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Multiple sclerosis (MS) changes the composition of the CSF. Here the authors use patient samples and aggregate CSF biomarkers into models that predict disability across all MS phenotypes, and identify potentially causal mechanisms and molecular disease heterogeneity.

While autopsy studies identify many abnormalities in the central nervous system (CNS) of subjects dying with neurological diseases, without their quantification in living subjects across the lifespan, pathogenic processes cannot be differentiated from epiphenomena. Using machine learning (ML), we searched for likely pathogenic mechanisms of multiple sclerosis (MS). We aggregated cerebrospinal fluid (CSF) biomarkers from 1305 proteins, measured blindly in the training dataset of untreated MS patients (N = 129), into models that predict past and future speed of disability accumulation across all MS phenotypes. Healthy volunteers (N = 24) data differentiated natural aging and sex effects from MS-related mechanisms. Resulting models, validated (Rho 0.40-0.51, p < 0.0001) in an independent longitudinal cohort (N = 98), uncovered intra-individual molecular heterogeneity. While candidate pathogenic processes must be validated in successful clinical trials, measuring them in living people will enable screening drugs for desired pharmacodynamic effects. This will facilitate drug development making, it hopefully more efficient and successful. Multiple sclerosis (MS) changes the composition of the CSF. Here the authors use patient samples and aggregate CSF biomarkers into models that predict disability across all MS phenotypes, and identify potentially causal mechanisms and molecular disease heterogeneity. [ABSTRACT FROM AUTHOR]

Supramolecular polymers are composed of monomers that self-assemble non-covalently, generating distributions of monodimensional fibres in continuous communication with each other and with the surrounding solution. Fibres, exchanging molecular species, and external environment constitute a sole complex system, which intrinsic dynamics is hard to elucidate. Here we report coarse-grained molecular simulations that allow studying supramolecular polymers at the thermodynamic equilibrium, explicitly showing the complex nature of these systems, which are composed of exquisitely dynamic molecular entities. Detailed studies of molecular exchange provide insights into key factors controlling how assemblies communicate with each other, defining the equilibrium dynamics of the system. Using minimalistic and finer chemically relevant molecular models, we observe that a rich concerted complexity is intrinsic in such self-assembling systems. This offers a new dynamic and probabilistic (rather than structural) picture of supramolecular polymer systems, where the travelling molecular species continuously shape the assemblies that statistically emerge at the equilibrium. The dynamic structure of supramolecular polymers is challenging to determine both in experiments and in simulations. Here the authors use coarse-grained molecular models to provide a comprehensive analysis of the molecular communication in these complex molecular systems. [ABSTRACT FROM AUTHOR]

Electrocatalytic nanocarbon (EN) is a class of material receiving intense interest as a potential replacement for expensive, metal-based electrocatalysts for energy conversion and chemical production applications. The further development of EN will require an intricate knowledge of its catalytic behaviors, however, the true nature of their electrocatalytic activity remains elusive. This review highlights work that contributed valuable knowledge in the elucidation of EN catalytic mechanisms. Experimental evidence from spectroscopic studies and well-defined molecular models, along with the survey of computational studies, is summarized to document our current mechanistic understanding of EN-catalyzed oxygen, carbon dioxide and nitrogen electrochemistry. We hope this review will inspire future development of synthetic methods and in situ spectroscopic tools to make and study well-defined EN structures. Electrocatalytic nanocarbon (EN) is a class of materials receiving intense interest as next generation electrocatalysts. Although impressive platforms, work is still required to develop our mechanistic understanding of them to that of molecular electrocatalysts. [ABSTRACT FROM AUTHOR]

The Mediator complex plays an essential and multi-faceted role in regulation of RNA polymerase II transcription in all eukaryotes. Structural analysis of yeast Mediator has provided an understanding of the conserved core of the complex and its interaction with RNA polymerase II but failed to reveal the structure of the Tail module that contains most subunits targeted by activators and repressors. Here we present a molecular model of mammalian (Mus musculus) Mediator, derived from a 4.0 Å resolution cryo-EM map of the complex. The mammalian Mediator structure reveals that the previously unresolved Tail module, which includes a number of metazoan specific subunits, interacts extensively with core Mediator and has the potential to influence its conformation and interactions. The Mediator complex regulates RNA polymerase II transcription in all eukaryotes. The mammalian Mediator cryo-EM structure reveals the architecture of previously unresolved Tail module and suggests its regulatory role in the complex conformation and interactions. [ABSTRACT FROM AUTHOR]

Many biological processes involve large-scale changes in membrane shape. Computer simulations of these processes are challenging since they occur across a wide range of spatiotemporal scales that cannot be investigated in full by any single current simulation technique. A potential solution is to combine different levels of resolution through a multiscale scheme. Here, we present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface (DTS) to its corresponding molecular model based on the coarse-grained (CG) Martini force field. Thus, we can use DTS simulations to equilibrate slow large-scale membrane conformational changes and then explore the local properties at CG resolution. We demonstrate the power of our method by backmapping a vesicular bud induced by binding of Shiga toxin and by transforming the membranes of an entire mitochondrion to near-atomic resolution. Our approach opens the way to whole cell simulations at molecular detail. Computer simulations of large-scale changes in membrane shape are challenging since they occur across a wide range of spatiotemporal scales. Here, authors present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface to its corresponding molecular model based on the coarse-grained Martini force field. [ABSTRACT FROM AUTHOR]

