Stable Ensembles Research Articles

Dynamics and Collective Behavior of Chemically Propelled Janus Sphere Dimers in Complex Solvents.

The propulsion mechanisms and collective dynamics of chemically powered Janus sphere dimers at the micro- and nanoscales, confined in a quasi-two-dimensional geometry, are investigated using a coarse-grained microscopic dynamical model. These active Janus dimers consist of two identical Janus spheres, featuring a catalytic cap on one hemisphere. The chemical reaction taking place on the catalytic surface generates asymmetric concentration gradients of product molecules around the Janus sphere, leading to the self-propulsion of the dimers. Depending on the dimer configuration, they exhibit various motion behaviors such as forward propulsion, rotation, and restricted stochastic motion. Due to chemotactic effects and self-diffusiophoretic forces, ensembles of dimers spontaneously form diverse structures, such as transient clusters, stable rotational ensembles, and antiparallel aligned doublets. This study demonstrates that the configurations of Janus sphere dimers significantly influence their self-propulsion and collective behaviors, providing crucial insights for the design and control of active micro- and nanoscale systems.

Directional Construction of the Highly Stable Active-Site Ensembles at Sub-2nm to Enhance Catalytic Activity and Selectivity.

Precise control over the size, species, and breakthrough of the activity-selectivity trade-off are great challenges for sub-nano non-noble metal catalysts. Here, for the first time, a "multiheteroatom induced SMSI + in situ P activation" strategy that enables high stability and effective construction of sub-2nm metal sites for optimizing selective hydrogenation performance is developed. It is synthesized the smallest metal phosphide clusters (<2 nm) including from unary to ternary non-noble metal systems, accompanied by unprecedented thermal stability. In the proof-of-concept demonstration, further modulation of size and species results in the creation of a sub-2nm site platform, directionally achieving single atom (Ni1), Ni1+metal cluster (Ni1+Nin), or novel Ni1+metal phosphide cluster synergistic sites (Ni1+Ni2Pn), respectively. Based on thorough structure and mechanism investigation, it is found the Ni1+Ni2Pn site is motivated to achieve electronic structure self-optimizing through synergistic SMSI and site coupling effect. Therefore, it speeds up the substrate adsorption-desorption kinetics in semihydrogenation of alkyne and achieves superior catalytic activity that is 56 times higher than the Ni1 site under mild conditions. Compared to traditional active sites, this may represent the highly effective integration of atom utilization, thermal stability, and favorable site requirements for chemisorption properties and reactivities of substrates.

Mechanistic insight into the mode of inhibition of dietary flavonoids; targeting macrophage migration inhibitory factor.

Introduction: The Macrophage Migration Inhibitory Factor (MIF), a key pro-inflammatory mediator, is responsible for modulating immune responses. An array of inflammatory and autoimmune diseases has been linked to the dysregulated activity of MIF. The significance in physiological as well as pathophysiological phenomena underscores the potential of MIF as an attractive target with pharmacological relevance. Extensive research in past has uncovered a number of inhibitors, while the ISO-1, or (S, R)-3-(4-hydroxyphenyl)-4,5-dihydro-5-isoxazole acetic acid methyl ester being recognized as a benchmark standard so far. Recent work by Yang and coworkers identified five promising dietary flavonoids, with superior activity compared to the standard ISO-1. Nevertheless, the exact atomic-level inhibitory mechanism is still elusive. Methods: To improve the dynamic research, and rigorously characterize, and compare molecular signatures of MIF complexes with ISO-1 and flavonoids, principal component analysis (PCA) was linked with molecular dynamics (MD) simulations and binding free energy calculations. Results: The results suggest that by blocking the tautomerase site these small molecule inhibitors could modify the MIF activity by disrupting the intrinsic dynamics in particular functional areas. The stability matrices revealed the average deviation values ranging from 0.27-0.32nm while the residue level fluctuations indicated that binding of the selected flavonoids confer enhanced stability relative to the ISO-1. Furthermore, the gyration values extracted from the simulated trajectories were found in the range of 1.80-1.83nm. Discussion: Although all the tested flavonoids demonstrated remarkable results, the one obtained for the potent inhibitors, particularly Morin and Amentoflavone exhibited a good correlation with biological activity. The PCA results featured relatively less variance and constricted conformational landscape than others. The stable ensembles and reduced variation in turns might be the possible reasons for their outstanding performance documented previously. The results from the present exploration provide a comprehensive understanding of the molecular complexes formed by flavonoids and MIF, shedding light on their potential roles and impacts. Future studies on MIF inhibitors may benefit from the knowledge gathered from this investigation.

