Gasdermins (GSDMs) are pore-forming proteins that trigger pyroptosis, an inflammatory cell death process that plays a crucial role in immunity. Recent experiments and atomistic simulations have shed light on GSDM molecular structure and their conformational transitions when inserting into the membrane to form pores. However, the dynamics of pore assembly remain incompletely understood. In this work, we propose a minimal coarse-grained model of GSDM proteins and run extensive molecular dynamics simulations that bridge the gap between atomistic simulations on a single molecule level and biological length and time scales relevant for membrane pore assembly. We observe supramolecular structures similar to those reported in experiments: rings, slits, and arcs with significantly different pore cross-sections. By informing our model with experimental observations, we show that the dominant regulatory factors for the assembly of pores are closely related to the kinetics of monomer conformational transition from prepore to pore state. When the monomer insertion kinetics is slow (late insertion), protein interaction strength is the key quantity promoting the formation of circular pores (rings), which maximize the pore area and consequentially the transport across the pore. In the case of fast (early) insertion, the ring formation is generally suppressed; we observe a prevalence of slit-like pores that are sub-optimal for transport. Different from the late insertion scenario, the rings are here promoted by increasing the membrane coverage with proteins. Our findings provide a mechanistic basis for understanding and potentially modulating pyroptotic cell death in various physiological and disease contexts.

Regulator of cell death-1 (RCD-1) governs the heteroallelic expression of RCD-1-1 and RCD-1-2, a pair of fungal gasdermin (GSDM)-like proteins, which prevent cytoplasmic mixing during allorecognition and safeguard against mycoparasitism, genome exploitation, and deleterious cytoplasmic elements (e.g., senescence plasmids) by effecting a form of cytolytic cell death. However, the underlying mechanisms by which RCD-1 acts on the cell membrane remain elusive. Here, we demonstrate that RCD-1 binds acidic lipid membranes, forms pores, and induces membrane bending. Using atomic force microscopy (AFM) and AlphaFold, we show that RCD-1-1 and RCD-1-2 form heterodimers that further self-assemble into 14.5 nm-wide transmembrane pores ( 10 heterodimers). Moreover, through AFM force spectroscopy and micropipette aspiration, we reveal that RCD-1 proteins bend membranes with low bending moduli. This combined action of pore formation and membrane deformation may constitute a conserved mechanism within the broader GSDM family. The mechanism of RCD-1 regulated cell death in fungal cells is unknown. Here, the authors use AFM to uncover two mechanisms by which RCD-1 proteins form pores in lipid membranes, and discover a membrane bending activity

This corrects the article DOI: 10.1103/PhysRevLett.123.047801.

The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong nonlinear elasticity effects that qualitatively affect their packing in confined spaces. Using analytical theory and numerical simulation we show that kink formation entails a mixed spool-nematic ordering of double-stranded DNA or RNA in spherical capsids, consisting of an outer spool domain and an inner, twisted nematic domain. These findings explain the experimentally observed nematic domains in viral capsids and imply that nonlinear elasticity must be considered to predict the configurations and dynamics of double-stranded genomes in viruses, bacterial nucleoids or gene-delivery vehicles. The nonlinear elastic theory suggests that spool-nematic ordering is a general feature of strongly confined kinkable polymers.

We propose a classical density functional theory model to study the self-assembly of polymeric surfactants on curved surfaces. We use this model to investigate the thermodynamics of phase separation of a binary mixture of size asymmetric miscible surfactants on cylindrical and spherical surfaces, and observe that phase separation driven by size alone is thermodynamically unfavorable on both cylindrical and spherical surfaces. We use the theory, supplemented by dissipative particle dynamics (DPD) simulations, to predict pattern formation on a non-uniform surface with regions of positive and negative curvature. Our results suggest potential ways to couple surface topography and polymeric surfactants to design surfaces coated with non-uniform patterns.

We explore how the stability of RNA viruses depends on genome topology and interactions between RNA and the capsid proteins. RNA is modeled as a branched polymer with 12 attractive sites (packaging signals) that can form bonds with 12 icosahedrally distributed capsid sites. The genome topology is encoded as a graph by mapping pairs of adjacent packaging signals to edges. We perform replica exchange molecular dynamics simulations and evaluate the osmotic pressure of all unique branched topologies of encapsulated RNA. We find that virion stability depends in a complex fashion on both genome topology and degree of confinement, and predict that MS2 bacteriophage should prefer a more linear genome topology.

