Incoming Molecules Research Articles

Temperature Dependence of Hydrotropy.

The solubility of hydrophobic solutes increases dramatically with the temperature when hydrotropes are added to water. In this paper, the mechanism of this well-known observation will be explained via statistical thermodynamics through (i) enhanced enthalpy-hydrotrope number correlation locally (around the solute) that promotes the temperature dependence and (ii) hydrotrope self-association in the bulk solution that suppresses the temperature dependence. The contribution from (i), demonstrated to be dominant for urea as a hydrotrope, signifies the weakening of interaction energies around the solute (local) than in the bulk that accompanies incoming hydrotrope molecules. Thus, studying hydrotropic solubilization along the temperature and hydrotrope concentration provides complementary information on the local-bulk difference: the local accumulation of hydrotropes around the solute, driven by the enhanced local hydrotrope self-association, is also accompanied by the overall local weakening of energetic interactions, reflecting the fluctuational nature of hydrotrope association and the mediating role of water molecules.

Orientation transitions and chiral assemblies of para-terphenyl molecules on Cd(0001).

The interplay between orientation transition and chiral self-assemblies of para-terphenyl (P3P) molecules on the Cd(0001) surface has been investigated using low temperature scanning tunneling microscopy and density functional theory calculations. Three distinct molecular orientations have been discerned from the self-assembled thin films of P3P. At the low coverage, flat-lying molecules appear in the homochiral domains with the incommensurate registry to the substrate. With the coverage increasing, the incoming molecules are incorporated into the first layer with edge-on orientation and form the self-assembled zigzag chains. The alternative arrangement of zigzag chains with opposite chirality leads to the formation of a c(4 × 2) superstructure, in which the tilted molecules exhibit orientational frustration and fuzzy noises. The analysis of the tunneling spectra reveals that the electronic structure of P3P layers is contingent upon the hybridization between the electronic states of P3P molecules and the Cd(0001) surface. These results provide important insights into the interplay between orientational transition and chiral assembly of P3P molecules on metal substrates.

Metal-Ligand Cooperation with Thiols as Transient Cooperative Ligands: Acceleration and Inhibition Effects in (De)Hydrogenation Reactions.

ConspectusOver the past two decades, we have developed a series of pincer-type transition metal complexes capable of activating strong covalent bonds through a mode of reactivity known as metal-ligand cooperation (MLC). In such systems, an incoming substrate molecule simultaneously interacts with both the metal center and ligand backbone, with one part of the molecule reacting at the metal center and another part at the ligand. The majority of these complexes feature pincer ligands with a pyridine core, and undergo MLC through reversible dearomatization/aromatization of this pyridine moiety. This MLC platform has enabled us to perform a variety of catalytic dehydrogenation, hydrogenation, and related reactions, with high efficiency and selectivity under relatively mild conditions.In a typical catalytic complex that operates through MLC, the cooperative ligand remains coordinated to the metal center throughout the entire catalytic process, and this complex is the only catalytic species involved in the reaction. As part of our ongoing efforts to develop new catalytic systems featuring MLC, we have recently introduced the concept of transient cooperative ligand (TCL), i.e., a ligand that is capable of MLC when coordinated to a metal center, but the coordination of which is reversible rather than permanent. We have thus far employed thiol(ate)s as TCLs, in conjunction with an acridanide-based ruthenium(II)-pincer catalyst, and this has resulted in remarkable acceleration and inhibition effects in various hydrogenation and dehydrogenation reactions. A cooperative thiol(ate) ligand can be installed in situ by the simple addition of an appropriate thiol in an amount equivalent to the catalyst, and this has been repeatedly shown to enable efficient bond activation by MLC without the need for other additives, such as base. The use of an ancillary thiol ligand that is not fixed to the pincer backbone allows the catalytic system to benefit from a high degree of tunability, easily implemented by varying the added thiol. Importantly, thiols are coordinatively labile enough under typical catalytic conditions to leave a meaningful portion of the catalyst in its original unsaturated form, thereby allowing it to carry out its own characteristic catalytic activity. This generates two coexisting catalyst populations─one that contains a thiol(ate) ligand and another that does not─and this may lead to different catalytic outcomes, namely, enhancement of the original catalytic activity, inhibition of this activity, or the occurrence of diverging reactivities within the same catalytic reaction mixture. These thiol effects have enabled us to achieve a series of unique transformations, such as thiol-accelerated base-free aqueous methanol reforming, controlled stereodivergent semihydrogenation of alkynes using thiol as a reversible catalyst inhibitor, and hydrogenative perdeuteration of C═C bonds without using D2, enabled by a combination of thiol-induced acceleration and inhibition. We have also successfully realized the unprecedented formation of thioesters through dehydrogenative coupling of alcohols and thiols, as well as the hydrogenation of organosulfur compounds, wherein the cooperative thiol serves as a reactant or product. In this Account, we present an overview of the TCL concept and its various applications using thiols.