Properties of stable ensembles of Euclidean random matrices.

We study the spectrum of a system of coupled disordered harmonic oscillators in the thermodynamic limit. This Euclidean random matrix ensemble has been suggested as a model for the low temperature vibrational properties of glass. Exact numerical diagonalization is performed in three and two spatial dimensions, which is accompanied by a detailed finite size analysis. It reveals a low-frequency regime of sound waves that are damped by Rayleigh scattering. At large frequencies localized modes exist. In between, the central peak in the vibrational density of states is well described by Wigner's semicircle law for not too large disorder, as is expected for simple random matrix systems. We compare our results with predictions from two recent self-consistent field theories.

Catalyst control over pentavalent stereocentres

A monumental diversity of catalytic methods imparts the ability to select one of two configurations of tetravalent stereocentres. Conversely, catalyst control over pentavalent stereocentres, where a fifth moiety bound to the central atom encodes an expanded stereochemical space, remained a challenge to be accomplished. Herein, we report the feasibility of the catalytic tractability of pentavalent stereocentres. A bifunctional iminophosphorane thiourea catalyst enables enantio- and diastereocontrol over pentavalent phosphoranes to differentiate configurationally stable enantiomers and ensembles of diastereomers which emerge together from a single stereocentre. The desired dioxophosphorane stereoisomers are obtained with excellent yield and selectivity (up to 99% yield, 96:4 e.r. and 99:1 d.r.), while stereodivergent catalysis reroutes the reaction for selective access to each of the viable stereoisomeric states of pentavalent phosphoranes. Considering the diversity of high-valent main group species, it is expected that catalyst control over pentavalent stereocentres significantly increases the synthetically addressable stereochemical space.

Inferring Pathways of Oxidative Folding from Prefolding Free Energy Landscapes of Disulfide-Rich Toxins.

Short, cysteine-rich peptides can exist in stable or metastable structural ensembles due to the number of possible patterns of formation of their disulfide bonds. One interesting subset of this peptide group is the conotoxins, which are produced by aquatic snails in the family Conidae. The μ conotoxins, which are antagonists and blockers of the voltage-gated sodium channel, exist in a folding spectrum: on one end of the spectrum are more hirudin-like folders, which form disulfide bonds and then reshuffle them, leading to an ensemble of kinetically trapped isomers, and on the other end are more BPTI-like folders, which form the native disulfide bonds one by one in a particular order, leading to a preponderance of conformations existing in a single stable state. In this Article, we employ the composite diffusion map approach to study the unified free energy surface of prefolding μ-conotoxin equilibrium. We identify the two most important nonlinear collective modes of the unified folding landscape and demonstrate that in the absence of their disulfides, the conotoxins can be thought of as largely disordered polymers. A small increase in the number of hydrophobic residues in the protein shifts the free energy landscape toward hydrophobically collapsed coil conformations responsible for cysteine proximity in hirudin-like folders, compared to semiextended coil conformations with more distal cysteines in BPTI-like folders. Overall, this work sheds important light on the folding processes and free energy landscapes of cysteine-rich peptides and demonstrates the extent to which sequence and length contribute to these landscapes.

Exercise accelerates place cell representational drift

Stable neural ensembles are often thought to underlie stable learned behaviors and memory. Recent longitudinal experiments, however, that tracked the activity of the same neurons over days to weeks have shown that neuronal activity patterns can change over extended timescales even if behaviors remain the same - a phenomenon termed representational drift1. We have tested whether neural circuit remodeling, defined as any change in structural connectivity, contributes to representational drift. To do this, we tracked how hippocampal CA1 spatial representations of a familiar environment change with time in conventionally housed mice relative to mice housed with a running wheel. Voluntary exercise is an environmental stimulus that promotes hippocampal circuit remodeling, primarily via promoting adult neurogenesis in the dentate gyrus. Adult neurogenesis alters structural connectivity patterns, as the integration of adult-generated granule cells (abGCs) is a competitive process where new input-output synaptic connections may co-exist and/or even replace existing synaptic connections2. Comparing the spatial activity of downstream hippocampal CA1 place cells in the same familiar environment over two weeks, we found that the activity of place cells in exercise mice exhibited accelerated representational drift compared to control mice, suggesting that hippocampal circuit remodeling may indeed drive representational drift.

