Molecular Origin Research Articles

Molecular Origins of Shock Dissipation in Polymer-Based Nanocomposites.

To explain the molecular origin of shock dissipation in polymer-based composites, a new method is proposed by absolutely quantifying the relative position between molecular chains, which directly reflects the shock dissipation energy between molecular chains and at the interfaces with nanofillers during mechanical deformation. The effects of nanofiller content and system temperature on energy dissipation were examined based on this newly proposed method, and the differences in energy dissipation between the thermosetting polymer (polydimethylsiloxane) and thermoplastic polymer (polyether-ether-ketone) under identical physical conditions were both studied to validate the reliability of the quantification method proposed in this paper. The present study offers a tool that provides theoretical insights to understand the molecular origins of shock dissipation in polymer composites as well as to facilitate the optimal design of composites with outstanding damping characteristics.

Nickel-organo compounds as potential enzyme precursors under simulated early Earth conditions

The transition from inorganic catalysis through minerals to organic catalysis by enzymes is a necessary step in the emergence of life. Our work is elucidating likely reactions at the earliest moments of Life, prior to the existence of enzymatic catalysis, by exploring essential intersections between nickel bioinorganic chemistry and pterin biochemistry. We used a prebiotically-inspired acetylene-containing volcanic hydrothermal experimental environment to shed light on the efficient formation of nickel-organo complexes. The simplest bis(dithiolene)nickel complex (C2H2S2)2Ni was identified by UV/Vis spectroscopy, mass spectrometry, nuclear magnetic resonance. Its temporal progression and possible function in this simulated early Earth atmosphere were investigated by isolating the main bis(dithiolene)nickel species from the primordial experimental setup. Using this approach, we uncovered a significant diversity of nickel-organo compositions by identifying 156 elemental annotations. The formation of acetaldehyde through the subsequent degradation of these organo-metal complexes is intriguing, as it is reminiscent of the ability of Pelobacter acetylenicus to hydrate acetylene to acetaldehyde via its bis(dithiolene)-containing enzyme acetylene hydratase. As our findings mechanistically characterize the role of nickel sulfide in catalyzing the formation of acetaldehyde, this fundamental pre-metabolic reaction could play the role of a primitive enzyme precursor of the enzymatic acetylene metabolism and further strengthen the role of acetylene in the molecular origin of life.

Fine-tuning activation specificity of G-protein-coupled receptors via automated path searching

Physics-based simulation methods can grant atomistic insights into the molecular origin of the function of biomolecules. However, the potential of such approaches has been hindered by their low efficiency, including in the design of selective agonists where simulations of myriad protein-ligand combinations are necessary. Here, we describe an automated input-free path searching protocol that offers (within 14 d using Graphics Processing Unit servers) a minimum free energy path (MFEP) defined in high-dimension configurational space for activating sphingosine-1-phosphate receptors (S1PRs) by arbitrary ligands. The free energy distributions along the MFEP for four distinct ligands and three S1PRs reached a remarkable agreement with Bioluminescence Resonance Energy Transfer (BRET) measurements of G-protein dissociation. In particular, the revealed transition state structures pointed out toward two S1PR3 residues F263/I284, that dictate the preference of existing agonists CBP307 and BAF312 on S1PR1/5. Swapping these residues between S1PR1 and S1PR3 reversed their response to the two agonists in BRET assays. These results inspired us to design improved agonists with both strong polar head and bulky hydrophobic tail for higher selectivity on S1PR1. Through merely three in silico iterations, our tool predicted a unique compound scaffold. BRET assays confirmed that both chiral forms activate S1PR1 at nanomolar concentration, 1 to 2 orders of magnitude less than those for S1PR3/5. Collectively, these results signify the promise of our approach in fine agonist design for G-protein-coupled receptors.

Viper Venom Phospholipase A2 Database: The Structural and Functional Anatomy of a Primary Toxin in Envenomation.

Viper venom phospholipase A2 enzymes (vvPLA2s) and phospholipase A2-like (PLA2-like) proteins are two of the principal toxins in viper venom that are responsible for the severe myotoxic and neurotoxic effects caused by snakebite envenoming, among other pathologies. As snakebite envenoming is the deadliest neglected tropical disease, a complete understanding of these proteins' properties and their mechanisms of action is urgently needed. Therefore, we created a database comprising information on the holo-form, cofactor-bound 3D structure of 217 vvPLA2 and PLA2-like proteins in their physiologic environment, as well as 79 membrane-bound viper species from 24 genera, which we have made available to the scientific community to accelerate the development of new anti-snakebite drugs. In addition, the analysis of the sequenced, 3D structure of the database proteins reveals essential aspects of the anatomy of the proteins, their toxicity mechanisms, and the conserved binding site areas that may anchor universal interspecific inhibitors. Moreover, it pinpoints hypotheses for the molecular origin of the myotoxicity of the PLA2-like proteins. Altogether, this study provides an understanding of the diversity of these toxins and how they are conserved, and it indicates how to develop broad, interspecies, efficient small-molecule inhibitors to target the toxin's many mechanisms of action.