The adsorption of carbon and nitrogen oxides on the PuO2 {110} surface: A DFT + U study

The adsorptions of CO, CO2, N2O, NO and NO2 on the PuO2 {110} surface have been studied using density functional theory with a Hubbard U correction. Different approaching pathways are analysed to locate physisorbed states. Starting from the most stable physisorbed structures, reaction paths leading to stable chemisorbed structures are determined. The chemisorptions of CO, CO2, N2O, NO and NO2 are extensively studied and the following aspects are compared: molecule/surface structures, atomic magnetic moments, surface work functions, density of states, adsorption energies and reaction barriers. With the exception of N2O, chemisorption is energetically favourable on PuO2 {110}. Dioxide adsorption is more favourable than monoxide, and the chemisorption of nitrogen monoxide/dioxide is easier than carbon monoxide/dioxide. Chemisorption of monoxides reduces a neighbouring surface Pu, thereby providing an active site for interaction with further incoming residual molecules.

Dynamic Transformation of High-Architectural Nanocrystal Superlattices upon Solvent Molecule Exposure.

The cluster-based body-centered-cubic superlattice (cBCC SL) represents one of the most complicated structures among reported nanocrystal assemblies, comprised of 72 truncated tetrahedral quantum dots per unit cell. Our previous report revealed that truncated tetrahedral quantum dots within cBCC SLs possessed highly controlled translational and orientational order owing to an unusual energetic landscape based on the balancing of entropic and enthalpic contributions during the assembly process. However, the cBCC SL's structural transformability and mechanical properties, uniquely originating from such complicated nanostructures, have yet to be investigated. Herein, we report that cBCC SLs can undergo dynamic transformation to face-centered-cubic SLs in response to post-assembly molecular exposure. We monitored the dynamic transformation process using in situ synchrotron-based small-angle X-ray scattering, revealing a dynamic transformation involving multiple steps underpinned by interactions between incoming molecules and TTQDs' surface ligands. Furthermore, our mechanistic study demonstrated that the precise configuration of TTQDs' ligand molecules in cBCC SLs was key to their high structural transformability and unique jelly-like soft mechanical properties. While ligand molecular configurations in nanocrystal SLs are often considered minor features, our findings emphasize their significance in controlling weak van der Waals interactions between nanocrystals within assembled SLs, leading to previously unremarked superstructural transformability and unique mechanical properties. Our findings promote a facile route toward further creation of soft materials, nanorobotics, and out-of-equilibrium assemblies based on nanocrystal building blocks.

Nickel-Catalyzed Ethylene Copolymerization with Vinylalkoxysilanes: A Computational Study.