Melanoma is the most lethal skin malignancy, driven by genetic and epigenetic alterations in the complex tumour microenvironment. While large-scale molecular profiling of melanoma has identified molecular signatures associated with melanoma progression, comprehensive systems-level modeling remains elusive. This study builds up predictive gene network models of molecular alterations in primary melanoma by integrating large-scale bulk-based multi-omic and single-cell transcriptomic data. Incorporating clinical, epigenetic, and proteomic data into these networks reveals key subnetworks, cell types, and regulators underlying melanoma progression. Tumors with high immune infiltrates are found to be associated with good prognosis, presumably due to induced CD8+ T-cell cytotoxicity, via MYO1F-mediated M1-polarization of macrophages. Seventeen key drivers of the gene subnetworks associated with poor prognosis, including the transcription factor ZNF180, are tested for their pro-tumorigenic effects in vitro. The anti-tumor effect of silencing ZNF180 is further validated using in vivo xenografts. Experimentally validated targets of ZNF180 are enriched in the ZNF180 centered network and the known pathways such as melanoma cell maintenance and immune cell infiltration. The transcriptional networks and their critical regulators provide insights into the molecular mechanisms of melanomagenesis and pave the way for developing therapeutic strategies for melanoma. While the molecular profiling of melanoma progression has been extensively characterised by large-scale studies, there is still need for the comprehensive integration of such datasets. Here the authors construct predictive gene network models for prognostic and therapeutic purposes. [ABSTRACT FROM AUTHOR]

Structure-forming systems are ubiquitous in nature, ranging from atoms building molecules to self-assembly of colloidal amphibolic particles. The understanding of the underlying thermodynamics of such systems remains an important problem. Here, we derive the entropy for structure-forming systems that differs from Boltzmann-Gibbs entropy by a term that explicitly captures clustered states. For large systems and low concentrations the approach is equivalent to the grand-canonical ensemble; for small systems we find significant deviations. We derive the detailed fluctuation theorem and Crooks' work fluctuation theorem for structure-forming systems. The connection to the theory of particle self-assembly is discussed. We apply the results to several physical systems. We present the phase diagram for patchy particles described by the Kern-Frenkel potential. We show that the Curie-Weiss model with molecule structures exhibits a first-order phase transition. Structure-forming systems, such as chemical reaction networks, are usually described with the grand-canonical ensemble, but this may be inaccurate for small-sized systems. Here, the authors propose a canonical ensemble approach for closed structure-forming systems, showing its application to physical problems including the self-assembly of soft matter. [ABSTRACT FROM AUTHOR]

Iron- and nitrogen-doped carbon (Fe-N-C) materials are leading candidates to replace platinum catalysts for the oxygen reduction reaction (ORR) in fuel cells; however, their active site structures remain poorly understood. A leading postulate is that the iron-containing active sites exist primarily in a pyridinic Fe-N4 ligation environment, yet, molecular model catalysts generally feature pyrrolic coordination. Herein, we report a molecular pyridinic hexaazacyclophane macrocycle, (phen2N2)Fe, and compare its spectroscopic, electrochemical, and catalytic properties for ORR to a typical Fe-N-C material and prototypical pyrrolic iron macrocycles. N 1s XPS and XAS signatures for (phen2N2)Fe are remarkably similar to those of Fe-N-C. Electrochemical studies reveal that (phen2N2)Fe has a relatively high Fe(III/II) potential with a correlated ORR onset potential within 150 mV of Fe-N-C. Unlike the pyrrolic macrocycles, (phen2N2)Fe displays excellent selectivity for four-electron ORR, comparable to Fe-N-C materials. The aggregate spectroscopic and electrochemical data demonstrate that (phen2N2)Fe is a more effective model of Fe-N-C active sites relative to the pyrrolic iron macrocycles, thereby establishing a new molecular platform that can aid understanding of this important class of catalytic materials. Iron- and nitrogen-doped carbon materials are effective catalysts for the oxygen reduction reaction whose active sites are poorly understood. Here, the authors establish a new pyridinic iron macrocycle complex as a more effective active site model relative to legacy pyrrolic model complexes. [ABSTRACT FROM AUTHOR]

During homologous recombination, Rad51 forms a nucleoprotein filament on single-stranded DNA to promote DNA strand exchange. This filament binds to double-stranded DNA (dsDNA), searches for homology, and promotes transfer of the complementary strand, producing a new heteroduplex. Strand exchange proceeds via two distinct three-strand intermediates, C1 and C2. C1 contains the intact donor dsDNA whereas C2 contains newly formed heteroduplex DNA. Here, we show that the conserved DNA binding motifs, loop 1 (L1) and loop 2 (L2) in site I of Rad51, play distinct roles in this process. L1 is involved in formation of the C1 complex whereas L2 mediates the C1–C2 transition, producing the heteroduplex. Another DNA binding motif, site II, serves as the DNA entry position for initial Rad51 filament formation, as well as for donor dsDNA incorporation. Our study provides a comprehensive molecular model for the catalytic process of strand exchange mediated by eukaryotic RecA-family recombinases. Rad51 drives DNA strand exchange, the central reaction in recombinational DNA repair. Two sites of Rad51 are responsible for DNA binding, but the function of these sites has proven elusive. Here, the authors employ real-time assays to reveal catalytic roles for the two DNA binding sites of Rad51. [ABSTRACT FROM AUTHOR]

Biomembranes are two-dimensional assemblies of phospholipids that are only a few nanometres thick, but form micrometre-sized structures vital to cellular function. Explicit molecular modelling of biologically relevant membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Coarse-grained solvent-free membrane models offer efficient sampling but sacrifice realistic kinetics, thereby limiting the ability to predict pathways and mechanisms of membrane processes. Here, we present a framework for integrating coarse-grained membrane models with continuum-based hydrodynamics. This framework facilitates efficient simulation of large biomembrane systems with large timesteps, while achieving realistic equilibrium and non-equilibrium kinetics. It helps to bridge between the nanometer/nanosecond spatiotemporal resolutions of coarse-grained models and biologically relevant time- and lengthscales. As a demonstration, we investigate fluctuations of red blood cells, with varying cytoplasmic viscosities, in 150-milliseconds-long trajectories, and compare kinetic properties against single-cell experimental observations. Explicit molecular modelling of biological membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Here authors present a framework for integrating coarse-grained membrane models with continuum-based hydrodynamics which facilitates efficient simulation of large biomembrane systems. [ABSTRACT FROM AUTHOR]