Disordered-ordered protein binary classification by circular dichroism spectroscopy.

Intrinsically disordered proteins are abundant in nature and responsible for a plethora of cellular functions. They lack a stable tertiary structure and form dynamic conformational ensembles due to their characteristic physicochemical properties and amino acid composition. While numerous bioinformatics tools have been developed for in silico disorder prediction in the last decades, there is a need for experimental methods to verify the disordered state. CD spectroscopy is widely used for protein secondary structure analysis. Even without providing high-resolution information, it is especially useful when NMR, X-ray, or other techniques are problematic or one simply needs a fast technique to verify the structure of proteins. Here, we proposed an automatized binary disorder-order classification method by analyzing far-UV CD spectroscopy data. The method needs CD data at only three wavelength points, making high-throughput data collection possible. The mathematical analysis applies the k-nearest neighbor algorithm with cosine distance function, which is independent of the spectral amplitude and thus free of concentration determination errors. To reach the best classification accuracy, CD of the protein should be measurable down to 197 nm in good quality. However, the method can be used even if the spectrum can be recorded down to the wavelength of 212 nm due to the strong absorbance of the samples. The method is implemented on a webserver (https://bestsel.elte.hu/idp_classification.php) and freely available for academic users to help the experimental identification of intrinsically disordered proteins (IDPs) and the verification of the results of bioinformatics tools. This study was supported by the National Research, Development and Innovation Office of Hungary (grants 2017-1.2.1-NKP-2017-00002, PD135510, K120391, K125340, K131702, K138937 and 2019-2.1.11-TÉT-2020-00101). SRCD measurements were supported by SOLEIL (Proposals 20181890, 20191810, and 20200751).

Long-term stability of cortical ensembles.

Neuronal ensembles, coactive groups of neurons found in spontaneous and evoked cortical activity, are causally related to memories and perception, but it is still unknown how stable or flexible they are over time. We used two-photon multiplane calcium imaging to track over weeks the activity of the same pyramidal neurons in layer 2/3 of the visual cortex from awake mice and recorded their spontaneous and visually evoked responses. Less than half of the neurons remained active across any two imaging sessions. These stable neurons formed ensembles that lasted weeks, but some ensembles were also transient and appeared only in one single session. Stable ensembles preserved most of their neurons for up to 46 days, our longest imaged period, and these 'core' cells had stronger functional connectivity. Our results demonstrate that neuronal ensembles can last for weeks and could, in principle, serve as a substrate for long-lasting representation of perceptual states or memories.

Crystal Packing‐Guided Construction of Hetero‐Oligomeric Peptidic Ensembles as Synthetic 3‐in‐1 Transporters

Strategies to generate heteromeric peptidic ensembles via a social self-sorting process are limited. Herein, we report a crystal packing-inspired social self-sorting strategy broadly applicable to diverse types of H-bonded peptidic frameworks. Specifically, a crystal structure of H-bonded alkyl chain-appended monopeptides reveals an inter-chain separation distance of 4.8 Å dictated by the H-bonded amide groups, which is larger than 4.1 Å separation distance desired by the tightly packed straight alkyl chains. This incompatibility results in loosely packed alkyl chains, prompting us to investigate and validate the feasibility of applying bulky tert-butyl groups, modified with an anion-binding group, to alternatively interpenetrate the straight alkyl chains, modified with a crown ether group. Structurally, this social self-sorting approach generates highly stable hetero-oligomeric ensembles, having alternated anion- and cation-binding units vertically aligned to the same side. Functionally, these hetero-oligomeric ensembles promote transmembrane transport of cations, anions and more interestingly zwitterionic species such as amino acids.

