH activity via end-specific conjugation of the reducing end of LMWH. LMHO can self-assemble into nanoparticles with an average size of 105 ± 1.7 nm in water without any nanocarrier and can be combined with serum albumin, resulting in a lipid-based albumin shuttling effect. Such molecules can circulate in the bloodstream for 4–5 days. We corroborate the self-assembly capability of LMHO and its interaction with albumin through molecular dynamics (MD) simulations and transmission electron microscopy (TEM) analysis. This innovative approach to carrier-free polysaccharide delivery, enhanced by nanoengineered albumin shuttling, represents a promising platform to address limitations in conventional therapies. Low-molecular-weight heparin (LMWH) has enhanced anticoagulant efficacy, long duration of action, and extended half-life, but achieving long-term efficacy is challenging. Here, the authors design and evaluate a nanoengineered LMWH and octadecylamine conjugate (LMHO) that can act for a long time while maintaining close to 97% of LMWH activity via end specific conjugation of the reducing end of LMWH. [ABSTRACT FROM AUTHOR]

Multidomain proteins with flexible linkers and disordered regions play important roles in many cellular processes, but characterizing their conformational ensembles is difficult. We have previously shown that the coarse-grained model, Martini 3, produces too compact ensembles in solution, that may in part be remedied by strengthening protein–water interactions. Here, we show that decreasing the strength of protein–protein interactions leads to improved agreement with experimental data on a wide set of systems. We show that the 'symmetry' between rescaling protein–water and protein–protein interactions breaks down when studying interactions with or within membranes; rescaling protein-protein interactions better preserves the binding specificity of proteins with lipid membranes, whereas rescaling protein-water interactions preserves oligomerization of transmembrane helices. We conclude that decreasing the strength of protein–protein interactions improves the accuracy of Martini 3 for IDPs and multidomain proteins, both in solution and in the presence of a lipid membrane. Here, the authors show that decreasing the strength of protein-protein interactions leads to improved agreement of Martini 3 generated molecular dynamics simulations with experimental data on a wide set of systems. [ABSTRACT FROM AUTHOR]

ASCT2 is an obligate exchanger of neutral amino acids, contributing to cellular amino acid homeostasis. ASCT2 belongs to the same family (SLC1) as Excitatory Amino Acid Transporters (EAATs) that concentrate glutamate in the cytosol. The mechanism that makes ASCT2 an exchanger rather than a concentrator remains enigmatic. Here, we employ cryo-electron microscopy and molecular dynamics simulations to elucidate the structural basis of the exchange mechanism of ASCT2. We establish that ASCT2 binds three Na+ ions per transported substrate and visits a state that likely acts as checkpoint in preventing Na+ ion leakage, both features shared with EAATs. However, in contrast to EAATs, ASCT2 retains one Na+ ion even under Na+-depleted conditions. We demonstrate that ASCT2 cannot undergo the structural transition in TM7 that is essential for the concentrative transport cycle of EAATs. This structural rigidity and the high-affinity Na+ binding site effectively confine ASCT2 to an exchange mode. ASCT2 is a Na+-dependent obligatory amino acid exchanger. Here, the authors untangle the structural basis of the exchange mechanism in ASCT2, revealing that structural rigidity and a high-affinity Na+ binding site effectively confine ASCT2 to an exchange mode. [ABSTRACT FROM AUTHOR]

Most triblock copolymer-based physical hydrogels form three-dimensional networks through micellar packing, and formation of polymer loops represents a topological defect that diminishes hydrogel elasticity. This effect can be mitigated by maximizing the fraction of elastically effective bridges in the hydrogel network. Herein, we report hydrogels constructed by complexing oppositely charged multiblock copolymers designed with a sequence pattern that maximizes the entropic and enthalpic penalty of micellization. These copolymers self-assemble into branched and bridge-rich network units (netmers), instead of forming sparsely interlinked micelles. We find that the storage modulus of the netmer-based hydrogel is 11.5 times higher than that of the micelle-based hydrogel. Complementary coarse grained molecular dynamics simulations reveal that in the netmer-based hydrogels, the numbers of charge-complexed nodes and mechanically reinforcing bridges increase substantially relative to micelle-based hydrogels. In the formation of physical hydrogels from triblock copolymers, formation of polymer loops can result in topological defects. Here, the authors report the development of hydrogels from oppositely charged copolymers which assembled to form branched and bridge-rich networks. [ABSTRACT FROM AUTHOR]

Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands has offered promising avenues for biological and therapeutic applications. However, it remains elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, we present a computational framework for simulating chemo-mechanical change of structured DNA assemblies. We particularly quantify the effects of ethidium bromide (EtBr) intercalation on the geometry and mechanical properties of DNA base-pairs through molecular dynamics simulations and integrated them into finite-element-based structural analysis to predict the shape and properties of DNA objects. The proposed model captures various structural changes induced by EtBr-binding such as shape variation, flexibility modulation, and supercoiling instability. It enables a rational design of structured DNA assemblies with tunable shapes and mechanical properties by binding molecules. Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands is promising for biological and therapeutic applications, but it is elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, the authors present a computational framework for simulating chemo-mechanical change of structured DNA assemblies, using ethidium bromide intercalation as an example. [ABSTRACT FROM AUTHOR]

Phase behaviours of two-dimensional (2D) systems constitute a fundamental topic in condensed matter and statistical physics. Although hard polygons and interactive point-like particles are well studied, the phase behaviours of more realistic molecular systems considering intermolecular interaction and molecular shape remain elusive. Here we investigate by molecular dynamics simulation phase stabilities of 2D ball-stick polygons, serving as simplified models for molecular systems. Below the melting temperature Tm, we identify a critical edge number n c = 4 , at which a distorted square lattice emerges; when n < n c , the triangular system stabilizes at a spin-ice-like glassy state; when n > n c , the polygons stabilize at crystalline states. Moreover, in the crystalline state, Tm is higher for polygons with more edges at higher pressures but exhibits a crossover for hexagon and octagon at low pressures. A theoretical framework taking into account the competition between entropy and enthalpy is proposed to provide a comprehensive understanding of our results, which is anticipated to facilitate the design of 2D materials. The melting scenario of two-dimensional (2D) systems is sensitive to molecular details. Here the authors investigate the phase stabilities of 2D ball-stick polygons by molecular dynamics simulation and reveal a critical edge number of 4 emerging from the entropy-enthalpy balance. [ABSTRACT FROM AUTHOR]

The Maintenance of Lipid Asymmetry (Mla) pathway is a multicomponent system found in all gram-negative bacteria that contributes to virulence, vesicle blebbing and preservation of the outer membrane barrier function. It acts by removing ectopic lipids from the outer leaflet of the outer membrane and returning them to the inner membrane through three proteinaceous assemblies: the MlaA-OmpC complex, situated within the outer membrane; the periplasmic phospholipid shuttle protein, MlaC; and the inner membrane ABC transporter complex, MlaFEDB, proposed to be the founding member of a structurally distinct ABC superfamily. While the function of each component is well established, how phospholipids are exchanged between components remains unknown. This stands as a major roadblock in our understanding of the function of the pathway, and in particular, the role of ATPase activity of MlaFEDB is not clear. Here, we report the structure of E. coli MlaC in complex with the MlaD hexamer in two distinct stoichiometries. Utilising in vivo complementation assays, an in vitro fluorescence-based transport assay, and molecular dynamics simulations, we confirm key residues, identifying the MlaD β6-β7 loop as essential for MlaCD function. We also provide evidence that phospholipids pass between the C-terminal helices of the MlaD hexamer to reach the central pore, providing insight into the trajectory of GPL transfer between MlaC and MlaD. In this work, the authors present structural and functional evidence of lipid exchange within the gram-negative Mla pathway, broadening our understanding of lipid transport in bacteria and providing insight into the mechanism of a unique ABC transporter. [ABSTRACT FROM AUTHOR]