Neural-network quantum states have been successfully used to study a variety of lattice and continuous-space problems. Despite a great deal of general methodological developments, representing fermionic matter is however still early research activity. Here we present an extension of neural-network quantum states to model interacting fermionic problems. Borrowing techniques from quantum simulation, we directly map fermionic degrees of freedom to spin ones, and then use neural-network quantum states to perform electronic structure calculations. For several diatomic molecules in a minimal basis set, we benchmark our approach against widely used coupled cluster methods, as well as many-body variational states. On some test molecules, we systematically improve upon coupled cluster methods and Jastrow wave functions, reaching chemical accuracy or better. Finally, we discuss routes for future developments and improvements of the methods presented. Despite the importance of neural-network quantum states, representing fermionic matter is yet to be fully achieved. Here the authors map fermionic degrees of freedom to spin ones and use neural-networks to perform electronic structure calculations on model diatomic molecules to achieve chemical accuracy. [ABSTRACT FROM AUTHOR]

Recombinant T cell receptors (TCRs) can be used to redirect naïve T cells to eliminate virally infected or cancerous cells; however, they are plagued by low stability and uneven expression. Here, we use molecular modeling to identify mutations in the TCR constant domains (Cα/Cβ) that increase the unfolding temperature of Cα/Cβ by 20 °C, improve the expression of four separate α/β TCRs by 3- to 10-fold, and improve the assembly and stability of TCRs with poor intrinsic stability. The stabilizing mutations rescue the expression of TCRs destabilized through variable domain mutation. The improved stability and folding of the TCRs reduces glycosylation, perhaps through conformational stabilization that restricts access to N-linked glycosylation enzymes. The Cα/Cβ mutations enables antibody-like expression and assembly of well-behaved bispecific molecules that combine an anti-CD3 antibody with the stabilized TCR. These TCR/CD3 bispecifics can redirect T cells to kill tumor cells with target HLA/peptide on their surfaces in vitro. Recombinant T-cells receptors can redirect naïve T cells but often have low or uneven expression. Here, the authors model mutations in TCR constant domains to increase T cell receptor expression, assembly, and stability and generate bispecific molecules. [ABSTRACT FROM AUTHOR]

Motile bacteria sense chemical gradients with transmembrane receptors organised in supramolecular signalling arrays. Understanding stimulus detection and transmission at the molecular level requires precise structural characterisation of the array building block known as a core signalling unit. Here we introduce an Escherichia coli strain that forms small minicells possessing extended and highly ordered chemosensory arrays. We use cryo-electron tomography and subtomogram averaging to provide a three-dimensional map of a complete core signalling unit, with visible densities corresponding to the HAMP and periplasmic domains. This map, combined with previously determined high resolution structures and molecular dynamics simulations, yields a molecular model of the transmembrane core signalling unit and enables spatial localisation of its individual domains. Our work thus offers a solid structural basis for the interpretation of a wide range of existing data and the design of further experiments to elucidate signalling mechanisms within the core signalling unit and larger array. Motile bacteria sense chemical gradients with transmembrane receptors organised in supramolecular signalling arrays. Here authors introduce an E. coli strain that forms small minicells possessing extended and highly ordered chemosensory arrays that are visualized by cryo-electron tomography. [ABSTRACT FROM AUTHOR]

Water is a critical component in polyelectrolyte anion exchange membranes (AEMs). It plays a central role in ion transport in electrochemical systems. Gaining a better understanding of molecular transport and conductivity in AEMs has been challenged by the lack of a general methodology capable of capturing and connecting water dynamics, water structure, and ionic transport over time and length scales ranging from those associated with individual bond vibrations and molecular reorientations to those pertaining to macroscopic AEM performance. In this work, we use two-dimensional infrared spectroscopy and semiclassical simulations to examine how water molecules are arranged into successive solvation shells, and we explain how that structure influences the dynamics of bromide ion transport processes in polynorbornene-based materials. We find that the transition to the faster transport mechanism occurs when the reorientation of water molecules in the second solvation shell is fast, allowing a robust hydrogen bond network to form. Our findings provide molecular-level insights into AEMs with inherent transport of halide ions, and help pave the way towards a comprehensive understanding of hydroxide ion transport in AEMs. Water is vital for ion transport in anion exchange membranes (AEMs). Here, the authors used electrochemical impedance, ultrafast spectroscopy, and molecular models to reveal how water arrangements affect bromide ion transport in state-of-the-art AEMs, offering insights for better membrane design. [ABSTRACT FROM AUTHOR]

Post-graphene organic Dirac (PGOD) materials are ordered two-dimensional networks of triply bonded sp2 carbon nodes spaced by π-conjugated linkers. PGOD materials are natural chemical extensions of graphene that promise to have an enhanced range of properties and applications. Experimentally realised molecules based on two PGOD nodes exhibit a bi-stable closed-shell/multi-radical character that can be understood through competing Lewis resonance forms. Here, following the same rationale, we predict that similar states should be accessible in PGOD materials, which we confirm using accurate density functional theory calculations. Although for graphene the semimetallic state is always dominant, for PGOD materials this state becomes marginally meta-stable relative to open-shell multiradical and/or closed-shell states that are stabilised through symmetry breaking, in line with analogous molecular systems. These latter states are semiconducting, increasing the potential use of PGOD materials as highly tuneable platforms for future organic nanoelectronics and spintronics. [ABSTRACT FROM AUTHOR]

Hyperconnected network architectures can endow nanomaterials with remarkable mechanical properties that are fundamentally controlled by designing connectivity into the intrinsic molecular structure. For hybrid organic-inorganic nanomaterials, here we show that by using 1,3,5 silyl benzene precursors, the connectivity of a silicon atom within the network extends beyond its chemical coordination number, resulting in a hyperconnected network with exceptional elastic stiffness, higher than that of fully dense silica. The exceptional intrinsic stiffness of these hyperconnected glass networks is demonstrated with molecular dynamics models and these model predictions are calibrated through the synthesis and characterization of an intrinsically porous hybrid glass processed from 1,3,5(triethoxysilyl) benzene. The proposed molecular design strategy applies to any materials system wherein the mechanical properties are controlled by the underlying network connectivity. [ABSTRACT FROM AUTHOR]