Since the discovery of α-diimine catalysts in 1995, an extensive series of Brookhart-type complexes have shown their excellence in catalyzing ethylene polymerizations with remarkable activity and a high molecular weight. However, although this class of palladium complexes has proven proficiency in catalyzing ethylene copolymerization with various polar monomers, the α-diimine nickel catalysts have generally exhibited a much worse performance in these copolymerizations compared to their palladium counterparts. Recently, Brookhart et al. reported a notable exception, demonstrating that α-diimine nickel catalysts could catalyze the ethylene copolymerization with some vinylalkoxysilanes effectively, producing functionalized polyethylene incorporating trialkoxysilane (-Si(OR)3) groups. This breakthrough is significant since Pd-catalyzed copolymerizations are commercially less usable due to the high cost of palladium. Thus, the utilization of Ni, given its abundance in raw materials and cost-effectiveness, is a landmark in ethylene/polar vinyl monomer copolymerization. Inspired by these findings, we used density functional theory (DFT) calculations to investigate the mechanistic study of ethylene copolymerization with vinyltrimethoxysilane (VTMoS) catalyzed by Brookhart-type nickel catalysts, aiming to elucidate the molecular-level understanding of this unique reaction. Initially, the nickel complexes and cationic active species were optimized through DFT calculations. Subsequently, we explored the mechanisms including the chain initiation, chain propagation, and chain termination of ethylene homopolymerization and copolymerization catalyzed by Brookhart-type complexes. Finally, we conducted an energetic analysis of both the in-chain and chain-end of silane enchainment. It was found that chain initiation is the dominant step in the ethylene homopolymerization catalyzed by the α-diimine Ni complex. The 1,2- and 2,1-insertion of vinylalkoxysilane exhibit similar barriers, explaining the fact that both five-membered and four-membered chelates were identified experimentally. After the VTMoS insertion, the barriers of ethylene reinsertion become higher, indicating that this step is the rate-determining step, which could be attributed to the steric hindrance between the incoming ethylene and the bulky silane substrate. We have also reported the energetic analysis of the distribution of polar substrates. The dominant pathway of chain-end -Si(OR)3 incorporation is suggested as chain-walking → ring-opening → ethylene insertion, and the preference of chain-end -Si(OR)3 incorporation is primarily attributed to the steric repulsion between the pre-inserted silane group and the incoming ethylene molecule, reducing the likelihood of in-chain incorporation.

The elementary reactions for incorporation into crystals

The growth rates of crystals are largely dictated by the chemical reaction between solute and kinks, in which a solute molecule severs its bonds with the solvent and establishes new bonds with the kink. Details on this sequence of bond breaking and rebuilding remain poorly understood. To elucidate the reaction at the kinks we employ four solvents with distinct functionalities as reporters on the microscopic structures and their dynamics along the pathway into a kink. We combine time-resolved in situ atomic force microscopy and x-ray and optical methods with molecular dynamics simulations. We demonstrate that in all four solvents the solute, etioporphyrin I, molecules reach the steps directly from the solution; this finding identifies the measured rate constant for step growth as the rate constant of the reaction between a solute molecule and a kink. We show that the binding of a solute molecule to a kink divides into two elementary reactions. First, the incoming solute molecule sheds a fraction of its solvent shell and attaches to molecules from the kink by bonds distinct from those in its fully incorporated state. In the second step, the solute breaks these initial bonds and relocates to the kink. The strength of the preliminary bonds with the kink determines the free energy barrier for incorporation into a kink. The presence of an intermediate state, whose stability is controlled by solvents and additives, may illuminate how minor solution components guide the construction of elaborate crystal architectures in nature and the search for solution compositions that suppress undesirable or accelerate favored crystallization in industry.

Assembly mechanism of the inflammasome sensor AIM2 revealed by single molecule analysis

Pathogenic dsDNA prompts AIM2 assembly leading to the formation of the inflammasome, a multimeric complex that triggers the inflammatory response. The recognition of foreign dsDNA involves AIM2 self-assembly concomitant with dsDNA binding. However, we lack mechanistic and kinetic information on the formation and propagation of the assembly, which can shed light on innate immunity’s time response and specificity. Combining optical traps and confocal fluorescence microscopy, we determine here the association and dissociation rates of the AIM2-DNA complex at the single molecule level. We identify distinct mechanisms for oligomer growth via the binding of incoming AIM2 molecules to adjacent dsDNA or direct interaction with bound AIM2 assemblies, resembling primary and secondary nucleation. Through these mechanisms, the size of AIM2 oligomers can increase fourfold in seconds. Finally, our data indicate that single AIM2 molecules do not diffuse/scan along the DNA, suggesting that oligomerization depends on stochastic encounters with DNA and/or DNA-bound AIM2.