Adenine DNA glycosylase (MutY) is a monofunctional glycosylase, removing adenines (A) misinserted opposite 8-oxo-7,8-dihydroguanine (OG), a common product of oxidative damage to DNA. Through multiscale calculations, we decipher a detailed adenine excision mechanism of MutY that is consistent with all available experimental data, involving an initial protonation step and two nucleophilic displacement steps. During the first displacement step, N-glycosidic bond cleavage is accompanied by the attack of the carboxylate group of residue Asp144 at the anomeric carbon (C1'), forming a covalent glycosyl-enzyme intermediate to stabilize the fleeting oxocarbenium ion. After departure of the excised base, water nucleophiles can be recruited to displace Asp144, completing the catalytic cycle with retention of stereochemistry at the C1' position. The two displacement reactions are found to mostly involve the movement of the oxocarbenium ion, occurring with large charge reorganization and thus sensitive to the internal electric field (IEF) exerted by the polar protein environment. Intriguingly, we find that the negatively charged carboxylate group is a good nucleophile for the oxocarbenium ion, yet an unactivated water molecule is not, and that the electric field catalysis strategy is used by the enzyme to enable its unique double-displacement reaction mechanism. A strong IEF, pointing toward 5' direction of the substrate sugar ring, greatly facilitates the second displacement reaction at the expense of elevating the barrier of the first one, thereby allowing both reactions to occur. These findings not only increase our understanding of the strategies used by DNA glycosylases to repair DNA lesions, but also have important implications for how internal/external electric field can be applied to modulate chemical reactions.

Uracil-DNA glycosylase (UDG) is a monofunctional DNA glycosylase, which is involved in the base excision repair (BER) pathway and responsible for the excision of uracil from DNA. UDG is well known for its high catalytic efficiency and substrate autocatalysis character. Here, using quantum-mechanical/molecular-mechanical (QM/MM) and QM calculations as well as molecular dynamics (MD) simulations, we propose a revised catalytic mechanism of UDG and elucidate the nature of its strong catalytic efficiency. In the initial stage of the reaction, a heterolytic C-N bond cleavage is catalyzed by a strong internal electric field which stabilizes the charge distribution of the transition state more than that of the ground state, yielding an oxocarbenium-ion-uracil-anion species. The catalytic effect of substrate phosphate groups can be included in the effect of the internal electric field, which is counterbalanced by sodium ions, explaining the longstanding discrepancy between theory and experiment. Subsequently, Asp145 acts as the general base to activate the water nucleophile to attack the oxocarbenium ion, forming an abasic site. Interestingly, the proton further transfers from Asp145 to the neutral and more solvent-exposed residue His148 to facilitate its release, which is demonstrated to be driven by the internal electric field. This work deepens our understanding of the catalytic mechanism of UDG and more generally the catalytic effect of internal electric fields in enzymes.

Alternative ('repeat') determinations of organic crystal structures deposited in the Cambridge Structural Database are analysed to characterise the nature and magnitude of the differences between structure solutions obtained by diffraction methods. Of the 3132 structure pairs considered, over 20% exhibited local structural differences exceeding 0.25 Å. In most cases (about 83%), structural optimisation using density functional theory (DFT) resolved the differences. Many of the cases where distinct and chemically significant structural differences remained after optimisation involved differently positioned hydroxyl groups, with obvious implications for the correct description of hydrogen bonding. 1H and 13C chemical shifts from solid-state NMR experiments are proposed as an independent methodology in cases where DFT optimisation fails to resolve discrepancies.

Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes, attached to a surface, bind to specific nucleotide sequences in the DNA of a target pathogen. Typically, each probe binds to a single target sequence; i.e., target-probe binding is monovalent. Here we show using computer simulations that the detection sensitivity and specificity can be improved by designing probes that bind multivalently to the entire length of the pathogen genomic DNA, such that a given probe binds to multiple sites along the target DNA. Our results suggest that multivalent targeting of long pieces of genomic DNA can allow highly sensitive and selective binding of the target DNA, even if competing DNA in the sample also contains binding sites for the same probe sequences. Our results are robust to mild fragmentation of the bacterial genome. Our conclusions may also be relevant for DNA detection in other fields, such as disease diagnostics more broadly, environmental management, and food safety.

Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity driven, suggesting general solutions with DNA organized into spool-like domains. Using analytical calculations and computer simulations of a long elastic filament confined to a spherical container, we show that the ground state is not a single spool as assumed hitherto, but an ordering mosaic of multiple homogeneously ordered domains. At low densities, we observe concentric spools, while at higher densities, other morphologies emerge, which resemble topological links. We discuss our results in the context of metallic wires, viral DNA, and flexible polymers.

Using diode laser vibration-rotation-tunneling spectroscopy near 15 Thz (500 cm−1), we have measured and assigned 142 transitions to three a-type librational subbands of the water hexamer-d12 prism. These subbands reveal dramatically enhanced (ca. 1000×) tunneling splittings relative to the ground state. This enhancement is in agreement with that observed for the water dimer, trimer, and pentamer in this same frequency region. The water prism tunneling motion has been predicted to potentially describe the motions of water in interfacial and confined environments; hence, the results presented here indicate that excitation of librational vibrations has a significant impact on the hydrogen bond dynamics in these macroscopic environments.

We report the assignment and analysis of 176 transitions belonging to a librational band of the (H2O)6 cage isomer near 525 cm-1(15 THz). From a fit of the transitions to an asymmetric top model, we observe both dramatic changes in the rotational constants relative to the ground state, indicating significant nonrigidity, and striking enhancement in the tunneling motions that break and reform the hydrogen bonds in the cluster. This is the fifth water cluster system to display such an enhancement in the 15 THz librational region, the details of which may help to elucidate the hydrogen bond dynamics occurring in bulk liquid water.