Protein biogenesis is essential in all cells and initiates when a nascent polypeptide emerges from the ribosome exit tunnel, where multiple ribosome-associated protein biogenesis factors (RPBs) direct nascent proteins to distinct fates. How distinct RPBs spatiotemporally coordinate with one another to affect accurate protein biogenesis is an emerging question. Here, we address this question by studying the role of a cotranslational chaperone, nascent polypeptide-associated complex (NAC), in regulating substrate selection by signal recognition particle (SRP), a universally conserved protein targeting machine. We show that mammalian SRP and SRP receptors (SR) are insufficient to generate the biologically required specificity for protein targeting to the endoplasmic reticulum. NAC co-binds with and remodels the conformational landscape of SRP on the ribosome to regulate its interaction kinetics with SR, thereby reducing the nonspecific targeting of signalless ribosomes and pre-emptive targeting of ribosomes with short nascent chains. Mathematical modeling demonstrates that the NAC-induced regulations of SRP activity are essential for the fidelity of cotranslational protein targeting. Our work establishes a molecular model for how NAC acts as a triage factor to prevent protein mislocalization, and demonstrates how the macromolecular crowding of RPBs at the ribosome exit site enhances the fidelity of substrate selection into individual protein biogenesis pathways. Biochemistry combined with biophysical measurements and mathematical modeling offer insight into the mechanism by which the cotranslational chaperone, nascent polypeptide-associated complex (NAC), modulates substrate selection by signal recognition particle (SRP) and reduces aberrant, nonspecific targeting of ribosomes to the ER. [ABSTRACT FROM AUTHOR]

Hollow multishelled structures (HoMSs), with relatively isolated cavities and hierarchal pores in the shells, are structurally similar to cells. Functionally inspired by the different transmission forms in living cells, we studied the mass transport process in HoMSs in detail. In the present work, after introducing the antibacterial agent methylisothiazolinone (MIT) as model molecules into HoMSs, we discover three sequential release stages, i.e., burst release, sustained release and stimulus-responsive release, in one system. The triple-shelled structure can provide a long sterility period in a bacteria-rich environment that is nearly 8 times longer than that of the pure antimicrobial agent under the same conditions. More importantly, the HoMS system provides a smart responsive release mechanism that can be triggered by environmental changes. All these advantages could be attributed to chemical diffusion- and physical barrier-driven temporally-spatially ordered drug release, providing a route for the design of intelligent nanomaterials. Hollow multishell structures (HoMSs) consist of multiple shells with voids between them that provide separate reaction environments within the same assembly. Here, the authors used TiO2-HoMS to deliver a broad-spectrum antibacterial agent, in three-stages and in response to environmental changes. [ABSTRACT FROM AUTHOR]

The bottom-up synthesis of structurally well-defined motifs of graphitic materials is crucial to understanding their physicochemical properties and to elicit new functions. Herein, we report the design and synthesis of TriQuinoline (TQ) as a molecular model for pyridinic-nitrogen defects in graphene sheets. TQ is a trimer of quinoline units concatenated at the 2- and 8-positions in a head-to-tail fashion, whose structure leads to unusual aromatisation behaviour at the final stage of the synthesis. The central atomic-sized void endows TQ with high proton affinity, which was confirmed empirically and computationally. TQ•H+ is a two-dimensional cationic molecule that displays both π–π and CH–π contact modes, culminating in the formation of the ternary complex ([12]cycloparaphenylene(CPP) ⊃ (TQ•H+/coronene)) that consists of TQ•H+, coronene (flat), and [12]cycloparaphenylene ([12]CPP) (ring). The water-miscibility of TQ•H+ allows it to serve as an efficient DNA intercalator for e.g. the inhibition of topoisomerase I activity. In this paper, the authors introduce a structurally elegant 2D triquinoline molecule as a discrete model for graphitic materials with atom-sized voids. The compound has unusual chemical properties, including high proton affinity and rich supramolecular behavior, forming complexes via both π-π and CH-π contact modes. [ABSTRACT FROM AUTHOR]

A correction is presented to the article "Developing a molecular picture of soil organic matter-mineral interactions by quantifying organo-mineral binding" which appeared online in the August 30, 2017 issue.

High-throughput sequencing describes multiple alterations in individual tumors, but their functional relevance is often unclear. Clinic-close, individualized molecular model systems are required for functional validation and to identify therapeutic targets of high significance for each patient. Here, we establish a Cre-ERT2-loxP (causes recombination, estrogen receptor mutant T2, locus of X-over P1) based inducible RNAi- (ribonucleic acid interference) mediated gene silencing system in patient-derived xenograft (PDX) models of acute leukemias in vivo. Mimicking anti-cancer therapy in patients, gene inhibition is initiated in mice harboring orthotopic tumors. In fluorochrome guided, competitive in vivo trials, silencing of the apoptosis regulator MCL1 (myeloid cell leukemia sequence 1) correlates to pharmacological MCL1 inhibition in patients´ tumors, demonstrating the ability of the method to detect therapeutic vulnerabilities. The technique identifies a major tumor-maintaining potency of the MLL-AF4 (mixed lineage leukemia, ALL1-fused gene from chromosome 4) fusion, restricted to samples carrying the translocation. DUX4 (double homeobox 4) plays an essential role in patients' leukemias carrying the recently described DUX4-IGH (immunoglobulin heavy chain) translocation, while the downstream mediator DDIT4L (DNA-damage-inducible transcript 4 like) is identified as therapeutic vulnerability. By individualizing functional genomics in established tumors in vivo, our technique decisively complements the value chain of precision oncology. Being broadly applicable to tumors of all kinds, it will considerably reinforce personalizing anti-cancer treatment in the future. Preclinical molecular models are useful that mimic a patient´s response to targeted therapy. Here, the authors establish an in vivo inducible RNAi-mediated gene silencing system in patient-derived xenograft models of acute leukemia to identify individual vulnerabilities and therapeutic targets. [ABSTRACT FROM AUTHOR]