Plant-Derived Epi-Nutraceuticals as Potential Broad-Spectrum Anti-Viral Agents.

Although the COVID-19 pandemic appears to be diminishing, the emergence of SARS-CoV-2 variants represents a threat to humans due to their inherent transmissibility, immunological evasion, virulence, and invulnerability to existing therapies. The COVID-19 pandemic affected more than 500 million people and caused over 6 million deaths. Vaccines are essential, but in circumstances in which vaccination is not accessible or in individuals with compromised immune systems, drugs can provide additional protection. Targeting host signaling pathways is recommended due to their genomic stability and resistance barriers. Moreover, targeting host factors allows us to develop compounds that are effective against different viral variants as well as against newly emerging virus strains. In recent years, the globe has experienced climate change, which may contribute to the emergence and spread of infectious diseases through a variety of factors. Warmer temperatures and changing precipitation patterns can increase the geographic range of disease-carrying vectors, increasing the risk of diseases spreading to new areas. Climate change may also affect vector behavior, leading to a longer breeding season and more breeding sites for disease vectors. Climate change may also disrupt ecosystems, bringing humans closer to wildlife that transmits zoonotic diseases. All the above factors may accelerate the emergence of new viral epidemics. Plant-derived products, which have been used in traditional medicine for treating pathological conditions, offer structurally novel therapeutic compounds, including those with anti-viral activity. In addition, plant-derived bioactive substances might serve as the ideal basis for developing sustainable/efficient/cost-effective anti-viral alternatives. Interest in herbal antiviral products has increased. More than 50% of approved drugs originate from herbal sources. Plant-derived compounds offer diverse structures and bioactive molecules that are candidates for new drug development. Combining these therapies with conventional drugs could improve patient outcomes. Epigenetics modifications in the genome can affect gene expression without altering DNA sequences. Host cells can use epigenetic gene regulation as a mechanism to silence incoming viral DNA molecules, while viruses recruit cellular epitranscriptomic (covalent modifications of RNAs) modifiers to increase the translational efficiency and transcript stability of viral transcripts to enhance viral gene expression and replication. Moreover, viruses manipulate host cells' epigenetic machinery to ensure productive viral infections. Environmental factors, such as natural products, may influence epigenetic modifications. In this review, we explore the potential of plant-derived substances as epigenetic modifiers for broad-spectrum anti-viral activity, reviewing their modulation processes and anti-viral effects on DNA and RNA viruses, as well as addressing future research objectives in this rapidly emerging field.

Drug discovery and therapeutic perspectives for proximal tubulopathies

The efficient reabsorption of essential nutrients by epithelial cells in the proximal tubule of the kidney is crucial for maintaining homeostasis. This process relies heavily on a complex ecosystem of vesicular trafficking pathways. At the center of this network, the lysosome plays a pivotal role in processing incoming molecules, sensing nutrient availability, sorting receptors and transporters, and balancing differentiation and proliferation in the tubular epithelial cells. Disruptions in these fundamental processes can lead to proximal tubulopathy-a condition characterized by the dysfunction of the tubular cells followed by the presence of low-molecular-weight proteins and solutes in urine. If left untreated, proximal tubulopathy can progress to chronic kidney disease and severe complications. Functional studies of rare inherited disorders affecting the proximal tubule have gleaned actionable insights into fundamental mechanisms of homeostasis while revealing drug targets for therapeutic discovery and development. In this mini review, we explore hereditary proximal tubulopathies as a paradigm of kidney homeostasis disorders, discussing the factors contributing to tubular dysfunction. In addition, we shed light on the current landscape of drug discovery approaches used to identify actionable targets and summarize the preclinical pipeline of potential therapeutic agents. These efforts may ultimately lead to new treatment avenues for proximal tubulopathies, which are currently inadequately tackled by existing therapies. Through this article, our hope is to promote academia-industry partnerships and advocate for research consortia that can accelerate the effective translation of knowledge advances into innovative therapies addressing the huge unmet needs of individuals with these debilitating diseases.