Remediation of Wastewater from Chlorpyrifos Pesticide by Nano-Gold Photocatalyst

AbstractSuccessful disintegration of Chlorpyrifos pesticide by nearly monodisperse nano-gold photcatalyst (∼10 nm) for remediation of wastewater has been reported in current studies. Nano-Gold dispersion reaction with Chlorpyrifos solutions completes in 45 minutes at ambient temperature under the normal daylight and exhibit systematic variations in the solution color from wine red to pink to light sky blue and finally transforming into a transparent solution with fine precipitates. UV-Vis absorption studies correlates well with the systematic color changes as observed in the nano-gold treated Chlorpyrifos solutions with time. The characteristic localized surface plasmon resonance peak of nanogold dispersion observed at 529 nm red shifts to weak, medium and strong intensity peaks at ∼ 640 nm, 740 nm and 890 nm on increasing chlorpyrifos concentration owing to the aggregation of gold nanoparticles in small to bigger sized clusters. The fine turbidity in final transparent solution further confirms the aggregation of nanogold particles into stable bigger ensembles. IR transmission spectra of final transparent solutions showed disappearance of Chlorpyrifos νC-Cl and phosphorothioate functional group peaks indicating degradation of chlorpyrifos.

Formation of stable and responsive collective states in suspensions of active colloids

Many animal species organise into disordered swarms, polarised flocks or swirls to protect from predators or optimise foraging. Previous studies suggest that such collective states are related to a critical point, which could explain their balance between robustness to noise and high responsiveness regarding external perturbations. Here we provide experimental evidence for this idea by investigating the stability of swirls formed by light-responsive active colloids which adjust their individual motion to positions and orientations of neighbours. Because their behaviour can be precisely tuned, controlled changes between different collective states can be achieved. During the transition between stable swirls and swarms we observe a maximum of the group’s susceptibility indicating the vicinity of a critical point. Our results support the idea of system-independent organisation principles of collective states and provide useful strategies for the realisation of responsive yet stable ensembles in microrobotic systems.

Population dynamics of driven autocatalytic reactive mixtures.

Motivated by the effect of electroautocatalysis (explicit concentration dependence) on the stability of electrochemically driven phase-separating single particles, we apply the Fokker-Planck equation to describe the population dynamics of a general ensemble of chemically reactive particles. For phase-separating ensembles, we show that mosaic instability (from a homogeneous initial state to a multimodal probability distribution) may be suppressed or enhanced by autoinhibitory or autocatalytic reactions, respectively. In some cases, autocatalysis may induce two distinct populations in thermodynamically stable single-phase ensembles. Asymmetric reaction kinetics also results in qualitatively different population dynamics upon reversing the reaction direction. In the limit of negligible fluctuations, we use the method of characteristics and linearization to study the evolution of the concentration variance as well as the condition for mosaic instability, in good agreement with the full numerical solution. Applications include Li-ion batteries characterized by in situ x-ray diffraction.

Emergence of stable striatal D1R and D2R neuronal ensembles with distinct firing sequence during motor learning

The dorsolateral striatum (DLS) is essential for motor and procedure learning, but the role of DLS spiny projection neurons (SPNs) of direct and indirect pathways, as marked, respectively, by D1 and D2 receptor (D1R and D2R) expression, remains to be clarified. Long-term two-photon calcium imaging of the same neuronal population during mouse learning of a cued lever-pushing task revealed a gradual emergence of distinct D1R and D2R neuronal ensembles that reproducibly fired in a sequential manner, with more D1R and D2R neurons fired during the lever-pushing period and intertrial intervals (ITIs), respectively. This sequential firing pattern was specifically associated with the learned motor behavior, because it changed markedly when the trained mice performed other cued motor tasks. Selective chemogenetic silencing of D1R and D2R neurons impaired the initiation of learned motor action and suppression of erroneous lever pushing during ITIs, respectively. Thus, motor learning involves reorganization of DLS neuronal activity, forming stable D1R and D2R neuronal ensembles that fired sequentially to regulate different aspects of the learned behavior.

Tau monomer encodes strains.