Assembly of functional ribosomal subunits and successfully delivering them to the translating pool is a prerequisite for protein synthesis and cell growth. In S. cerevisiae, the ribosome assembly factor Reh1 binds to pre-60S subunits at a late stage during their cytoplasmic maturation. Previous work shows that the C-terminus of Reh1 inserts into the polypeptide exit tunnel of the pre-60S subunit. Here, we show that Reh1-bound nascent 60S subunits associate with 40S subunits to form actively translating ribosomes. Using selective ribosome profiling, we found that Reh1-bound ribosomes populate open reading frames near start codons. Reh1-bound ribosomes are also strongly enriched for initiator tRNA, indicating they are associated with early elongation. Using cryo-electron microscopy to image Reh1-bound 80S ribosomes, we found they contain A site peptidyl tRNA, P site tRNA and eIF5A, indicating that Reh1 does not dissociate from 60S until translation elongation. We propose that Reh1 is displaced by the elongating peptide chain, making it the last assembly factor released from the nascent 60S subunit during its initial round of translation. Assembly of functional ribosomal subunits is aided by dedicated assembly factors. Here, the authors show that the Reh1 is positioned in the polypeptide exit tunnel of 80S ribosomes, suggesting that the growing polypeptide chain displaces Reh1 during first round of translation. [ABSTRACT FROM AUTHOR]

The self-assembly of small molecules through non-covalent interactions is an emerging and promising strategy for building dynamic, stable, and large-scale structures. One remaining challenge is making the non-covalent interactions occur in the ideal positions to generate strength comparable to that of covalent bonds. This work shows that small molecule YAWF can self-assemble into a liquid-crystal hydrogel (LCH), the mechanical properties of which could be controlled by water. LCH can be used to construct stable solid threads with a length of over 1 meter by applying an external force on 2 µL of gel solution followed by water-regulated crystallization. These solid threads can support 250 times their weight. Cryogenic electron microscopy (Cryo-EM) analysis unravels the three-dimensional structure of the liquid-crystal fiber (elongated helix with C2 symmetry) at an atomic resolution. The multiscale mechanics of this material depend on the specificity of the molecular structure, and the water-controlled hierarchical and sophisticated self-assembly. Assembly of small molecules offers possibilities in the preparation of materials, but obtaining desirable mechanical strength can be challenging. Here, the authors report the assembly of a tetrapeptide to form a liquid crystal hydrogel, able to support significant weight. [ABSTRACT FROM AUTHOR]

Cryo-electron tomography (cryoET) provides sub-nanometer protein structure within the dense cellular environment. Existing sample preparation methods are insufficient at accessing the plasma membrane and its associated proteins. Here, we present a correlative cryo-electron tomography pipeline optimally suited to image large ultra-thin areas of isolated basal and apical plasma membranes. The pipeline allows for angstrom-scale structure determination with subtomogram averaging and employs a genetically encodable rapid chemically-induced electron microscopy visible tag for marking specific proteins within the complex cellular environment. The pipeline provides efficient, distributable, low-cost sample preparation and enables targeted structural studies of identified proteins at the plasma membrane of mammalian cells. Cryo-electron tomography requires thin samples. Few cell-thinning techniques have been standardized. Here, the authors provide and validate a method to prepare, label, and image proteins at mammalian cell plasma membranes for sub-nanometer structural analysis. [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]

The feasibility of carbon mineralization relies on the carbonation efficiency of CO2-reactive minerals, which is largely governed by the water content and state within material mesopores. Yet, the pivotal role of confined water in regulating carbonation efficiency at the nanoscale is not well understood. Here, we show that the maximum CO2 intake occurs at an optimal relative humidity (RHopt) when capillary condensation initiates within the hydrophilic mesopores. At this transition state, the pore becomes filled with metastable low-density water, providing an ideal docking site for CO2 adsorption and forming a mixed metastable state of water/CO2. We prove that RHopt depends on the mesopore size through a Kelvin-like relationship, which yields a robust engineering model to predict RHopt for realistic mineral carbonation. Building upon classical theories of phase transition in hydrophilic mesopores, this study unveils the capacity of the metastable water in CO2 intake and enhances the high-efficiency carbon mineralization with natural ore and industrial wastes in real-world applications. CO2 can be captured in mesoporous alkaline waste materials. Here the authors provide atomistic insight for CO2 adsorption in calcium hydroxide to identify optimal relative humidity conditions for maximum CO2 intake. [ABSTRACT FROM AUTHOR]

The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, leaving only three protein-coding genes and highly fragmented mitoribosomal rRNAs, raising challenging questions about mitoribosome composition, assembly and structure. Our study reveals how Toxoplasma gondii assembles over 40 mt-rRNA fragments using exclusively nuclear-encoded mitoribosomal proteins and three lineage-specific families of RNA-binding proteins. Among these are four proteins from the Apetala2/Ethylene Response Factor (AP2/ERF) family, originally known as transcription factors in plants and Apicomplexa, now repurposed as essential mitoribosome components. Cryo-EM analysis of the mitoribosome structure demonstrates how these AP2 proteins function as RNA binders to maintain mitoribosome integrity. The mitoribosome is also decorated with members of lineage-specific RNA-binding proteins belonging to RAP (RNA-binding domain abundant in Apicomplexa) proteins and HPR (heptatricopeptide repeat) families, highlighting the unique adaptations of these parasites. Solving the molecular puzzle of apicomplexan mitoribosome could inform the development of therapeutic strategies targeting organellar translation. The authors uncover one of the largest mitoribosomes, dedicated to translating only three proteins in lethal human eukaryotic pathogens of the Apicomplexa phylum. All members of mitochondrial DNA-containing Myzozoa, including Toxoplasma gondii, have commandeered three lineage-specific families of RNA-binding proteins to meticulously piece together over 40 mitochondrial rRNA fragments to build an operational mitoribosome. [ABSTRACT FROM AUTHOR]

Abstract Tetrahydrocannabinol (THC) is the principal psychoactive compound derived from the cannabis plant Cannabis sativa and approved for emetic conditions, appetite stimulation and sleep apnea relief. THC’s psychoactive actions are mediated primarily by the cannabinoid receptor CB1. Here, we determine the cryo-EM structure of HU210, a THC analog and widely used tool compound, bound to CB1 and its primary transducer, Gi1. We leverage this structure for docking and 1000 ns molecular dynamics simulations of THC and 10 structural analogs delineating their spatiotemporal interactions at the molecular level. Furthermore, we pharmacologically profile their recruitment of Gi and β-arrestins and reversibility of binding from an active complex. By combining detailed CB1 structural information with molecular models and signaling data we uncover the differential spatiotemporal interactions these ligands make to receptors governing potency, efficacy, bias and kinetics. This may help explain the actions of abused substances, advance fundamental receptor activation studies and design better medicines.