Enhanced Spectral Resolution and Two-Dimensional Correlation Spectroscopy (2D-COS).

The apparent enhancement of spectral resolution is one of the attractive features of two-dimensional correlation spectroscopy (2D-COS). Highly overlapped adjacent bands often encountered in one-dimensional spectra may be effectively differentiated and identified by spreading peaks along the second dimension. This differentiating feature or selectivity is especially prominent in asynchronous spectra, where even a slight difference in the variation patterns of overlapped bands in response to a given perturbation results in the generation of cross-peaks. While cross-peaks in asynchronous spectra can identify signals originating from different moieties or bands, they do not effectively specify which regions of spectra actually share the same molecular origin. Overreliance on asynchronous spectra alone risks the potential false negative assessment or lack of sufficient specificity, leading to the failure of classifying signals into a reasonable set of component groups. The combined use of synchronous and asynchronous spectra coupled with the scaling techniques, elimination of anti-correlated negative synchronous peaks, and a robust line shape narrowing method provides a means to achieve both selectivity and specificity for resolution-enhancement of 2D-COS.

Improving separation of CH4 and N2 by adsorption on zeolite Y Ion–Exchanged with ammonium Cations: An experimental and Grand–Canonical Monte Carlo (GCMC) simulation investigation

The separation of methane (CH4) from industrially–important nitrogen (N2)-rich vent streams such as those in liquefied natural gas processing plants is challenging. Pressure swing adsorption (PSA) is a promising, cost–effective solution in gas separation, especially for small–scale units. Further development and commercialisation of PSA–based technologies require access to low–cost, selective adsorbent materials. The current work investigates the improved separation of CH4 from N2 by TMA–Y zeolite which is obtained from the ion exchange treatment of Na–Y zeolite with the ammonium salt tetramethylammonium chloride (TMACl). TMA–Y is commercially called Ionic Liquidic Zeolite (ILZ), patented at The University of Western Australia, and has now been demonstrated on tonne–scale. In particular, we use a combination of experimental and molecular simulation techniques to provide insights into the high CH4–over–N2 selectivity of TMA–Y. For this, we obtain equilibrium isotherms of CH4 and N2 on Na–Y at different temperatures and pressures before and after ion exchange. The true selectivities of the zeolite samples are determined using the Ideal Adsorbed Solution Theory (IAST) and binary–gas grand–canonical Monte Carlo (GCMC) molecular simulations. From experiments and IAST calculations, we report an increase of >110% in the CH4/N2 selectivity of Na–Y after treatment with TMACl (from 2.2 to 4.7 at 5.0 MPa and 303.15 K for a mixture of 0.1 CH4+0.9 N2 mol.mol−1). GCMC molecular simulations provide a detailed picture of the molecular origins of this effect. Specifically, the introduction of TMA+ ions into the structure of Na–Y zeolite leads to a reduction of the available adsorption volume by more than 40% (from 0.30 to 0.17 cm3.g−1 with N2 as the probe molecule) for both adsorbing gas species (i.e. CH4 and N2). However, at the same time, this leads to stronger CH4–cation interactions due to the much higher affinity of TMA+ cations (5 kJ.mol−1) than extra–framework Na+ cations (1 kJ.mol−1) towards CH4. The overall effect of these two trends combined is the higher selectivity of the resulting TMA–Y zeolite for CH4. These molecular insights are useful in the systematic engineering of new materials with improved separation performance.

Self-terminating, heterogeneous solid–electrolyte interphase enables reversible Li–ether cointercalation in graphite anodes

Ether solvents are suitable for formulating solid-electrolyte interphase (SEI)-less ion-solvent cointercalation electrolytes in graphite for Na-ion and K-ion batteries. However, ether-based electrolytes have been historically perceived to cause exfoliation of graphite and cell failure in Li-ion batteries. In this study, we develop strategies to achieve reversible Li-solvent cointercalation in graphite through combining appropriate Li salts and ether solvents. Specifically, we design 1M LiBF4 1,2-dimethoxyethane (G1), which enables natural graphite to deliver ~91% initial Coulombic efficiency and >88% capacity retention after 400 cycles. We captured the spatial distribution of LiF at various length scales and quantified its heterogeneity. The electrolyte shows self-terminated reactivity on graphite edge planes and results in a grainy, fluorinated pseudo-SEI. The molecular origin of the pseudo-SEI is elucidated by ab initio molecular dynamics (AIMD) simulations. The operando synchrotron analyses further demonstrate the reversible and monotonous phase transformation of cointercalated graphite. Our findings demonstrate the feasibility of Li cointercalation chemistry in graphite for extreme-condition batteries. The work also paves the foundation for understanding and modulating the interphase generated by ether electrolytes in a broad range of electrodes and batteries.