Tauopathies have diverse presentation, progression, and neuropathology. They are linked to tau prion strains, self-replicating assemblies of unique quaternary conformation, whose origin is unknown. Strains can be propagated indefinitely in cultured cells, and induce unique patterns of transmissible neuropathology upon inoculation into mice. DS9 and DS10 cell lines propagate different synthetic strains that derive from recombinant tau. We previously observed that tau monomer adopts two conformational states: one that is inert (Mi) and one that is seed-competent (Ms) (Mirbaha et al., 2018). We have now found that Ms itself is comprised of multiple stable ensembles that encode unique strains. DS9 monomer inoculated into naive cells encoded only DS9, whereas DS10 monomer encoded multiple sub-strains. Sub-strains each induced distinct pathology upon inoculation into a tauopathy mouse model (PS19). Ms purified from an Alzeimer's disease brain encoded a single strain. Conversely, Ms from a corticobasal degeneration brain encoded three sub-strains, in which monomer from any one re-established all three upon inoculation into cells. Seed competent tau monomer thus adopts multiple, stable seed-competent conformations, each of which encodes a limited number of strains. This provides insight into the emergence of distinct tauopathies, and may improve diagnosis and therapy.

Propylene polymerization reactions with supported Ziegler–Natta catalysts: Observing polymer material produced by a single active center

ABSTRACTMedium‐ and high‐resolution SEM analysis of several Ti‐based MgCl2‐supported Ziegler–Natta catalysts and isotactic polypropylene produced with them is carried out. Each catalyst particle, 35–55 μ in size, produces one polymer particle with an average size of 1.5–2 mm, which replicates the shape of the catalyst particle. Polymer particles contain two distinct morphological features. The larger of them are globules with Dav ∼400 nm; from 1 to 2 × 1011 globules per particle. Each globule represents the combined polymer output of a single active center. The globules consist of ∼2500 microglobules with an average size of ∼20 nm. The microglobules contain several folded polymer molecules; they are the smallest thermodynamically stable macromolecular ensembles in propylene polymerization reactions. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017, 55, 3832–3841

Recombination, reassortment, and many-to-one genotypes in natural arenavirus infections

Mutation, recombination, and reassortment generate virus particles with variable genotypes, some of which may be better adapted to infect a new host, resist drug treatment, or escape immune pressure. The arenaviruses are a family of viruses that package a large (L) and small (S) genome segment. Arenaviruses infect mammals and snakes and are associated with fatal disease in both groups of animals. Although recombination and reassortment are well documented in some virus families, neither process has been observed in natural arenavirus infections. In this study, we documented a surprising degree of genetic diversity in arenavirus-infected snakes. Instead of one or two viral species or quasispecies, individual animals harbored complex populations of viral genotypes composed of up to 5 S and 11 L genotypes, which replicated as stable ensembles in culture. S and L segment genotype accumulation was not balanced and a particular S segment genotype dominated, both in individual animals and at a population level. Numerous instances of recombination and reassortment were detected. Some recombinant segments had unusual organizations with 2 intergenic regions. This genetic fluidity is closer to that observed in influenza viruses than to the relatively placid genetics of mammalian arenavirus. However, the observed imbalance between the S and L segments and the intrahost accumulation and persistence of multiple genotypes is previously undocumented. Overall, this provides an opportunity to study basic mechanisms of viral adaptation and stretches the idea of what it means to be infected by “a virus”.

Structural and Functional Analysis of Novel Human Cytochrome c Targets in Apoptosis

Since the first description of apoptosis four decades ago, great efforts have been made to elucidate, both in vivo and in vitro, the molecular mechanisms involved in its regulation. Although the role of cytochrome c during apoptosis is well established, relatively little is known about its participation in signaling pathways in vivo due to its essential role during respiration. To obtain a better understanding of the role of cytochrome c in the onset of apoptosis, we used a proteomic approach based on affinity chromatography with cytochrome c as bait in this study. In this approach, novel cytochrome c interaction partners were identified whose in vivo interaction and cellular localization were facilitated through bimolecular fluorescence complementation. Modeling of the complex interface between cytochrome c and its counterparts indicated the involvement of the surface surrounding the heme crevice of cytochrome c, in agreement with the vast majority of known redox adducts of cytochrome c. However, in contrast to the high turnover rate of the mitochondrial cytochrome c redox adducts, those occurring under apoptosis led to the formation of stable nucleo-cytoplasmic ensembles, as inferred mainly from surface plasmon resonance and nuclear magnetic resonance measurements, which permitted us to corroborate the formation of such complexes in vitro. The results obtained suggest that human cytochrome c interacts with pro-survival, anti-apoptotic proteins following its release into the cytoplasm. Thus, cytochrome c may interfere with cell survival pathways and unlock apoptosis in order to prevent the spatial and temporal coexistence of antagonist signals.