Contraction of striated muscles is driven by cyclic interactions of myosin head projecting from the thick filament with actin filament and is regulated by Ca2+ released from sarcoplasmic reticulum. Muscle thin filament consists of actin, tropomyosin and troponin, and Ca2+ binding to troponin triggers conformational changes of troponin and tropomyosin to allow actin-myosin interactions. However, the structural changes involved in this regulatory mechanism remain unknown. Here we report the structures of human cardiac muscle thin filament in the absence and presence of Ca2+ by electron cryomicroscopy. Molecular models in the two states built based on available crystal structures reveal the structures of a C-terminal region of troponin I and an N-terminal region of troponin T in complex with the head-to-tail junction of tropomyosin together with the troponin core on actin filament. Structural changes of the thin filament upon Ca2+ binding now reveal the mechanism of Ca2+ regulation of muscle contraction. The contraction of cardiac and skeletal muscles is regulated by Ca2+ released from the sarcoplasmic reticulum in muscle cells. Here the authors provide molecular insights into Ca2+ regulation of muscle contraction by determining the cryo-EM structures of the human cardiac muscle thin filament in the absence and presence of Ca2+. [ABSTRACT FROM AUTHOR]

Halogen-mediated interactions play an important role in molecular recognition and crystallization in many chemical and biological systems, whereas their effect on homochiral versus heterochiral recognition and crystallization has rarely been explored. Here we demonstrate the evolution of Br⋯Br contacts in chiral recognition during 2D crystallization. On Ag(100), type I contacts prevail at low coverage and lead to homochiral recognition and the formation of 2D conglomerates; whereas type II contacts mediating heterochiral recognition are suppressed at medium coverage and appear in the racemates induced by structural transitions at high coverage. On Ag(111), type I contacts dominate the 2D crystallization and generate 2D conglomerates exclusively. DFT calculations suggest that the energy difference between type I and type II contacts is reversed upon adsorption due to the substrate induced mismatch energy penalty. This result provides fundamental understanding of halogen-mediated interactions in molecular recognition and crystallization on surface. Halogen-mediated interactions control molecular recognition in many chemical and biological systems. Here, the authors demonstrate two types of Br⋯Br contacts and their importance in chiral on-surface crystallization. [ABSTRACT FROM AUTHOR]

Kainate receptors (KARs) are a subtype of ionotropic glutamate receptor (iGluR) channels, a superfamily of ligand-gated ion channels which mediate the majority of excitatory neurotransmission in the central nervous system. KARs modulate neuronal circuits and plasticity during development and are implicated in neurological disorders, including epilepsy, depression, schizophrenia, anxiety, and autism. Calcium-permeable KARs undergo ion channel block, but the therapeutic potential of channel blockers remains underdeveloped, mainly due to limited structural knowledge. Here, we present closed-state structures of GluK2 KAR homotetramers in complex with ion channel blockers NpTx-8, PhTx-74, Kukoamine A, and spermine. We find that blockers reside inside the GluK2 ion channel pore, intracellular to the closed M3 helix bundle-crossing gate, with their hydrophobic heads filling the central cavity and positively charged polyamine tails spanning the selectivity filter. Molecular dynamics (MD) simulations of our structures illuminate interactions responsible for different affinity and binding poses of the blockers. Our structures elucidate the trapping mechanism of KAR channel block and provide a template for designing new blockers that can selectively target calcium-permeable KARs in neuropathologies. Kainate receptors (KARs) contribute to excitatory neurotransmission, neuronal plasticity and neurological disorders. Here, Gangwar et al. present KAR structures in complex with channel blockers NpTx8, PhTx74, KukoA, and spermine, which become trapped inside the channel upon its closure. [ABSTRACT FROM AUTHOR]

The interconversion dynamics between charge transfer state charges (CTCs) and separated charges (SCs) is still an unresolved issue in the field of organic photovoltaics. Here, a transient absorption spectroscopy (TAS) study of a thermally evaporated small-molecule:fullerene system (α6T:C60) in different morphologies (dilute intermixed and phase separated) is presented. Spectral decomposition reveals two charge species with distinct absorption characteristics and different dynamics. Using time-dependent density functional theory, these species are identified as CTCs and SCs, where the spectral differences arise from broken symmetry in the charge transfer state that turns forbidden transitions into allowed ones. Based on this assignment, a kinetic model is formulated allowing the characterization of the charge generation, separation, and recombination mechanisms. We find that SCs are either formed directly from excitons within a few picoseconds or more slowly (~30–80 ps) from reversible splitting of CTCs. These findings constitute the first unambiguous observation of spectrally resolved CTCs and SCs. The interconversion dynamics between charge transfer state charges and separated charges remains an unresolved issue. Here, the authors spectrally resolve those charges and report a kinetic model to reveal the charge generation, separation, and recombination mechanism in α6T:C60 systems. [ABSTRACT FROM AUTHOR]

Amid the ongoing Global Plastics Treaty, high-quality circulation of halogen-containing plastics in an environmentally sound manner is a globally pressing issue. Current chemical dechlorination methods are limited by their inability to recycle PVC at the long-chain carbon level and the persistence of eco-toxic organochlorine byproducts. Herein, we propose a click dechlorination strategy for transforming waste PVC into valuable vitrimers via a one-step cascade thiol-ene click reaction and dynamic polymerization. Thermal activation of C-Cl bonds initiates β-elimination dechlorination, while disulfide bonds synchronously undergo homolytic cleavage, generating sulfur-centered radicals that drive precise sulfur-chlorine substitution and the formation of disulfide dynamic networks. This strategy achieves nearly complete chlorine extraction (93.88%) and produces vitrimers with tailorable mechanical and reprocessing properties, spanning from soft elastomers with 784% elongation to rigid plastics with a yield strength of 34 MPa. The significant advantage of this strategy is backbone protective precise dechlorination, enabling ecosystem toxicity reduced by 99.51% compared with widely adopted pyrolysis methods. This work introduces a sustainable pathway for upcycling PVC into valuable materials, marking significant progress in chlorinated plastic recycling. Current chemical dechlorination methods are limited by their inability to recycle PVC at the long-chain carbon level and the persistence of eco-toxic organochlorine byproducts. Here, the authors propose a click dechlorination strategy for transforming waste PVC into valuable vitrimers via a one-step cascade thiol-ene click reaction and dynamic polymerization. [ABSTRACT FROM AUTHOR]