Historical Aspects of Restriction Endonucleases as Intelligent Scissors for Genetic Engineering

Restriction endonucleases are a component of restriction–modification systems, where the main biological function is to protect bacterial cells from incoming foreign DNA molecules. There are four main types of restriction enzymes (types I, II, III, and IV), which differ in protein composition, cofactor requirements, and mode of action. The most studied are representatives of type II, which specifically recognize DNA sequences of 4–8 bp and catalyze DNA cleavage within these sequences or not far from them. The exceptional precision of type II enzymes has made them indispensable for DNA manipulations. Although hundreds of DNA restriction enzymes are currently known, there is still a need for enzymes that recognize new DNA targets. For this reason, the discovery of new natural restriction endonucleases and rational design of their properties (to obtain enzymes with high specificity for a unique nucleotide sequence at a restriction site and without nonspecific activity) will expand the list of enzymes for use in biotechnology and genetic engineering. This review briefly touches upon the main types of restriction endonucleases, their classification, nomenclature, and typical properties, and it concisely describes approaches to the construction of enzymes with altered properties.

Fast Water Transport in UTSA‐280 via a Knock‐Off Mechanism

AbstractWater and other small molecules frequently coordinate within metal‐organic frameworks (MOFs). These coordinated molecules may actively engage in mass transfer, moving together with the transport molecules, but this phenomenon has yet to be examined. In this study, we explore a unique water transfer mechanism in UTSA‐280, where an incoming water molecule can displace a coordinated molecule for mass transfer. We refer to this process as the “knock‐off” mechanism. Despite UTSA‐280 possessing one‐dimensional channels, the knock‐off transport enables water movement along the other two axes, effectively simulating a pseudo‐three‐dimensional mass transfer. Even with a relatively narrow pore width, the knock‐off mechanism enables a high water flux in the UTSA‐280 membrane. The knock‐off mechanism also renders UTSA‐280 superior water/ethanol diffusion selectivity for pervaporation. To validate this unique mechanism, we conducted 1H and 2H solid‐state NMR on UTSA‐280 after the adsorption of deuterated water. We also derived potential energy diagrams from the density functional theory to gain atomic‐level insight into the knock‐off and the direct‐hopping mechanisms. The simulation findings reveal that the energy barrier of the knock‐off mechanism is marginally lower than the direct‐hopping pathway, implying its potential role in enhancing water diffusion in UTSA‐280.

Fast Water Transport in UTSA-280 via a Knock-Off Mechanism.

Water and other small molecules frequently coordinate within metal-organic frameworks (MOFs). These coordinated molecules may actively engage in mass transfer, moving together with the transport molecules, but this phenomenon has yet to be examined. In this study, we explore a unique water transfer mechanism in UTSA-280, where an incoming water molecule can displace a coordinated molecule for mass transfer. We refer to this process as the "knock-off" mechanism. Despite UTSA-280 possessing one-dimensional channels, the knock-off transport enables water movement along the other two axes, effectively simulating a pseudo-three-dimensional mass transfer. Even with a relatively narrow pore width, the knock-off mechanism enables a high water flux in the UTSA-280 membrane. The knock-off mechanism also renders UTSA-280 superior water/ethanol diffusion selectivity for pervaporation. To validate this unique mechanism, we conducted 1 H and 2 H solid-state NMR on UTSA-280 after the adsorption of deuterated water. We also derived potential energy diagrams from the density functional theory to gain atomic-level insight into the knock-off and the direct-hopping mechanisms. The simulation findings reveal that the energy barrier of the knock-off mechanism is marginally lower than the direct-hopping pathway, implying its potential role in enhancing water diffusion in UTSA-280.

Desolvation Induced Conformational Transition in a Cryptophane Host: Crystal To Crystal Transformation.