Probing T-cell activation in nanoliter tumor co-cultures using membrane displacement trap arrays.

Immune responses against cancer are inherently stochastic, with small numbers of individual T cells within a larger ensemble of lymphocytes initiating the molecular cascades that lead to tumor cytotoxicity. A potential source of this intra-tumor variability is the differential ability of immune cells to respond to tumor cells. Classical microwell co-cultures of T cells and tumor cells are inadequate for reliably culturing and analyzing low cell numbers needed to probe this variability, and have failed in recapitulating the heterogeneous small domains observed in tumors. Here we leverage a membrane displacement trap array technology that overcomes limitations of conventional microwell plates for immunodynamic studies. The microfluidic platform supports on-demand formation of dense nanowell cultures under continuous perfusion reflecting the tumor microenvironment, with real-time monitoring of T cell proliferation and activation within each nanowell. The system enables selective ejection of cells for profiling by fluorescence activated cell sorting, allowing observed on-chip variability in immune response to be correlated with off-chip quantification of T cell activation. The technology offers new potential for probing the molecular origins of T cell heterogeneity and identifying specific cell phenotypes responsible for initiating and propagating immune cascades within tumors. Insight Box Variability in T cell activation plays a critical role in the immune response against cancer. New tools are needed to unravel the mechanisms that drive successful anti-tumor immune response, and to support the development of novel immunotherapies utilizing rare T cell phenotypes that promote effective immune surveillance. To this end, we present a microfluidic cell culture platform capable of probing differential T cell activation in an array of nanoliter-scale wells coupled with off-chip cell analysis, enabling a high resolution view of variable immune response within tumor / T cell co-cultures containing cell ensembles orders of magnitude smaller than conventional well plate studies.

Tracing the slow Arrhenius process deep in the glassy state-quantitative evaluation of the dielectric relaxation of bulk samples and thin polymer films in the temperature domain.

The slow Arrhenius process (SAP) is a dielectric mode connected to thermally activated equilibration mechanisms, allowing for a fast reduction in free energy in liquids and glasses. The SAP, however, is still poorly understood, and so far, this process has mainly been investigated at temperatures above the glass transition. By employing a combination of methods to analyze dielectric measurements under both isochronal and isothermal conditions, we were able to quantitatively reproduce the dielectric response of the SAP of different polymers and to expand the experimental regime over which this process can be observed down to lower temperatures, up to 70K below the glass transition. Employing thin films of thicknesses varying between 10 and 800nm, we further verified that the peak shape and activation energy of the SAP of poly(4-bromostyrene) are not sensitive to temperature, nor do they vary upon confinement at the nanoscale level. These observations confirm the preliminary trends reported for other polymers. We find that one single set of parameters-meaning the activation barrier and the pre-exponential factor, respectively, linked to the enthalpic and entropic components of the process-can describe the dynamics of the SAP in both the supercooled liquid and glassy states, in bulk and thin films. These results are discussed in terms of possible molecular origins of the slow Arrhenius process in polymers.

Pathway to the Molecular Origins of Drought Escape and Early Flowering Illuminated via the Phosphorylation of SnRK2-Substrate 1 in Arabidopsis.

Pathway to the Molecular Origins of Drought Escape and Early Flowering Illuminated via the Phosphorylation of SnRK2-Substrate 1 in Arabidopsis.

Why Are Nucleosome Breathing Dynamics Asymmetric?

In eukaryotic cells, DNA is bound to nucleosomes, but DNA segments occasionally unbind in the process known as nucleosome breathing. Although DNA can unwrap simultaneously from both ends of the nucleosome (symmetric breathing), experiments indicate that DNA prefers to dissociate from only one end (asymmetric breathing). However, the molecular origin of the asymmetry is not understood. We developed a new theoretical approach that gives microscopic explanations of asymmetric breathing. It is based on a stochastic description that leads to a comprehensive evaluation of dynamics by using effective free-energy landscapes. It is shown that asymmetric breathing follows the kinetically preferred pathways. In addition, it is also found that asymmetric breathing leads to a faster target search by transcription factors. Theoretical predictions, supported by computer simulations, agree with experiments. It is proposed that nature utilizes the symmetry of nucleosome breathing to achieve a better dynamic accessibility of chromatin for more efficient genetic regulation.