Segregation of Negatively Charged Phospholipids by the Polycationic and Farnesylated Membrane Anchor of Kras

The Kras protein, a member of the Ras family of bio-switches that are frequently mutated in cancer and developmental disorders, becomes functional when anchored to the inner surface of the plasma membrane. It is well known that membrane attachment involves the farnesylated and poylcationic C-terminus of the protein. However, little is known about the structure of the complex and the specific protein-lipid interactions that are responsible for the binding. On the basis of data from extensive (>0.55 μs) molecular dynamics simulations of multiple Kras anchors in bilayers of POPC/POPG lipids (4:1 ratio), we show that, as expected, Kras is tethered to the bilayer surface by specific lysine-POPG salt bridges and by nonspecific farnesyl-phospholipid van der Waals interactions. Unexpectedly, however, only the C-terminal five of the eight Kras Lys side chains were found to directly interact with the bilayer, with the N-terminal ones staying in water. Furthermore, the positively charged Kras anchors pull the negatively charged POPG lipids together, leading to the clustering of the POPG lipids around the proteins. This selective Kras-POPG interaction is directly related to the specific geometry of the backbone, which exists in two major conformational states: 1), a stable native-like ensemble of structures characterized by an extended geometry with a pseudohelical turn; and 2), less stable nonnative ensembles of conformers characterized by severely bent geometries. Finally, although the interface-bound anchor has little effect on the overall structure of the bilayer, it induces local thinning within a persistence length of ∼12 Å. Our results thus go beyond documenting how Kras attaches to a mixed bilayer of charged and neutral lipids; they highlight a fascinating process of protein-induced lipid sorting coupled with the (re)shaping of a surface-bound protein by the host lipids.

Massive non-natural proteins structure prediction using grid technologies

BackgroundThe number of natural proteins represents a small fraction of all the possible protein sequences and there is an enormous number of proteins never sampled by nature, the so called "never born proteins" (NBPs). A fundamental question in this regard is if the ensemble of natural proteins possesses peculiar chemical and physical properties or if it is just the product of contingency coupled to functional selection. A key feature of natural proteins is their ability to form a well defined three-dimensional structure. Thus, the structural study of NBPs can help to understand if natural protein sequences were selected for their peculiar properties or if they are just one of the possible stable and functional ensembles.MethodsThe structural characterization of a huge number of random proteins cannot be approached experimentally, thus the problem has been tackled using a computational approach. A large random protein sequences library (2 × 104 sequences) was generated, discarding amino acid sequences with significant similarity to natural proteins, and the corresponding structures were predicted using Rosetta. Given the highly computational demanding problem, Rosetta was ported in grid and a user friendly job submission environment was developed within the GENIUS Grid Portal. Protein structures generated were analysed in terms of net charge, secondary structure content, surface/volume ratio, hydrophobic core composition, etc.ResultsThe vast majority of NBPs, according to the Rosetta model, are characterized by a compact three-dimensional structure with a high secondary structure content. Structure compactness and surface polarity are comparable to those of natural proteins, suggesting similar stability and solubility. Deviations are observed in α helix-β strands relative content and in hydrophobic core composition, as NBPs appear to be richer in helical structure and aromatic amino acids with respect to natural proteins.ConclusionThe results obtained suggest that the ability to form a compact, ordered and water-soluble structure is an intrinsic property of polypeptides. The tendency of random sequences to adopt α helical folds indicate that all-α proteins may have emerged early in pre-biotic evolution. Further, the lower percentage of aromatic residues observed in natural proteins has important evolutionary implications as far as tolerance to mutations is concerned.