Immune checkpoint blockade (ICB) therapy has emerged as a new therapeutic paradigm for a variety of advanced cancers, but wide clinical application is hindered by low response rate. Here we use a peptide-based, biomimetic, self-assembly strategy to generate a nanoparticle, TPM1, for binding PD-L1 on tumour cell surface. Upon binding with PD-L1, TPM1 transforms into fibrillar networks in situ to facilitate the aggregation of both bound and unbound PD-L1, thereby resulting in the blockade of the PD-1/PD-L1 pathway. Characterizations of TPM1 manifest a prolonged retention in tumour (> 7 days) and anti-cancer effects associated with reinvigorating CD8+ T cells in multiple mice tumour models. Our results thus hint TPM1 as a potential strategy for enhancing the ICB efficacy. Immune checkpoint blockade therapy such as anti-PD-L1 is efficient for treating specific cancer types, but poor response rates remain a caveat. Here the authors generate a peptide-based, self-assembly nanomaterial that binds and aggregates PD-L1 as a fibrillar networks to enhance the anti-tumour efficacy of anti-PD-L1 in multiple mouse tumour models. [ABSTRACT FROM AUTHOR]

The massed-spaced effect is a hallmark feature of memory formation. We now demonstrate this effect in two separate non-neural, immortalized cell lines stably expressing a short-lived luciferase reporter controlled by a CREB-dependent promoter. We emulate training using repeated pulses of forskolin and/or phorbol ester, and, as a proxy for memory, measure luciferase expression at various points after training. Four spaced pulses of either agonist elicit stronger and more sustained luciferase expression than a single "massed" pulse. Spaced pulses also result in stronger and more sustained activation of molecular factors critical for memory formation, ERK and CREB, and inhibition of ERK or CREB blocks the massed-spaced effect. Our findings show that canonical features of memory do not necessarily depend on neural circuitry, but can be embedded in the dynamics of signaling cascades conserved across different cell types. When learning is spaced in time, memory is enhanced, but so far this was only observed in neural systems. Here, the authors show that non-neural cells, including kidney cells, also show a spaced effect in terms of transcriptional responses. [ABSTRACT FROM AUTHOR]

The deep continental crust represents a vast potential habitat for microbial life where its activity remains poorly constrained. Organic acids like acetate are common in these ecosystems, but their role in the subsurface carbon cycle - including the mechanism and rate of their turnover - is still unclear. Here, we develop an isotope-exchange 'clock' based on the abiotic equilibration of H-isotopes between acetate and water, which can be used to define the maximum in situ acetate residence time. We apply this technique to the fracture fluids in Birchtree and Kidd Creek mines within the Canadian Precambrian crust. At both sites, we find that acetate residence times are <1 million years and calculated a rate of turnover that could theoretically support microbial life. However, radiolytic water-rock reactions could also contribute to acetate production and degradation, a process that would have global relevance for the deep biosphere. More broadly, our study demonstrates the utility of isotope-exchange clocks in determining residence times of biomolecules with possible applications to other environments. Trapped in rock fractures miles below the surface are saline waters that have been isolated for millions of years. In these most remote environments exists an active turnover of dissolved organic molecules, an active carbon cycle. [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 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]

We report bio-structural, bio-chemical and bio-physical evidence demonstrating how small molecules can bind to both wild-type and mutant IDH1, but only inhibit the enzymatic activity of the mutant isoform. Enabled through x-ray crystallography, we characterized a series of small molecule inhibitors that bound to mutant IDH1 differently than the marketed inhibitor Ivosidenib, for which we have determined the x-ray crystal structure. Across the industry several mutant IDH1 inhibitor chemotypes bind to this allosteric IDH1 pocket and selectively inhibit the mutant enzyme. Detailed characterization by a variety of biophysical techniques and NMR studies led us to propose how compounds binding in the allosteric IDH1 R132H pocket inhibit the production of 2-Hydroxy glutarate. Mutations in the IDH1 gene that generate neomorphic metabolites are linked to multiple human tumors including glioma. Here, the authors disclose novel mutant IDH1 inhibitors and contrast their mechanism and binding mode to molecules in clinical use. [ABSTRACT FROM AUTHOR]

Metabolic dysfunction-associated steatohepatitis (MASH) poses challenges for targeted delivery and retention of therapeutic proteins due to excess extracellular matrix (ECM). Here we present a new approach to treat MASH, termed “Fibrosis overexpression and retention (FORT)”. In this strategy, we design (1) retinoid-derivative lipid nanoparticle (LNP) to enable enhanced mRNA overexpression in fibrotic regions, and (2) mRNA modifications which facilitate anchoring of therapeutic proteins in ECM. LNPs containing carboxyl-retinoids, rather than alcohol- or ester-retinoids, effectively deliver mRNA with over 10-fold enhancement of protein expression in fibrotic livers. The carboxyl-retinoid rearrangement on the LNP surface improves protein binding and membrane fusion. Therapeutic proteins are then engineered with an endogenous collagen-binding domain. These fusion proteins exhibit increased retention in fibrotic lesions and reduced systemic toxicity. In vivo, fibrosis-targeting LNPs encoding fusion proteins demonstrate superior therapeutic efficacy in three clinically relevant male-animal MASH models. This approach holds promise in fibrotic diseases unsuited for protein injection.Metabolic dysfunction-associated steatohepatitis (MASH) poses challenges for targeted delivery and retention of therapeutic proteins due to excess extracellular matrix (ECM). To address this, the authors developed a “Fibrosis Overexpression and Retention (FORT) strategy” that can improve mRNA expression in the fibrotic region and extend the expressed protein in situ. [ABSTRACT FROM AUTHOR]