We investigate solvent effects in the hydrodeoxygenation of 4-propylguaiacol (4PG, 166 amu), a key lignin-derived monomer, over Ru/C catalyst by combined operando synchrotron photoelectron photoion coincidence (PEPICO) spectroscopy and molecular dynamics simulations. With and without isooctane co-feeding, ring-hydrogenated 2-methoxy-4-propylcyclohexanol (172 amu) is the first product, due to the favorable flat adsorption configuration of 4PG on the catalyst surface. In contrast, tetrahydrofuran (THF)—a polar aprotic solvent that is representative of those used for lignin solubilization and upgrading—strongly coordinates to the catalyst surface at the oxygen atom. This induces a local steric hindrance, blocking the flat adsorption of 4PG more effectively, as it needs more Ru sites than the tilted adsorption configuration revealed by molecular dynamics simulations. Therefore, THF suppresses benzene ring hydrogenation, favoring a demethoxylation route that yields 4-propylphenol (136 amu), followed by dehydroxylation to propylbenzene (120 amu). Solvent selection may provide new avenues for controlling catalytic selectivity. Solvents play a crucial role in catalysis, affecting both activity and selectivity. Here the authors demonstrate how solvent affinity to the catalyst surface influences the reaction pathways of 4-propylguaiacol. [ABSTRACT FROM AUTHOR]

Photoionization can initiate structural reorganization of molecular matter and drive formation of new chemical bonds. Here, we used time-resolved extreme ultraviolet (EUV) pump – EUV probe Coulomb explosion imaging of carbon dioxide dimer ion C O 2 2 + dynamics, that combined with ab initio molecular dynamics simulations, revealed unexpected asymmetric structural rearrangement. We show that ionization by the pump pulse induces rearrangement from the slipped-parallel (C2h) geometry of the neutral C O 2 dimer towards a T-shaped (C2v) structure on the ~100 fs timescale, although the most stable slipped-parallel (C2h) structure of the ionic dimer. Moreover, we find that excited states of the ionized C O 2 dimer can exhibit formation of a CO 3 moiety in the C 2 O 4 + complex that can persist even after a suitably time-delayed second photoionization in a metastable C 2 O 4 2 + dication. Our results suggest that charge asymmetry plays an important role in the ionization-induced dynamics in such dimers that are present in C O 2 rich environments. In a time-resolved Coulomb explosion imaging study using ultrafast extreme ultraviolet pulses, combined with theoretical simulations, authors reveal unexpected asymmetric rearrangement of carbon dioxide dimer ion, including a CO3 moiety formation. [ABSTRACT FROM AUTHOR]

Ice nucleation is a crucial process in nature and industries; however, the role of the free surface of water in this process remains unclear. To address this, we investigate the microscopic freezing process using brute-force molecular dynamics simulations. We discover that the free surface assists ice nucleation through an unexpected mechanism. The surface-induced negative pressure enhances the formation of local structures with a ring topology characteristic of Ice 0-like symmetry, promoting ice nucleation despite the symmetry differing from ordinary ice crystals. Unlike substrate-induced nucleation via water-solid interactions that occurs directly on the surface, this negative-pressure-induced mechanism promotes ice nucleation slightly inward the surface. Our findings provide a molecular-level understanding of the mechanism and pathway behind free-surface-induced ice formation, resolving the longstanding debate. The implications of our discoveries are of substantial importance in areas such as cloud formation, food technology, and other fields where ice nucleation plays a pivotal role. Ice nucleation is pivotal, yet the role of water's free surface remains unclear. Here, authors elucidate how the free surface aids ice nucleation through an unexpected mechanism involving negative pressure-induced formation of Ice 0-like structures. [ABSTRACT FROM AUTHOR]