Cryptophanes show different conformations in solution and solid state depending upon various factors, such as the length of connecting linkers, medium, and nature of the incoming guest molecule(s). A cyclotriguaiacylenes (CTG) based cryptophane molecule was synthesized using click chemistry containing three triazole linkers and studied as well. This molecule shows two conformations, out-out crown-crown (CC), and out-in CC, in the presence or absence of guest molecule(s), as studied both in solution and solid state. The out-in CC, in which both CTG fragments are in crown conformation with one crown sitting above the other, could be obtained by slow escape of the trapped acetone molecules from out-out CC in solid state. This transformation could be obtained through a single-crystal-to-single-crystal (SCSC) transformation from a large volume out-out CC to a smaller volume out-in CC conformation which is also supported by density functional theory calculations.

A DFT Study of the Copolymerization of Methyl Vinyl Sulfone and Ethylene Catalyzed by Phosphine–Sulfonate and α-Diimine Palladium Complexes

Density functional theory (DFT) calculations were comparatively carried out to reveal the origins of different catalytic performances from phosphine–benzene sulfonate (A, [{P^O}PdMe(L)] (P^O = Κ2-P,O-Ar2PC6H4SO3 with Ar = 2-MeOC6H4)) and α-diimine (B, [{N^N}PdMe(Cl)] (N^N = (ArN=C(Me)-C(Me)=NAr) with Ar = 2,6-iPr2C6H3)) palladium complexes toward the copolymerization of ethylene and methyl vinyl sulfone (MVS). Having achieved agreement between theory and experiment, it was found that the favorable 2,1-selective insertion of MVS into phosphine–sulfonate palladium complex A was due to there being less structural deformations in the catalyst and monomer. Both the MVS and ethylene insertions were calculated, and the former was found to be more favorable for chain initiation and chain propagation. In the case of α-diimine palladium system B, the resulting product of the first MVS insertion was quite stable, and the stronger O-backbiting interaction hampered the insertion of the incoming ethylene molecule. These computational results are expected to provide some hints for the design of transition metal copolymerization catalysts.

Electrostatic Modulation of Intramolecular and Intermolecular Interactions during the Formation of an Amyloid-like Assembly.

The mechanism of protein aggregation can be broadly viewed as a shift from the native-state stabilizing intramolecular to the aggregated-phase sustaining intermolecular interactions. Understanding the role of electrostatic forces on the extent of modulation of this switch has recently evolved as a topic of monumental significance as protein aggregation has lately been connected to charge modifications of an aging proteome. To decipher the distinctive role of electrostatic forces on the extremely complicated phase separation landscape, we opted for a combined in vitro-in silico approach to ascertain the structure-dynamics-stability-aggregability relationship of the functional tandem RRM domains of the ALS-related protein TDP-43 (TDP-43tRRM), under a bivariate solution condition in terms of pH and salt concentration. Under acidic pH conditions, the native TDP-43tRRM protein creates an aggregation-prone entropically favorable partially unfolded conformational landscape due to enthalpic destabilization caused by the protonation of the buried ionizable residues and consequent overwhelming fluctuations of selective segments of the sequence leading to anti-correlated movements of the two domains of the protein. The evolved fluffy ensemble with a comparatively exposed backbone then easily interacts with incoming protein molecules in the presence of salt via typical amyloid-aggregate-like intermolecular backbone hydrogen bonds with a considerable contribution originating from the dispersion forces. Subsequent exposure to excess salt at low pH conditions expedites the aggregation process via an electrostatic screening mechanism where salt shows preferential binding to the positively charged side chain. The applied target observable-specific approach complementarity unveils the hidden information landscape of an otherwise complex process with unquestionable conviction.