A stress tensor eigenvector projection space is created to describe reaction pathways on the (H2O)5 MP2 potential energy surface. Evidence for the stabilizing role of the O---O bonding interactions is found from the length of the recently introduced stress tensor trajectory in the stress tensor eigenvector projection space. The stress tensor trajectories demonstrate coupling behavior of the adjoining covalent (σ) O-H and hydrogen bonds due to sharing of covalent character. Additionally, the stress tensor trajectories can show dynamic coupling effects of pairs of σ bonds and of pairs of hydrogen bonds.

A stress tensor eigenvector projection space is created to describe reaction pathways on the (H2O)5 MP2 potential energy surface. Evidence for the stabilizing role of the O---O bonding interactions is found from the length of the recently introduced stress tensor trajectory in the stress tensor eigenvector projection space. The stress tensor trajectories demonstrate coupling behavior of the adjoining covalent (σ) O-H and hydrogen bonds due to sharing of covalent character. Additionally, the stress tensor trajectories can show dynamic coupling effects of pairs of σ bonds and of pairs of hydrogen bonds.

The emergence of observable properties from the organisation of the underlying potential energy landscape is analysed, spanning a full range of complexity from self-organising to glassy and jammed systems. The examples include atomic and molecular clusters, a β-barrel protein, the GNNQQNY peptide dimer, and models of condensed matter that exhibit structural glass formation and jamming. We have considered measures based on several different properties, namely, the Shannon entropy, an equilibrium thermodynamic measure that uses a sample of local minima, and indices that require additional information about the connections between local minima in the form of transition states. A frustration index is defined that correlates directly with key properties that distinguish relaxation behaviour within this diverse set. The index uses the ratio of the energy barrier to the energy difference with reference to the global minimum. The contributions for each local minimum are weighted by the equilibrium occupation probabilities. Hence we obtain fundamental insight into the connections and distinctions between systems that cover the continuum from efficient structure-seekers to landscapes that exhibit broken ergodicity and rare event dynamics.

A 3-D microfluidic system consisting of microchamber arrays embedded in a collagen hydrogel with tuneable biochemical gradients that mimics the tumour microenvironment of mammary glands was constructed for the investigation on the interactions between invasive breast cancer cells and stromal cells. The hollow microchambers in collagen provide a very similar 3-D environment to that in vivo that regulates collective cellular dynamics and behaviour, while the microfluidic channels surrounding the collagen microchamber arrays allow one to impose complex concentration gradients of specific biological molecules or drugs. We found that breast epithelial cells (MCF-10A) seeded in the microchambers formed lumen-like structures similar to those in epithelial layers. When MCF-10A cells were co-cultured with invasive breast cancer cells (MDA-MB-231), the formation of lumen-like structures in the microchambers was inhibited, indicating the capability of cancer cells to disrupt the structures formed by surrounding cells for further invasion and metastasis. Subsequent mechanism studies showed that down regulation of E-cad expression due to MMPs produced by the cancer cells plays a dominant role in determining the cellular behaviour. Our microfluidic system offers a robust platform for high throughput studies that aim to understand combinatorial effects of multiple biochemical and microenvironmental factors.

Clusters of eight water molecules play an important role in theoretical analysis of aqueous structure and dynamics but have proven to be challenging experimental targets. Here we report the high-resolution spectroscopic characterization of the water octamer. Terahertz (THz) vibration-rotation-tunneling (VRT) spectroscopy resolved 99 transitions with 1 part per million precision in a narrow range near 46.5 wave numbers, which were assigned to the h(16) octamer via detailed isotope dilution experiments. Fitting to a semi-rigid symmetric top model supports predictions of two coexisting cuboidal structures and provides precise values for the changes in their rotational constants. Comparison with theory and previous spectroscopic data provides a characterization of the two structures and the observed torsional vibration and supports the prediction that the D-2d symmetry structure is lower in energy than the S-4 isomer.

Using the quantum theory of atoms in molecules a near complete combined directed spanning quantum topology phase diagram (QTPD) was constructed from the nine (H2O)5 reaction‐pathways and five unique Poincaré–Hopf solutions that were found after an extensive search of the MP2 potential energy surface. Two new energy minima that were predicted from earlier work are found and include the first (H2O)5 conformer with a 3‐DQT quantum topology. The stress tensor Poincaré–Hopf relation indicated a preference for 2‐DQT (H2O)5 topologies as well as the presence of coupling between shared‐shell OH BCPs to the hydrogen‐bond BCPs that share an H NCP. The complexity of the near complete combined QTPD was explained in terms of the O…O bonding interactions that were found in six of the nine (H2O)5 reaction‐pathways and for all points of the combined QTPD. The stabilizing role of the O…O bonding interactions from the values of the total local energy density was explored. © 2016 Wiley Periodicals, Inc.