Strategies for designing biocatalysts with new functions.

The engineering of natural enzymes has led to the availability of a broad range of biocatalysts that can be used for the sustainable manufacturing of a variety of chemicals and pharmaceuticals. However, for many important chemical transformations there are no known enzymes that can serve as starting templates for biocatalyst development. These limitations have fuelled efforts to build entirely new catalytic sites into proteins in order to generate enzymes with functions beyond those found in Nature. This bottom-up approach to enzyme development can also reveal new fundamental insights into the molecular origins of efficient protein catalysis. In this tutorial review, we will survey the different strategies that have been explored for designing new protein catalysts. These methods will be illustrated through key selected examples, which demonstrate how highly proficient and selective biocatalysts can be developed through experimental protein engineering and/or computational design. Given the rapid pace of development in the field, we are optimistic that designer enzymes will begin to play an increasingly prominent role as industrial biocatalysts in the coming years.

Molecular origins of enhanced bioproduct properties by pretreatment of agricultural residues with deep eutectic solvents

The present work provides a multiscale picture of the effect of a promising DES on biomass pretreatment by combining computational and experimental approaches.

Non-affine deformation analysis and 3D packing defects: A new way to probe membrane heterogeneity in molecular simulations.

Here, we discuss a new framework developed over the last 5 years in our group to probe nanoscale membrane heterogeneity. The framework is based on the idea of characterizing lateral heterogeneity through non-affine deformation (NAD) measurements, transverse heterogeneity through three dimensional (3D) lipid packing defects, and using these approaches to formalize the seemingly trivial correlation between lateral organization and lipid packing in biological membranes. We find that measurements from NAD analysis, a prescription which is borrowed from Physics of glasses and granular material, can faithfully distinguish between liquid-ordered and disordered phases in membranes at molecular length scalesand, can also be used to identify phase boundaries with high precision. Concomitantly, 3D-packing defects can not only distinguish between the two co-existing fluid phases based on their molecular scale packing (or membrane free volume), but also provide a route to connect the membrane domains to their functionality, such as exploring the molecular origins of inter-leaflet domain registration and peptide partitioning. The correlation between lateral membrane order and transverse packing presents novel molecular design-level features that can explain functions such as protein/peptide partitioning and small-molecule permeation dynamics in complex and heterogeneous membranes with high-fidelity. The framework allows us to explore the nature of lateral organization and molecular packing as a manifestation of intricate molecular interactions among a chemically rich variety of lipids and other molecules in a membrane with complex membrane composition and asymmetry across leaflets.

Computational investigation of the effects of polymer grafting on the effective interaction between silica nanoparticles in water.

Understanding and control of the effective interaction between nanoscale building blocks (colloids or nanoparticles) dispersed in a solvent is an important prerequisite for the development of bottom-up design strategies for soft functional materials. Here, we have employed all-atom molecular dynamics simulations to investigate the impact of polymer grafting on the solvent-mediated effective interaction between the silica nanoparticles (Si-NPs) in water, and in turn, on its bulk structural and thermodynamic properties. We found that the nature of the short grafting polymers [characterized by their interaction with water (hydrophobicity or hydrophilicity) and molecular weight] has a profound effect on the range and strength of the effective interaction between the Si-NPs. The hydrophobic polymer [such as polyethylene (PE)]-grafting of Si-NP gives rise to a more attractive interaction between the Si-NPs compared to the hydrophilic polymer [such as polyethylene glycol (PEG)] and non-grafted cases. This study further provides fundamental insights into the molecular origin of the observed behavior of the effective pair interactions between the grafted Si-NPs. For PE-grafted Si-NPs, the confined water (water inside the cavity formed by a pair of Si-NPs) undergoes a partial dewetting transition on approaching below a critical inter-particle separation leading to a stronger attractive interaction. Furthermore, we report that the effective attraction between the PE-grafted Si-NPs can be reliably controlled by changing the grafting PE density. We have also investigated the bulk structural and thermodynamic behavior of the coarse-grained Si-NP system where the particles interact via effective interaction in the absence of water. We believe that the insights gained from this work are important prerequisites for formulating rational bottom-up design strategies for functional materials where nano- (or, colloidal) particles are the building blocks.

Cell invasive amyloid assemblies from SARS-CoV-2 peptides can form multiple polymorphs with varying neurotoxicity.