With protein databases growing rapidly due to advances in structural and computational biology, the ability to accurately align and rapidly search protein structures has become essential for biological research. In response to the challenge posed by vast protein structure repositories, GTalign offers an innovative solution to protein structure alignment and search—an algorithm that achieves optimal superposition at high speeds. Through the design and implementation of spatial structure indexing, GTalign parallelizes all stages of superposition search across residues and protein structure pairs, yielding rapid identification of optimal superpositions. Rigorous evaluation across diverse datasets reveals GTalign as the most accurate among structure aligners while presenting orders of magnitude in speedup at state-of-the-art accuracy. GTalign's high speed and accuracy make it useful for numerous applications, including functional inference, evolutionary analyses, protein design, and drug discovery, contributing to advancing understanding of protein structure and function. GTalign introduces spatial structure indexing for accelerated and deep superposition search and protein alignment derivation. Its parallel algorithms facilitate massive protein similarity searches, offering speed and accuracy advantages. [ABSTRACT FROM AUTHOR]

CASTs use both CRISPR-associated proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we report that CASTs can co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that CASTs co-occur with defense-associated CRISPR systems, with the highest prevalence for type I-B and type V CAST sub-types. Using an E. coli quantitative transposition assay and in vitro reconstitution, we show that CASTs can use CRISPR RNAs from these defense systems. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B CRISPR RNA reveals that Cas6 recognizes direct repeats via sequence-independent π − π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via an unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA or a single guide RNA reduces, but does not abrogate, off-target integration for type V CASTs. Our findings suggest that some CASTs may exploit defense-associated CRISPR arrays and that this fact must be considered when porting CASTs to heterologous bacterial hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications. Here, the authors show that CRISPR-associated transposons can co-opt other CRISPR arrays found in the same cell. Such interactions must be considered when porting these systems into new hosts. [ABSTRACT FROM AUTHOR]

Fluorinated phenyl azides (FPA) enable photo-structuring of π-conjugated polymer films for electronic device applications. Despite their potential, FPAs have faced limitations regarding their crosslinking efficiency, and more importantly, their impact on critical semiconductor properties, such as charge-carrier mobility. Here, we report that azide photolysis and photocrosslinking can achieve unity quantum efficiencies for specific FPAs. This suggests preferential nitrene insertion into unactivated C‒H bonds over benzazirine and ketenimine reactions, which we attribute to rapid interconversion between the initially formed hot states. Furthermore, we establish a structure‒activity relationship for carrier mobility quenching. The binding affinity of FPA crosslinker to polymer π-stacks governs its propensity for mobility quenching in both PM6 and PBDB-T used as model conjugated polymers. This binding affinity can be suppressed by FPA ring substitution, but varies in a non-trivial way with π-stack order. Utilizing the optimal FPA, photocrosslinking enables the fabrication of morphology-stabilized, acceptor-infiltrated donor polymer networks (that is, PBDB-T: ITIC and PM6: Y6) for solar cells. Our findings demonstrate the exceptional potential of the FPA photochemistry and offer a promising approach to address the challenges of modelling realistic molecular interactions in complex polymer morphologies, moving beyond the limitations of Flory‒Huggins mean field theory.The general photocrosslinking of semiconducting polymers is limited by efficiency and semiconductor property degradation. Here, the authors show that fluorinated phenyl azides can be molecularly designed to improve photolysis efficiency, and induce favourable partitioning of the crosslinker amongst the alkyl side chains of the polymer, thereby achieving high crosslinking efficiency without diminishing semiconducting properties. [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]

Tigecycline is widely used for treating complicated bacterial infections for which there are no effective drugs. It inhibits bacterial protein translation by blocking the ribosomal A-site. However, even though it is also cytotoxic for human cells, the molecular mechanism of its inhibition remains unclear. Here, we present cryo-EM structures of tigecycline-bound human mitochondrial 55S, 39S, cytoplasmic 80S and yeast cytoplasmic 80S ribosomes. We find that at clinically relevant concentrations, tigecycline effectively targets human 55S mitoribosomes, potentially, by hindering A-site tRNA accommodation and by blocking the peptidyl transfer center. In contrast, tigecycline does not bind to human 80S ribosomes under physiological concentrations. However, at high tigecycline concentrations, in addition to blocking the A-site, both human and yeast 80S ribosomes bind tigecycline at another conserved binding site restricting the movement of the L1 stalk. In conclusion, the observed distinct binding properties of tigecycline may guide new pathways for drug design and therapy. Tigecycline is widely used to treat complex bacterial infections. Here, authors present cryo-EM structures of tigecycline-bound eukaryotic ribosomes, revealing how it also targets the human mitoribosome with distinct binding properties. [ABSTRACT FROM AUTHOR]

Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials. Building atomistic models with molecules of varying size and density requires significant time and expertize. Here, authors describe CHARMM-GUI Multicomponent Assembler that guides complex molecular assembly and simulation input preparation under periodic boundary conditions. [ABSTRACT FROM AUTHOR]

Solid–water interfaces are crucial for clean water, conventional and renewable energy, and effective nuclear waste management. However, reflecting the complexity of reactive interfaces in continuum-scale models is a challenge, leading to oversimplified representations that often fail to predict real-world behavior. This is because these models use fixed parameters derived by averaging across a wide physicochemical range observed at the molecular scale. Recent studies have revealed the stochastic nature of molecular-level surface sites that define a variety of reaction mechanisms, rates, and products even across a single surface. To bridge the molecular knowledge and predictive continuum-scale models, we propose to represent surface properties with probability distributions rather than with discrete constant values derived by averaging across a heterogeneous surface. This conceptual shift in continuum-scale modeling requires exponentially rising computational power. By incorporating our molecular-scale understanding of solid–water interfaces into continuum-scale models we can pave the way for next generation critical technologies and novel environmental solutions. Chemistry at solid-water interfaces is crucial for all aspects of human life. Here, authors propose to use a probability-based paradigm for formalizing chemical reactions at solid-water interfaces in continuum scale models. [ABSTRACT FROM AUTHOR]