Computational Investigation of Precursor Blocking during Area-Selective Atomic Layer Deposition Using Aniline as a Small-Molecule Inhibitor

Area-selective atomic layer deposition using small-molecule inhibitors (SMIs) involves vapor-phase dosing of inhibitor molecules, resulting in an industry-compatible approach. However, the identification of suitable SMIs that yield a high selectivity remains a challenging task. Recently, aniline (C6H5NH2) was shown to be an effective SMI during the area-selective deposition (ASD) of TiN, giving 6 nm of selective growth on SiO2 in the presence of Ru and Co non-growth areas. In this work, using density functional theory (DFT) and random sequential adsorption (RSA) simulations, we investigated how aniline can effectively block precursor adsorption on specific areas. Our DFT calculations confirmed that aniline selectively adsorbs on Ru and Co non-growth areas, whereas its adsorption on the SiO2 growth area is limited to physisorption. DFT reveals two stable adsorption configurations of aniline on the metal surfaces. Further calculations on the aniline-functionalized surfaces show that the aniline inhibitor significantly reduces the interaction of Ti precursor, tetrakis(dimethylamino)titanium, with the non-growth area. In addition, RSA simulations showed that the co-presence of two stable adsorption configurations allows for a high surface inhibitor coverage on both Co and Ru surfaces. As the surface saturates, there is a transition from the thermodynamically most favorable adsorption configuration to the sterically most favorable adsorption configuration, which results in a sufficiently dense inhibition layer, such that an incoming precursor molecule cannot fit in between the adsorbed precursor molecules. We also found that, as a result of the catalytic activity of the metallic non-growth area, further reactions of inhibitor molecules, such as hydrogenolysis, can play a role in precursor blocking.

Определение оптимальной системы скачков воздухозаборного устройства с учетом диссоциации молекул набегающего воздуха

Определение оптимальной системы скачков воздухозаборного устройства с учетом диссоциации молекул набегающего воздуха

Spatial organisation of the E. coli outer membrane from multiscale computer simulations.

The cell envelope that surrounds Gram-negative bacteria is composed of two membranes (the inner and outer) which are separated by an aqueous region known as the periplasm. Together these three regions provide the bacterium with a formidable defence against unwanted incoming molecules, including antibiotics. The outer membrane contains a range of beta-barrel proteins of varying sizes and functions and in terms of its lipidic composition, it has lipopolysaccharides (LPS) in the outer leaflet and phospholipids in the inner leaflet. We are using multiscale simulations in combination with the experimental work (including native mass spectrometry, cross-linking studies and AFM) of our colleagues to develop a picture of the spatial organisation of the outer membrane of E. coli. Our work has shown that outer membrane proteins (OMPs) are not uniformly distributed throughout the membrane but occupy high protein density regions or ‘OMP islands’. These islands are separated by regions of high LPS (upper leaflet) and phospholipid (lower leaflet), in which there are hardly any proteins. We provide details of our current view of the organisation of OMP islands and briefly describe how this is being incorporated into our efforts to study antimicrobial penetration into the outer membrane. We also discuss the advancements in our computational models that are enabling us to expand the scope of our studies to larger systems by using ultra coarse-grained approaches. Overall, our studies are now revealing a very different picture of the E. coli surface than the one presented in textbooks.

Lattice light-sheet microscopy and evaluation of dendritic transport in cultured hippocampal tissue reveal high variability in mobility of the KIF1A motor domain and entry into dendritic spines

The unique morphology of neurons consists of a long axon and a highly variable arbour of dendritic processes, which assort neuronal cells into the main classes. The dendritic tree serves as the main domain for receiving synaptic input. Therefore, to maintain the structure and to be able to plastically change according to the incoming stimuli, molecules and organelles need to be readily available. This is achieved mainly via bi-directional transport of cargo along the microtubule lattices. Analysis of dendritic transport is lagging behind the investigation of axonal transport. Moreover, addressing transport mechanisms in tissue environment is very challenging and, therefore, rare. We employed high-speed volumetric lattice light-sheet microscopy and single particle tracking of truncated KIF1A motor protein lacking the cargo-binding domain. We focused our analysis on dendritic processes of CA1 pyramidal neurons in cultured hippocampal tissue. Analysis of individual trajectories revealed detailed information about stalling and high variability in movement and speed, and biased directionality of KIF1A. Furthermore, we could also observe KIF1A shortly entering into dendritic spines. We provide a workflow to analyse variations in the speed and direction of motor protein movement in dendrites that are either intrinsic properties of the motor domain or depend on the structure and modification of the microtubule trails.