The neurological symptoms of COVID-19, often referred to as neuro-COVID include neurological pain, memory loss, cognitive and sensory disruption. These neurological symptoms can persist for months and are known as Post-Acute Sequalae of COVID-19 (PASC). The molecular origins of neuro-COVID, and how it contributes to PASC are unknown, however a growing body of research highlights that the self-assembly of protein fragments from SARS-CoV-2 into amyloid nanofibrils may play a causative role. Previously, we identified two fragments from the SARS-CoV-2 proteins, Open Reading Frame (ORF) 6 and ORF10, that self-assemble into neurotoxic amyloid assemblies. Here we further our understanding of the self-assembly mechanisms and nano-architectures formed by these fragments and their biological responses. By solubilising the peptides in a fluorinated solvent, we eliminate insoluble aggregates in the starting materials (seeds) that change the polymorphic landscape of the assemblies. The resultant assemblies are dominated by structures with higher free energies (e.g. ribbons and amorphous aggregates) that are less toxic to cultured neurons but do affect their mitochondrial respiration. We also show the first direct evidence of cellular uptake of viral amyloids. This work highlights the importance of understanding the polymorphic behaviour of amyloids and the correlation to neurotoxicity, particularly in the context of neuro-COVID and PASC.

Thermal evolution of a polymer-nanoparticle binary mixture.

We experimentally probe the microscopic variations in a model polymer-nanoparticle (NP) binary mixture (mixture of polybutadiene and clay nanoplatelets) across a thermal evolution path for which Tevolution > Tg(polymer). The evolution of the NP dispersion, NP crystallinity, polymer chain-NP interface, and nature of polymer chain-NP interaction are mapped for a spectrum of temperatures and NP concentrations constrained by experiments. Multiple pieces of evidence indicate that thermal evolution does not influence the nature of interparticle dispersion and is also independent of NP concentration in the binary mixture. However, the NP crystalline order significantly reduces across the thermal evolution path. Thermal evolution induces a transition of a sharp polymer chain-NP interface to a diffuse interfacial layer. In contrast, an already diffuse polymer-NP interface existing in the binary mixture due to particle crowding at high NP concentrations undergoes no significant change in its nature across the evolution path. At all particle concentrations, thermal evolution changes the dominant interaction from polymer chain-polymer chain to polymer chain-NP. These insights aid in explaining the molecular origins of unique and anomalous behaviors shown by polymer-nanoparticle binary mixtures while undergoing thermal evolution.

A molecular origin of non-reciprocal interactions between interacting active catalysts

A molecular origin of non-reciprocal interactions between interacting active catalysts

Elementary and Advanced Mechanisms for Genetic Engineering in Crops

Presently, the field of plant breeding is in the genomics era, where innovative techniques are being integrated to accelerate and enhance the efficiency of breeding. Traditional plant breeding methods rely on maintaining plant germplasm with desirable agronomic traits from distinct plants produced through crosses or mutagenesis. However, advancements in genetic engineering encompass all forms of genetic modification through recombinant DNA technology (RDT) and cell fusion mechanisms. These approaches shed light on areas involving mutant organisms, DNA replication, genetic linkage resolution, genetically modified organisms (GMOs), protein sequencing, functional genomics, and computational genomics alterations in genetic engineering. The integration of structural genomics into breeding and eugenics analysis has resulted in a vast knowledge base on crop genetics, species divergence, and molecular origin of traits, as well as the evolutionary history of crop lineage from ancient ancestral species. The genomic data and advancements have proven essential in identifying rare genes, alleles, or local lesions crucial to significant agronomic traits, thereby expediting breeding cycles. This article aims to explore the potential of emerging genetic engineering technologies, including synthetic biology and genome editing, to further advance crop genetics and plant breeding.

Molecular determinants of ligand efficacy and potency in GPCR signaling.

Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) bind to extracellular ligands and drugs and modulate intracellular responses through conformational changes. Despite their importance as drug targets, the molecular origins of pharmacological properties such as efficacy (maximum signaling response) and potency (the ligand concentration at half-maximal response) remain poorly understood for any ligand-receptor-signaling system. We used the prototypical adrenaline-β2 adrenergic receptor-G protein system to reveal how specific receptor residues decode and translate the information encoded in a ligand to mediate a signaling response. We present a data science framework to integrate pharmacological and structural data to uncover structural changes and allosteric networks relevant for ligand pharmacology. These methods can be tailored to study any ligand-receptor-signaling system, and the principles open possibilities for designing orthosteric and allosteric compounds with defined signaling properties.